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9v0b

Cryo-EM structure of avadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly

Method: ELECTRON MICROSCOPY Dmax: 186.2 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cullin-4A

Homo sapiens

UniProt Q13619

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 2–759 Not recorded DNA damage-binding protein 1 × 1 （Q16531） Protein cereblon × 1 （Q96SW2） Ubiquitin-conjugating enzyme E2 D1 × 1 （P51668） Zinc finger protein Aiolos × 1 （Q9UKT9） NEDD8 × 1 （Q15843） E3 ubiquitin-protein ligase RBX1, N-terminally processed × 1 （P62877） Ubiquitin × 1 （P62979） ZINC ION × 6 (3S)-3-(5-azanyl-2-methyl-4-oxidanylidene-quinazolin-3-yl)piperidine-2,6-dione × 1 ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 3.54 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9V0B Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2HYE Crystal Structure of the DDB1-Cul4A-Rbx1-SV5V Complex Deposited 2006-08-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–759（759 aa）
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；100mM NaHEPES, 7-9% PEG4000, 10% iso-propanol, 5mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.316
4A0K STRUCTURE OF DDB1-DDB2-CUL4A-RBX1 BOUND TO A 12 BP ABASIC SITE CONTAINING DNA-DUPLEX Deposited 2011-09-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 38–759（722 aa） Fragment：RESIDUES 38-759
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.3；100MM TRIS-HCL PH 8.3, 33% PEG 200
Resolution 5.93 Å R-free 0.270
7OKQ Cryo-EM Structure of the DDB1-DCAF1-CUL4A-RBX1 Complex Deposited 2021-05-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: Hexadecameric
Chain C 35–759（725 aa）
Chain G 35–759（725 aa）
Chain K 35–759（725 aa）
Chain O 35–759（725 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.40 Å
7OPC Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 4) Deposited 2021-05-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 25 PDB declaration: 28-meric
Chain e 1–759（759 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7OPD Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 5) Deposited 2021-05-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 25 PDB declaration: 28-meric
Chain e 1–759（759 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8B3G C(N)RL4CSA-UVSSA-E2-ubiquitin complex. Deposited 2022-09-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain e 1–759（759 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8B3I CRL4CSA-E2-Ub (state 2) Deposited 2022-09-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain e 1–759（759 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9EG8 Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-4A Deposited 2024-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain J 1–759（759 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9LWI The head region of HBx-Smc5/6 ubiquitination complex Deposited 2025-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain G 1–759（759 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9LWJ The head-arm region of HBx-Smc5/6 ubiquitination complex Deposited 2025-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain G 1–759（759 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.19 Å
9LWL HBx-Smc5/6 ubiquitination complex Deposited 2025-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain G 1–759（759 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.25 Å
9PVH Human Cullin-4 in complex with CAND2 Deposited 2025-08-01 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 37–759（723 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 4.38 Å
9UUM Cryo-EM structure of mezigdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-07 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 2–759（758 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.41 Å
9V0A Cryo-EM structure of pomalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 2–759（758 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.69 Å
9V0F Cryo-EM structure of cemsidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 2–759（758 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.71 Å

15 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CUL4A_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 18–775； UniProt 2–759

DNA damage-binding protein 1

Homo sapiens

UniProt Q16531

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain B； UniProt 1–1140 Not recorded Cullin-4A × 1 （Q13619） Protein cereblon × 1 （Q96SW2） Ubiquitin-conjugating enzyme E2 D1 × 1 （P51668） Zinc finger protein Aiolos × 1 （Q9UKT9） NEDD8 × 1 （Q15843） E3 ubiquitin-protein ligase RBX1, N-terminally processed × 1 （P62877） Ubiquitin × 1 （P62979） ZINC ION × 6 (3S)-3-(5-azanyl-2-methyl-4-oxidanylidene-quinazolin-3-yl)piperidine-2,6-dione × 1 ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 3.54 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9V0B Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
10AY Cryo-EM structure of CRBN-DDB1 in complex with HBS1L and TNG961 Deposited 2026-01-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–1140（1140 aa）
Chain F 1–1140（1140 aa）
Not recorded A1C4S N-{6-[(3R)-2,6-dioxopiperidin-3-yl]naphthalen-1-yl}-N'-{2-[6-(trifluoromethyl)-1-benzothiophen-2-yl]propan-2-yl}urea × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；0.1 M HEPES (pH 7.5), 0.24 M sodium chloride, 3 mM TCEP, 0.2 % n-octylglucoside
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
2HYE Crystal Structure of the DDB1-Cul4A-Rbx1-SV5V Complex Deposited 2006-08-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；100mM NaHEPES, 7-9% PEG4000, 10% iso-propanol, 5mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.316
3E0C Crystal Structure of DNA Damage-Binding protein 1(DDB1) Deposited 2008-07-31 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M Bis tris, pH 6.5,0.2 M Lithium sulfate, 25% PEG 3350, 1:6000 Protein:Chymotrypsin , VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.41 Å R-free 0.283
3EI1 Structure of hsDDB1-drDDB2 bound to a 14 bp 6-4 photoproduct containing DNA-duplex Deposited 2008-09-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Not recorded PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；298 K；100mM Ca-Acetate, 100mM MES pH 5.7, 12-14 % PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.80 Å R-free 0.278
3EI2 Structure of hsDDB1-drDDB2 bound to a 16 bp abasic site containing DNA-duplex Deposited 2008-09-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Not recorded PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；298 K；100mM Ca-Acetate, 100mM MES pH 5.7, 12-14% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.60 Å R-free 0.268
3EI3 Structure of the hsDDB1-drDDB2 complex Deposited 2008-09-15 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded PG4 TETRAETHYLENE GLYCOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；298 K；100mM Ca-Acetate, 100mM MES pH 5.7, 12-14% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.30 Å R-free 0.251
3EI4 Structure of the hsDDB1-hsDDB2 complex Deposited 2008-09-15 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；200 mM (NH4)2SO4; 800 mM LiSO2; 100 mM Na-Citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.30 Å R-free 0.288
3EI4 Structure of the hsDDB1-hsDDB2 complex Deposited 2008-09-15 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；200 mM (NH4)2SO4; 800 mM LiSO2; 100 mM Na-Citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.30 Å R-free 0.288
3EI4 Structure of the hsDDB1-hsDDB2 complex Deposited 2008-09-15 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；200 mM (NH4)2SO4; 800 mM LiSO2; 100 mM Na-Citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.30 Å R-free 0.288
3I7H Crystal Structure of DDB1 in Complex with the H-Box Motif of HBX Deposited 2009-07-08 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.90 Å R-free 0.279
3I7K Crystal Structure of DDB1 in Complex with the H-Box Motif of WHX Deposited 2009-07-08 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005 M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.271
3I7L Crystal Structure of DDB1 in Complex with the H-Box Motif of DDB2 Deposited 2009-07-08 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005 M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.289
3I7N Crystal Structure of DDB1 in Complex with the H-Box Motif of WDTC1 Deposited 2009-07-08 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.290
3I7O Crystal Structure of DDB1 in Complex with the H-Box Motif of IQWD1 Deposited 2009-07-08 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.320
3I7P Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR40A Deposited 2009-07-08 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.301
3I89 Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR22 Deposited 2009-07-09 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.304
3I8C Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR21A Deposited 2009-07-09 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.308
3I8E Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR42A Deposited 2009-07-09 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.40 Å R-free 0.338
3I8E Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR42A Deposited 2009-07-09 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.40 Å R-free 0.338
4A08 Structure of hsDDB1-drDDB2 bound to a 13 bp CPD-duplex (purine at D-1 position) at 3.0 A resolution (CPD 1) Deposited 2011-09-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Mutation：YES MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 CA CALCIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；100 MM MES, 25 MM NAOH, 18% PEG 350MME., pH 5.6
Resolution 3.00 Å R-free 0.294
4A09 Structure of hsDDB1-drDDB2 bound to a 15 bp CPD-duplex (purine at D-1 position) at 3.1 A resolution (CPD 2) Deposited 2011-09-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Mutation：YES CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.3；100 MM MES, 15 MM NAOH, 21% PEG 200, pH 5.3
Resolution 3.10 Å R-free 0.308
4A0A Structure of hsDDB1-drDDB2 bound to a 16 bp CPD-duplex (pyrimidine at D-1 position) at 3.6 A resolution (CPD 3) Deposited 2011-09-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Mutation：YES CA CALCIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；100 MM MES, 28 MM NAOH, 16% PEG 350MME., pH 5.6
Resolution 3.60 Å R-free 0.347
4A0B Structure of hsDDB1-drDDB2 bound to a 16 bp CPD-duplex (pyrimidine at D-1 position) at 3.8 A resolution (CPD 4) Deposited 2011-09-08 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.3；100 MM MES, 15 MM NAOH, 18% PEG 350MME., pH 5.3
Resolution 3.80 Å R-free 0.319
4A0B Structure of hsDDB1-drDDB2 bound to a 16 bp CPD-duplex (pyrimidine at D-1 position) at 3.8 A resolution (CPD 4) Deposited 2011-09-08 Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain C 1–1140（1140 aa）
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.3；100 MM MES, 15 MM NAOH, 18% PEG 350MME., pH 5.3
Resolution 3.80 Å R-free 0.319
4A0K STRUCTURE OF DDB1-DDB2-CUL4A-RBX1 BOUND TO A 12 BP ABASIC SITE CONTAINING DNA-DUPLEX Deposited 2011-09-09 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain C 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.3；100MM TRIS-HCL PH 8.3, 33% PEG 200
Resolution 5.93 Å R-free 0.270
4A0L Structure of DDB1-DDB2-CUL4B-RBX1 bound to a 12 bp abasic site containing DNA-duplex Deposited 2011-09-09 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.2；100MM MES PH 6.2, 3.1% PEG 6000, 4% ETHYLENEGLYCOL
Resolution 7.40 Å R-free 0.320
4A0L Structure of DDB1-DDB2-CUL4B-RBX1 bound to a 12 bp abasic site containing DNA-duplex Deposited 2011-09-09 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain C 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.2；100MM MES PH 6.2, 3.1% PEG 6000, 4% ETHYLENEGLYCOL
Resolution 7.40 Å R-free 0.320
4A11 Structure of the hsDDB1-hsCSA complex Deposited 2011-09-13 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；1.4-1.58 M NAKPO4, 0.1 M NAMALONATE, 0-0.1 M LI2SO4, pH 8.0
Resolution 3.31 Å R-free 0.233
4CI1 Structure of the DDB1-CRBN E3 ubiquitin ligase bound to thalidomide Deposited 2013-12-05 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 EF2 S-Thalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6；PROTEIN WAS CRYSTALLIZED FROM 100 MM NA-CACODYLATE; 80 MM NAH2PO4; 120 MM K2HPO4; 800 MM TRI-NA CITRATE., pH 6
Resolution 2.98 Å R-free 0.233
4CI2 Structure of the DDB1-CRBN E3 ubiquitin ligase bound to lenalidomide Deposited 2013-12-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 LVY S-Lenalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 100 MM NA-CACODYLATE PH 6.2, 80 MM NAH2PO4, 120 MM K2HPO4, 950 MM TRI-NA CITRATE.
Resolution 2.95 Å R-free 0.234
4CI3 Structure of the DDB1-CRBN E3 ubiquitin ligase bound to Pomalidomide Deposited 2013-12-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 100 MM NA-CACOCYLATE, 80 MM NAH2PO4, 120 MM K2HPO4, 700 MM TRI-NA CITRATE., pH 6.5
Resolution 3.50 Å R-free 0.235
4E54 Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair Deposited 2012-03-14 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 2–1140（1139 aa） Fragment：DNA DAMAGE-BINDING PROTEIN 1 (DDB1; p127)
Mutation：NT-His10-DDB1 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；20mM Tris pH 7.5, 2mM MgCl2, 1mM EDTA, 2mM TECP, 5% Glycerol, 0.02% azide. UV-DDB-AP24 complex (molar ratio of 1:3 UV-DDB:DNA) at 2.5 mg/mL. 'AP24' refers to synthetic DNA substrate of 24-bpr with a central abasic site mimic., VAPOR DIFFUSION, temperature 277K
Resolution 2.85 Å R-free 0.281
4E5Z Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair Deposited 2012-03-15 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 2–1140（1139 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；20mM Tris pH 7.5, 2mM MgCl2, 1mM EDTA, 2mM TECP, 5% Glycerol, 0.02% azide. UV-DDB-AP24 complex (molar ratio of 1:3 UV-DDB:DNA) at 2.5 mg/mL. 'AP24' refers to synthetic DNA substrate of 24-bpr with a central abasic site mimic., VAPOR DIFFUSION, temperature 277K
Resolution 3.22 Å R-free 0.284
4TZ4 Crystal Structure of Human Cereblon in Complex with DDB1 and Lenalidomide Deposited 2014-07-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–1140（1139 aa）
Not recorded ZN ZINC ION × 1 LVY S-Lenalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；100mM HEPES pH 7.5, 18% PEG 10K
Resolution 3.01 Å R-free 0.271
5FQD Structural basis of Lenalidomide induced CK1a degradation by the crl4crbn ubiquitin ligase Deposited 2015-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded ZN ZINC ION × 1 LVY S-Lenalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 70 MM TRIS PH 7.0 140 MM MGCL2 7% W/V PEG 8000
Resolution 2.45 Å R-free 0.210
5FQD Structural basis of Lenalidomide induced CK1a degradation by the crl4crbn ubiquitin ligase Deposited 2015-12-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded ZN ZINC ION × 1 LVY S-Lenalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 70 MM TRIS PH 7.0 140 MM MGCL2 7% W/V PEG 8000
Resolution 2.45 Å R-free 0.210
5HXB Cereblon in complex with DDB1, CC-885, and GSPT1 Deposited 2016-01-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Y 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 85C 1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；280 K；200mM Sodium Citrate, Tris pH 8.5, 18% PEG 3350
Resolution 3.60 Å R-free 0.273
5HXB Cereblon in complex with DDB1, CC-885, and GSPT1 Deposited 2016-01-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 85C 1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；280 K；200mM Sodium Citrate, Tris pH 8.5, 18% PEG 3350
Resolution 3.60 Å R-free 0.273
5JK7 The X-ray structure of the DDB1-DCAF1-Vpr-UNG2 complex Deposited 2016-04-26 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；289.15 K；100 mM Na Ctrate, pH 5.6, 11% PEG 20000
Resolution 3.49 Å R-free 0.206
5JK7 The X-ray structure of the DDB1-DCAF1-Vpr-UNG2 complex Deposited 2016-04-26 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions BATCH MODE；289.15 K；100 mM Na Ctrate, pH 5.6, 11% PEG 20000
Resolution 3.49 Å R-free 0.206
5V3O Cereblon in complex with DDB1 and CC-220 Deposited 2017-03-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded 8W7 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；200mM NaCl, 20% PEG 3350
Resolution 3.20 Å R-free 0.267
6BN7 Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET23 PROTAC. Deposited 2017-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded ZN ZINC ION × 1 RN3 methyl {(6S)-4-(4-chlorophenyl)-2-[(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl)carbamoyl]-3,9-dimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl}acetate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9% (w/v) PEG20K, 18% (v/v) PEG MME 550, 0.09M BICINE pH8.5, 9% Silver bullet B5 (0.33% w/v 2,7-Naphthalenedisulfonic acid disodium salt, 0.33% w/v Azelaic acid, 0.33% w/v trans-Cinnamic acid, 0.02 M HEPES sodium pH 6.8)
Resolution 3.50 Å R-free 0.256
6BN8 Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET55 PROTAC. Deposited 2017-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9% PEG20K, 18% PEG MME 550, 0.09M BICINE pH8.5, 9% Silver bullet G4 (0.16% w/v 3-Indolebutyric acid, 0.16% w/v Hexadecanedioic acid, 0.16% w/v Oxamic acid, 0.16% w/v Pyromellitic acid, 0.16% w/v Sebacic acid, 0.16% w/v Suberic acid, 0.02 M HEPES sodium pH 6.8)
Resolution 3.99 Å R-free 0.333
6BN9 Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET70 PROTAC Deposited 2017-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；10% (w/v) PEG20K, 20% (v/v) PEG MME 550, 0.1M BICINE pH8.5, Silver Bullet F2 (0.2% w/v D-Fructose 1,6-bisphosphate trisodium salt hydrate, 0.2% w/v Glycerol phosphate disodium salt hydrate, 0.2% w/v L-O-Phosphoserine, 0.2% w/v O-Phospho-L-tyrosine, 0.2% w/v Phytic acid sodium salt hydrate, 0.02 M HEPES sodium pH 6.8)
Resolution 4.38 Å R-free 0.301
6BNB Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET57 PROTAC Deposited 2017-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.34M NaH2PO4, 0.33M K2HPO4
Resolution 6.34 Å R-free 0.381
6BOY Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET6 PROTAC. Deposited 2017-11-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded ZN ZINC ION × 1 RN6 2-[(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]-N-(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl)acetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9% (w/v) PEG20K, 18% (v/v) PEG MME 550, 0.09M BICINE pH8.5, 9% (v/v) Silver bullet D11 (0.25% w/v 2,6-Naphthalenedisulfonic acid disodium salt, 0.25% w/v 4-Aminobenzoic acid, 0.25% w/v 5-Sulfosalicylic acid dihydrate, 0.25% w/v Naphthalene-1,3,6-trisulfonic acid trisodium salt hydrate, 0.02 M HEPES sodium pH 6.8)
Resolution 3.33 Å R-free 0.234
6DSZ Crystal structure of DDB1 in complex with DET1- and DDB1-associated protein 1 (DDA1) Deposited 2018-06-14 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.5, 20% (w/v) PEG4000, 180 mM NaCl, 5 mM DTT
Resolution 3.09 Å R-free 0.307
6DSZ Crystal structure of DDB1 in complex with DET1- and DDB1-associated protein 1 (DDA1) Deposited 2018-06-14 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.5, 20% (w/v) PEG4000, 180 mM NaCl, 5 mM DTT
Resolution 3.09 Å R-free 0.307
6FCV Structure of the human DDB1-CSA complex Deposited 2017-12-21 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M sodium citrate, 24% PEG 3350, 0.1 M bis-tris propane pH 8.0, 3% glycerol
Resolution 2.92 Å R-free 0.245
6H0G Structure of the DDB1-CRBN-pomalidomide complex bound to ZNF692(ZF4) Deposited 2018-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Mutation：;Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG) ; Mutation：;Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG) ; ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；Protein-drug solution: 350 uM ZNF692-ZF4, 70 uM DDB1/CRBN, 80 uM pomalidomide and in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP Crystallisation solution: 14.1% (w/v) PEG 5K MME and 70 mM Tris-HCl pH 7.5
Resolution 4.25 Å R-free 0.256
6H0G Structure of the DDB1-CRBN-pomalidomide complex bound to ZNF692(ZF4) Deposited 2018-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 706–1140（435 aa）
Mutation：;Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG) ; Mutation：;Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG) ; ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；Protein-drug solution: 350 uM ZNF692-ZF4, 70 uM DDB1/CRBN, 80 uM pomalidomide and in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP Crystallisation solution: 14.1% (w/v) PEG 5K MME and 70 mM Tris-HCl pH 7.5
Resolution 4.25 Å R-free 0.256
6PAI Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and sulfonamide E7820 Deposited 2019-06-11 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Not recorded EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 O6M 3-cyano-N-(3-cyano-4-methyl-1H-indol-7-yl)benzene-1-sulfonamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M sodium HEPES, pH 7.0, 15% w/v PEG4000
Resolution 2.90 Å R-free 0.252
6Q0R Structure of DDB1-DDA1-DCAF15 complex bound to E7820 and RBM39 Deposited 2019-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–395（395 aa） Fragment：internal deletion of the BPB domain
Chain A 706–1140（435 aa） Fragment：internal deletion of the BPB domain
Not recorded OXM OXAMIC ACID × 1 O6M 3-cyano-N-(3-cyano-4-methyl-1H-indol-7-yl)benzene-1-sulfonamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；300 K；20% PEG 4000
Resolution 2.90 Å R-free 0.251
6Q0V Structure of DDB1-DDA1-DCAF15 complex bound to tasisulam and RBM39 Deposited 2019-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–395（395 aa） Fragment：internal deletion of the BPB domain
Chain A 706–1140（435 aa） Fragment：internal deletion of the BPB domain
Not recorded P7M N-[(5-bromothiophen-2-yl)sulfonyl]-2,4-dichlorobenzamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；300 K；20% PEG 4000
Resolution 2.90 Å R-free 0.242
6Q0W Structure of DDB1-DDA1-DCAF15 complex bound to Indisulam and RBM39 Deposited 2019-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 1–395（395 aa） Fragment：internal deletion of the BPB domain
Chain A 706–1140（435 aa） Fragment：internal deletion of the BPB domain
Not recorded EF6 N~1~-(3-chloro-1H-indol-7-yl)benzene-1,4-disulfonamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；300 K；20% PEG 4000
Resolution 2.90 Å R-free 0.264
6R8Y Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB Deposited 2019-04-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
6R8Z Cryo-EM structure of NCP_THF2(-1)-UV-DDB Deposited 2019-04-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6R90 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class A Deposited 2019-04-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6R91 Cryo-EM structure of NCP_THF2(-3)-UV-DDB Deposited 2019-04-02 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6R92 Cryo-EM structure of NCP-THF2(+1)-UV-DDB class B Deposited 2019-04-02 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain K 1–395（395 aa）
Chain K 706–1140（435 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
6SJ7 Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and Indisulam Deposited 2019-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–1140（1140 aa）
Not recorded EF6 N~1~-(3-chloro-1H-indol-7-yl)benzene-1,4-disulfonamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
6TD3 Structure of DDB1 bound to CR8-engaged CDK12-cyclinK Deposited 2019-11-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 708–1140（433 aa）
Not recorded RC8 (2R)-2-({9-(1-methylethyl)-6-[(4-pyridin-2-ylbenzyl)amino]-9H-purin-2-yl}amino)butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；0.9 M ammonium citrate tribasic
Resolution 3.46 Å R-free 0.220
6TD3 Structure of DDB1 bound to CR8-engaged CDK12-cyclinK Deposited 2019-11-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 708–1140（433 aa）
Not recorded RC8 (2R)-2-({9-(1-methylethyl)-6-[(4-pyridin-2-ylbenzyl)amino]-9H-purin-2-yl}amino)butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；0.9 M ammonium citrate tribasic
Resolution 3.46 Å R-free 0.220
6TD3 Structure of DDB1 bound to CR8-engaged CDK12-cyclinK Deposited 2019-11-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 708–1140（433 aa）
Not recorded RC8 (2R)-2-({9-(1-methylethyl)-6-[(4-pyridin-2-ylbenzyl)amino]-9H-purin-2-yl}amino)butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；0.9 M ammonium citrate tribasic
Resolution 3.46 Å R-free 0.220
6UD7 Crystal structure of full-length human DCAF15-DDB1(deltaBPB)-DDA1-RBM39 in complex with indisulam Deposited 2019-09-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–395（395 aa）
Chain B 706–1140（435 aa）
Not recorded GOL GLYCEROL × 2 EF6 N~1~-(3-chloro-1H-indol-7-yl)benzene-1,4-disulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；2% (v:v) TacsimateTM, pH 5.0, 0.1 M sodium citrate tribasic dihydrate, pH 5.6, and 10-20% (w:v) polyethylene glycol 3350
Resolution 2.30 Å R-free 0.248
6UE5 Crystal structure of full-length human DCAF15-DDB1-deltaPBP-DDA1-RBM39 in complex with 4-(aminomethyl)-N-(3-cyano-4-methyl-1H-indol-7-yl)benzenesulfonamide Deposited 2019-09-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–395（395 aa）
Chain B 706–1140（435 aa）
Not recorded Q5J 4-(aminomethyl)-N-(3-cyano-4-methyl-1H-indol-7-yl)benzene-1-sulfonamide × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291.5 K；2% (v:v) TacsimateTM, pH 5.0, 0.1 M sodium citrate tribasic 676 dihydrate, pH 5.6, and 10-20% (w:v) polyethylene glycol 3350
Resolution 2.61 Å R-free 0.266
6UML Structural Basis for Thalidomide Teratogenicity Revealed by the Cereblon-DDB1-SALL4-Pomalidomide Complex Deposited 2019-10-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；10% PEG MME 500, 8% PEG 20K, 210mM calcium acetate, 100mM tris pH 7.5
Resolution 3.58 Å R-free 0.267
6XK9 Cereblon in complex with DDB1, CC-90009, and GSPT1 Deposited 2020-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Y 1–1140（1140 aa）
Not recorded V4M 2-(4-chlorophenyl)-N-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)-2,2-difluoroacetamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 100mM Tris-HCl (pH 7.5), 300mM sodium citrate
Resolution 3.64 Å R-free 0.245
6XK9 Cereblon in complex with DDB1, CC-90009, and GSPT1 Deposited 2020-06-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–1140（1140 aa）
Not recorded V4M 2-(4-chlorophenyl)-N-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)-2,2-difluoroacetamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 100mM Tris-HCl (pH 7.5), 300mM sodium citrate
Resolution 3.64 Å R-free 0.245
6ZUE Crystal structure of human DDB1 bound to human DCAF1 (amino acid residues 1046-1396) Deposited 2020-07-22 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；100 mM Tri-Na citrate pH 5.5 18% PEG 1000
Resolution 3.09 Å R-free 0.279
6ZX9 Crystal structure of SIV Vpr,fused to T4 lysozyme, isolated from moustached monkey, bound to human DDB1 and human DCAF1 (amino acid residues 1046-1396) Deposited 2020-07-29 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded GOL GLYCEROL × 8 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；8-10% PEG 4000 (w/v), 200 mM MgCl2, 100 mM HEPES-NaOH, pH 7.0-8.2.
Resolution 2.52 Å R-free 0.260
7LPS Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) Deposited 2021-02-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 2 RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.57；293 K；30% (w/v) PEG3350, 0.1 M Tris pH 8.57
Resolution 3.78 Å R-free 0.303
7LPS Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) Deposited 2021-02-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–1140（1140 aa）
Not recorded ZN ZINC ION × 2 RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.57；293 K；30% (w/v) PEG3350, 0.1 M Tris pH 8.57
Resolution 3.78 Å R-free 0.303
7LPS Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) Deposited 2021-02-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–1140（1140 aa）
Not recorded ZN ZINC ION × 2 RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.57；293 K；30% (w/v) PEG3350, 0.1 M Tris pH 8.57
Resolution 3.78 Å R-free 0.303
7LPS Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) Deposited 2021-02-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–1140（1140 aa）
Not recorded ZN ZINC ION × 2 RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.57；293 K；30% (w/v) PEG3350, 0.1 M Tris pH 8.57
Resolution 3.78 Å R-free 0.303
7OKQ Cryo-EM Structure of the DDB1-DCAF1-CUL4A-RBX1 Complex Deposited 2021-05-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: Hexadecameric
Chain A 1–1140（1140 aa）
Chain E 1–1140（1140 aa）
Chain I 1–1140（1140 aa）
Chain M 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.40 Å
7OO3 Pol II-CSB-CSA-DDB1-UVSSA (Structure1) Deposited 2021-05-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7OOB Pol II-CSB-CSA-DDB1-UVSSA-ADPBeF3 (Structure2) Deposited 2021-05-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 15 PDB declaration: octadecameric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7OOP Pol II-CSB-CSA-DDB1-UVSSA-PAF-SPT6 (Structure 3) Deposited 2021-05-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7OPC Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 4) Deposited 2021-05-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 25 PDB declaration: 28-meric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7OPD Pol II-CSB-CRL4CSA-UVSSA-SPT6-PAF (Structure 5) Deposited 2021-05-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 25 PDB declaration: 28-meric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7U8F Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2) and the molecular glue DKY709 Deposited 2022-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–395（395 aa）
Chain B 706–1140（435 aa）
Not recorded ZN ZINC ION × 2 LWK (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5
Resolution 3.15 Å R-free 0.243
7U8F Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2) and the molecular glue DKY709 Deposited 2022-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–395（395 aa）
Chain E 706–1140（435 aa）
Not recorded ZN ZINC ION × 2 LWK (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 SO4 SULFATE ION × 4 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5
Resolution 3.15 Å R-free 0.243
7UKN Crystal Structure of DDB1 in Complex with the H-Box Motif of pUL145 Deposited 2022-04-01 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；100 mM MES (pH 6.5-6.7), 16% PEG 4000, 50 mM NaCl, 5 mM DTT
Resolution 2.90 Å R-free 0.261
7V7B CryoEM structure of DDB1-VprBP complex in ARM-up conformation Deposited 2021-08-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–1140（1140 aa）
Chain D 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
7V7C CryoEM structure of DDB1-VprBP-Vpr-UNG2(94-313) complex Deposited 2021-08-21 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–1140（1140 aa）
Chain F 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7ZN7 Cryo-EM structure of RCMV-E E27 bound to human DDB1 (deltaBPB) and rat STAT2 CCD Deposited 2022-04-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–396（396 aa）
Chain A 706–1140（435 aa）
Mutation：delta396-705 GNGNSG Mutation：delta396-705 GNGNSG ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE；45 seconds adsorption 2 seconds blot
Resolution 3.78 Å
7ZNN Cryo-EM structure of RCMV-E E27 bound to human DDB1 (deltaBPB) and full-length rat STAT2 Deposited 2022-04-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–396（396 aa）
Chain A 706–1140（435 aa）
Mutation：Residues 396-705 have been replaced by a GNGNSG-linker Mutation：Residues 396-705 have been replaced by a GNGNSG-linker ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE；45 seconds adsorption 2 seconds blot
Resolution 4.80 Å
8AJM Structure of human DDB1-DCAF12 in complex with the C-terminus of CCT5 Deposited 2022-07-28 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.83 Å
8AJN Structure of the human DDB1-DCAF12 complex Deposited 2022-07-28 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8AJO Negative-stain electron microscopy structure of DDB1-DCAF12-CCT5 Deposited 2022-07-28 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
Resolution 30.60 Å
8B3D Structure of the Pol II-TCR-ELOF1 complex. Deposited 2022-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 17 PDB declaration: eicosameric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8B3F Pol II-CSB-CSA-DDB1-ELOF1 Deposited 2022-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 16 PDB declaration: nonadecameric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 9 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8B3G C(N)RL4CSA-UVSSA-E2-ubiquitin complex. Deposited 2022-09-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8B3I CRL4CSA-E2-Ub (state 2) Deposited 2022-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8BU1 Structure of DDB1 bound to DS17-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded GOL GLYCEROL × 5 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, NDSB-256 additive
Resolution 2.98 Å R-free 0.218
8BU1 Structure of DDB1 bound to DS17-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded GOL GLYCEROL × 5 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, NDSB-256 additive
Resolution 2.98 Å R-free 0.218
8BU1 Structure of DDB1 bound to DS17-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded GOL GLYCEROL × 5 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, NDSB-256 additive
Resolution 2.98 Å R-free 0.218
8BU2 Structure of DDB1 bound to DS18-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 12 RVQ ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-2-morpholin-4-yl-9-propan-2-yl-purin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.13 Å R-free 0.217
8BU2 Structure of DDB1 bound to DS18-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 16 RVQ ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-2-morpholin-4-yl-9-propan-2-yl-purin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.13 Å R-free 0.217
8BU2 Structure of DDB1 bound to DS18-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 13 RVQ ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-2-morpholin-4-yl-9-propan-2-yl-purin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.13 Å R-free 0.217
8BU3 Structure of DDB1 bound to DS19-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 6 RSI 2-morpholin-4-yl-9-propan-2-yl-~{N}-[(4-pyridin-2-ylphenyl)methyl]purin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.49 M ammonium sulfate, ammonium citrate, 0.07 M HEPES pH 6.8
Resolution 3.42 Å R-free 0.213
8BU3 Structure of DDB1 bound to DS19-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 706–1140（435 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 5 RSI 2-morpholin-4-yl-9-propan-2-yl-~{N}-[(4-pyridin-2-ylphenyl)methyl]purin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.49 M ammonium sulfate, ammonium citrate, 0.07 M HEPES pH 6.8
Resolution 3.42 Å R-free 0.213
8BU3 Structure of DDB1 bound to DS19-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 9 RSI 2-morpholin-4-yl-9-propan-2-yl-~{N}-[(4-pyridin-2-ylphenyl)methyl]purin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.49 M ammonium sulfate, ammonium citrate, 0.07 M HEPES pH 6.8
Resolution 3.42 Å R-free 0.213
8BU4 Structure of DDB1 bound to DS22-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 5 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 M ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.09 Å R-free 0.223
8BU4 Structure of DDB1 bound to DS22-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 6 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 M ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.09 Å R-free 0.223
8BU4 Structure of DDB1 bound to DS22-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 3 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 M ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.09 Å R-free 0.223
8BU5 Structure of DDB1 bound to SR-4835-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 1 RMF ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1 CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.28 M ammonium sulphate, 0.72 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0
Resolution 3.13 Å R-free 0.220
8BU5 Structure of DDB1 bound to SR-4835-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 706–1140（435 aa）
Not recorded RMF ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1 CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.28 M ammonium sulphate, 0.72 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0
Resolution 3.13 Å R-free 0.220
8BU5 Structure of DDB1 bound to SR-4835-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 2 RMF ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1 CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.28 M ammonium sulphate, 0.72 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0
Resolution 3.13 Å R-free 0.220
8BU6 Structure of DDB1 bound to DS55-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 2 RQE ~{N}-(1~{H}-benzimidazol-2-ylmethyl)-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.3
Resolution 3.45 Å R-free 0.249
8BU6 Structure of DDB1 bound to DS55-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 2 RQE ~{N}-(1~{H}-benzimidazol-2-ylmethyl)-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.3
Resolution 3.45 Å R-free 0.249
8BU6 Structure of DDB1 bound to DS55-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 2 RQE ~{N}-(1~{H}-benzimidazol-2-ylmethyl)-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.3
Resolution 3.45 Å R-free 0.249
8BU7 Structure of DDB1 bound to 21195-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 RS5 1-[2,6-bis(chloranyl)phenyl]-6-[[4-(2-hydroxyethyloxy)phenyl]methyl]-3-propan-2-yl-5H-pyrazolo[3,4-d]pyrimidin-4-one × 1 SO4 SULFATE ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.33 M ammonium sulfate, 0.045 M ammonium citrate, 0.07M HEPES pH 7
Resolution 3.25 Å R-free 0.219
8BU7 Structure of DDB1 bound to 21195-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 706–1140（435 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 RS5 1-[2,6-bis(chloranyl)phenyl]-6-[[4-(2-hydroxyethyloxy)phenyl]methyl]-3-propan-2-yl-5H-pyrazolo[3,4-d]pyrimidin-4-one × 1 SO4 SULFATE ION × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.33 M ammonium sulfate, 0.045 M ammonium citrate, 0.07M HEPES pH 7
Resolution 3.25 Å R-free 0.219
8BU7 Structure of DDB1 bound to 21195-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 706–1140（435 aa）
Not recorded RS5 1-[2,6-bis(chloranyl)phenyl]-6-[[4-(2-hydroxyethyloxy)phenyl]methyl]-3-propan-2-yl-5H-pyrazolo[3,4-d]pyrimidin-4-one × 1 SO4 SULFATE ION × 11 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.33 M ammonium sulfate, 0.045 M ammonium citrate, 0.07M HEPES pH 7
Resolution 3.25 Å R-free 0.219
8BU9 Structure of DDB1 bound to roscovitine-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 5 RRC R-ROSCOVITINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.42 M ammonium sulphate, 0.63 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0
Resolution 3.51 Å R-free 0.223
8BU9 Structure of DDB1 bound to roscovitine-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 5 RRC R-ROSCOVITINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.42 M ammonium sulphate, 0.63 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0
Resolution 3.51 Å R-free 0.223
8BU9 Structure of DDB1 bound to roscovitine-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 5 RRC R-ROSCOVITINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.42 M ammonium sulphate, 0.63 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0
Resolution 3.51 Å R-free 0.223
8BUA Structure of DDB1 bound to 919278-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded CIT CITRIC ACID × 2 RVH (2~{R})-~{N}-(1~{H}-benzimidazol-2-yl)-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate, 100 %w/v SB38D2, 0.07 M HEPES pH 7
Resolution 3.19 Å R-free 0.225
8BUA Structure of DDB1 bound to 919278-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 706–1140（435 aa）
Not recorded CIT CITRIC ACID × 3 RVH (2~{R})-~{N}-(1~{H}-benzimidazol-2-yl)-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate, 100 %w/v SB38D2, 0.07 M HEPES pH 7
Resolution 3.19 Å R-free 0.225
8BUA Structure of DDB1 bound to 919278-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 706–1140（435 aa）
Not recorded CIT CITRIC ACID × 4 RVH (2~{R})-~{N}-(1~{H}-benzimidazol-2-yl)-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate, 100 %w/v SB38D2, 0.07 M HEPES pH 7
Resolution 3.19 Å R-free 0.225
8BUB Structure of DDB1 bound to dCeMM4-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded CIT CITRIC ACID × 2 RNU ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 1 M sodium malonate additive
Resolution 3.42 Å R-free 0.237
8BUB Structure of DDB1 bound to dCeMM4-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded CIT CITRIC ACID × 3 RNU ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 1 M sodium malonate additive
Resolution 3.42 Å R-free 0.237
8BUB Structure of DDB1 bound to dCeMM4-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded CIT CITRIC ACID × 2 RNU ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 1 M sodium malonate additive
Resolution 3.42 Å R-free 0.237
8BUC Structure of DDB1 bound to dCeMM3-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 4 RKO 2-(1~{H}-benzimidazol-2-ylsulfanyl)-~{N}-(5-chloranylpyridin-2-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.85 Å R-free 0.224
8BUC Structure of DDB1 bound to dCeMM3-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 1 RKO 2-(1~{H}-benzimidazol-2-ylsulfanyl)-~{N}-(5-chloranylpyridin-2-yl)ethanamide × 1 CIT CITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.85 Å R-free 0.224
8BUC Structure of DDB1 bound to dCeMM3-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 4 RKO 2-(1~{H}-benzimidazol-2-ylsulfanyl)-~{N}-(5-chloranylpyridin-2-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.85 Å R-free 0.224
8BUD Structure of DDB1 bound to Z7-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 10 RP9 ~{N}-(5-bromanylpyridin-2-yl)-3-(4-oxidanylidenequinazolin-3-yl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.20 Å R-free 0.220
8BUD Structure of DDB1 bound to Z7-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 15 RP9 ~{N}-(5-bromanylpyridin-2-yl)-3-(4-oxidanylidenequinazolin-3-yl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.20 Å R-free 0.220
8BUD Structure of DDB1 bound to Z7-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 14 RP9 ~{N}-(5-bromanylpyridin-2-yl)-3-(4-oxidanylidenequinazolin-3-yl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.20 Å R-free 0.220
8BUE Structure of DDB1 bound to Z11-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 12 RVU ~{N}-(1~{H}-benzimidazol-2-yl)-1-(2-methoxy-5-methyl-phenyl)-5-oxidanylidene-pyrrolidine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.45 M ammonium sulphate, 0.07 M HEPES, pH 7.1
Resolution 3.25 Å R-free 0.213
8BUE Structure of DDB1 bound to Z11-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 16 RVU ~{N}-(1~{H}-benzimidazol-2-yl)-1-(2-methoxy-5-methyl-phenyl)-5-oxidanylidene-pyrrolidine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.45 M ammonium sulphate, 0.07 M HEPES, pH 7.1
Resolution 3.25 Å R-free 0.213
8BUE Structure of DDB1 bound to Z11-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 15 RVU ~{N}-(1~{H}-benzimidazol-2-yl)-1-(2-methoxy-5-methyl-phenyl)-5-oxidanylidene-pyrrolidine-3-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.45 M ammonium sulphate, 0.07 M HEPES, pH 7.1
Resolution 3.25 Å R-free 0.213
8BUF Structure of DDB1 bound to Z12-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 12 RW6 2-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-ylmethyl)-6,7-dimethoxy-3~{H}-quinazolin-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.47 M amonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.30 Å R-free 0.220
8BUF Structure of DDB1 bound to Z12-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 17 RW6 2-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-ylmethyl)-6,7-dimethoxy-3~{H}-quinazolin-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.47 M amonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.30 Å R-free 0.220
8BUF Structure of DDB1 bound to Z12-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 17 RW6 2-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-ylmethyl)-6,7-dimethoxy-3~{H}-quinazolin-4-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.47 M amonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.30 Å R-free 0.220
8BUG Structure of DDB1 bound to HQ461-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded CIT CITRIC ACID × 2 RPW 2-[2-[(6-methylpyridin-2-yl)amino]-1,3-thiazol-4-yl]-~{N}-(5-methyl-1,3-thiazol-2-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 0.1 M TMA additive
Resolution 3.53 Å R-free 0.231
8BUG Structure of DDB1 bound to HQ461-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded CIT CITRIC ACID × 2 RPW 2-[2-[(6-methylpyridin-2-yl)amino]-1,3-thiazol-4-yl]-~{N}-(5-methyl-1,3-thiazol-2-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 0.1 M TMA additive
Resolution 3.53 Å R-free 0.231
8BUG Structure of DDB1 bound to HQ461-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded CIT CITRIC ACID × 3 RPW 2-[2-[(6-methylpyridin-2-yl)amino]-1,3-thiazol-4-yl]-~{N}-(5-methyl-1,3-thiazol-2-yl)ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 0.1 M TMA additive
Resolution 3.53 Å R-free 0.231
8BUH Structure of DDB1 bound to WX3-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 5 RR9 6-[[[2-[[(2~{R})-1-oxidanylbutan-2-yl]amino]-9-propan-2-yl-purin-6-yl]amino]methyl]-3-pyridin-2-yl-1~{H}-pyridin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.7 M ammonium sulfate, 0.45 M ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.79 Å R-free 0.232
8BUH Structure of DDB1 bound to WX3-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 3 RR9 6-[[[2-[[(2~{R})-1-oxidanylbutan-2-yl]amino]-9-propan-2-yl-purin-6-yl]amino]methyl]-3-pyridin-2-yl-1~{H}-pyridin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.7 M ammonium sulfate, 0.45 M ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.79 Å R-free 0.232
8BUH Structure of DDB1 bound to WX3-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 4 RR9 6-[[[2-[[(2~{R})-1-oxidanylbutan-2-yl]amino]-9-propan-2-yl-purin-6-yl]amino]methyl]-3-pyridin-2-yl-1~{H}-pyridin-2-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.7 M ammonium sulfate, 0.45 M ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.79 Å R-free 0.232
8BUI Structure of DDB1 bound to DRF-053-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 7 RV6 (2~{R})-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)amino]purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.50 Å R-free 0.221
8BUI Structure of DDB1 bound to DRF-053-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 7 RV6 (2~{R})-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)amino]purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.50 Å R-free 0.221
8BUI Structure of DDB1 bound to DRF-053-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 7 RV6 (2~{R})-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)amino]purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.50 Å R-free 0.221
8BUJ Structure of DDB1 bound to DS06-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 5 RUW (2~{R})-2-[[6-(octylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.38 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.62 Å R-free 0.206
8BUJ Structure of DDB1 bound to DS06-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 4 RUW (2~{R})-2-[[6-(octylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.38 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.62 Å R-free 0.206
8BUJ Structure of DDB1 bound to DS06-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 5 RUW (2~{R})-2-[[6-(octylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.38 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.62 Å R-free 0.206
8BUK Structure of DDB1 bound to DS08-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 7 RWE (2~{R})-2-[[6-(naphthalen-2-ylmethylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.84 M ammonium sulfate, 0.36 M ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.41 Å R-free 0.210
8BUK Structure of DDB1 bound to DS08-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 6 RWE (2~{R})-2-[[6-(naphthalen-2-ylmethylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 CIT CITRIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.84 M ammonium sulfate, 0.36 M ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.41 Å R-free 0.210
8BUK Structure of DDB1 bound to DS08-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 7 RWE (2~{R})-2-[[6-(naphthalen-2-ylmethylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.84 M ammonium sulfate, 0.36 M ammonium citrate, 0.07 M HEPES pH 7
Resolution 3.41 Å R-free 0.210
8BUL Structure of DDB1 bound to DS11-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 8 RSU (2~{R})-2-[[6-(3-phenylpropylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M amonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.40 Å R-free 0.215
8BUL Structure of DDB1 bound to DS11-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 706–1140（435 aa）
Not recorded EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 8 RSU (2~{R})-2-[[6-(3-phenylpropylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M amonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.40 Å R-free 0.215
8BUL Structure of DDB1 bound to DS11-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 9 RSU (2~{R})-2-[[6-(3-phenylpropylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M amonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.40 Å R-free 0.215
8BUM Structure of DDB1 bound to DS15-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 11 T6X (2R)-2-[[6-(5-naphthalen-1-ylpentylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M amonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.36 Å R-free 0.212
8BUM Structure of DDB1 bound to DS15-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 15 T6X (2R)-2-[[6-(5-naphthalen-1-ylpentylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M amonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.36 Å R-free 0.212
8BUM Structure of DDB1 bound to DS15-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 13 T6X (2R)-2-[[6-(5-naphthalen-1-ylpentylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M amonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.36 Å R-free 0.212
8BUN Structure of DDB1 bound to DS16-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 10 RNF (2~{R})-2-[[6-[(4-phenylphenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.08 Å R-free 0.211
8BUN Structure of DDB1 bound to DS16-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 12 RNF (2~{R})-2-[[6-[(4-phenylphenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.08 Å R-free 0.211
8BUN Structure of DDB1 bound to DS16-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 12 RNF (2~{R})-2-[[6-[(4-phenylphenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.08 Å R-free 0.211
8BUO Structure of DDB1 bound to DS24-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 9 RLC (2~{R})-2-[[6-[(3-fluoranyl-4-pyridin-2-yl-phenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.47 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.58 Å R-free 0.219
8BUO Structure of DDB1 bound to DS24-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 7 RLC (2~{R})-2-[[6-[(3-fluoranyl-4-pyridin-2-yl-phenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.47 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.58 Å R-free 0.219
8BUO Structure of DDB1 bound to DS24-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 10 RLC (2~{R})-2-[[6-[(3-fluoranyl-4-pyridin-2-yl-phenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.47 M ammonium sulphate, 0.07 M HEPES, pH 6.8
Resolution 3.58 Å R-free 0.219
8BUP Structure of DDB1 bound to DS30-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 11 RWN (2~{R})-2-[[6-[3-(3-methylphenyl)propylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.44 M ammonium sulphate, 2.143 %v/v PEG 200, 0.07 M HEPES pH 7.5
Resolution 3.41 Å R-free 0.223
8BUP Structure of DDB1 bound to DS30-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 22 RWN (2~{R})-2-[[6-[3-(3-methylphenyl)propylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.44 M ammonium sulphate, 2.143 %v/v PEG 200, 0.07 M HEPES pH 7.5
Resolution 3.41 Å R-free 0.223
8BUP Structure of DDB1 bound to DS30-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 24 RWN (2~{R})-2-[[6-[3-(3-methylphenyl)propylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.44 M ammonium sulphate, 2.143 %v/v PEG 200, 0.07 M HEPES pH 7.5
Resolution 3.41 Å R-free 0.223
8BUQ Structure of DDB1 bound to DS43-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded CIT CITRIC ACID × 2 RQ9 (2~{R})-2-[[6-[[1-(3-chlorophenyl)pyrazol-3-yl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, Jeff600 additive
Resolution 3.20 Å R-free 0.216
8BUQ Structure of DDB1 bound to DS43-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded CIT CITRIC ACID × 2 RQ9 (2~{R})-2-[[6-[[1-(3-chlorophenyl)pyrazol-3-yl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, Jeff600 additive
Resolution 3.20 Å R-free 0.216
8BUQ Structure of DDB1 bound to DS43-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded CIT CITRIC ACID × 2 RQ9 (2~{R})-2-[[6-[[1-(3-chlorophenyl)pyrazol-3-yl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, Jeff600 additive
Resolution 3.20 Å R-free 0.216
8BUR Structure of DDB1 bound to DS50-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 7 RQU ~{N}-[2-(2-methoxyphenyl)ethyl]-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.64 Å R-free 0.234
8BUR Structure of DDB1 bound to DS50-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 10 RQU ~{N}-[2-(2-methoxyphenyl)ethyl]-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.64 Å R-free 0.234
8BUR Structure of DDB1 bound to DS50-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 7 RQU ~{N}-[2-(2-methoxyphenyl)ethyl]-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]ethanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.64 Å R-free 0.234
8BUS Structure of DDB1 bound to DS59-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 5 RMX 1,3-dimethyl-5-[[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]methyl]pyrazole-4-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.26 Å R-free 0.228
8BUS Structure of DDB1 bound to DS59-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 3 RMX 1,3-dimethyl-5-[[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]methyl]pyrazole-4-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.26 Å R-free 0.228
8BUS Structure of DDB1 bound to DS59-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 706–1140（435 aa）
Not recorded SO4 SULFATE ION × 6 RMX 1,3-dimethyl-5-[[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]methyl]pyrazole-4-sulfonamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 7.0
Resolution 3.26 Å R-free 0.228
8BUT Structure of DDB1 bound to DS61-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 7 RQ5 2-[[6-[[4-(2-hydroxyethyloxy)phenyl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.374 M ammonium sulfate, 0.07 M HEPES pH 7.3
Resolution 3.25 Å R-free 0.217
8BUT Structure of DDB1 bound to DS61-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 6 RQ5 2-[[6-[[4-(2-hydroxyethyloxy)phenyl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.374 M ammonium sulfate, 0.07 M HEPES pH 7.3
Resolution 3.25 Å R-free 0.217
8BUT Structure of DDB1 bound to DS61-engaged CDK12-cyclin K Deposited 2022-11-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa）
Chain G 709–1140（432 aa）
Not recorded SO4 SULFATE ION × 8 RQ5 2-[[6-[[4-(2-hydroxyethyloxy)phenyl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.374 M ammonium sulfate, 0.07 M HEPES pH 7.3
Resolution 3.25 Å R-free 0.217
8CVP Cereblon-DDB1 in the Apo form Deposited 2022-05-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4? coldroom
Resolution 3.40 Å
8D7U Cereblon~DDB1 bound to CC-92480 with DDB1 in the linear conformation Deposited 2022-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.10 Å
8D7V Cereblon~DDB1 bound to CC-92480 with DDB1 in the twisted conformation Deposited 2022-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.20 Å
8D7W Cereblon~DDB1 bound to CC-92480 with DDB1 in the hinged conformation Deposited 2022-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.10 Å
8D7X Cereblon~DDB1 in the Apo form with DDB1 in the hinged conformation Deposited 2022-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.40 Å
8D7Y Cereblon-DDB1 in the Apo form with DDB1 in the twisted conformation Deposited 2022-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.40 Å
8D7Z Cereblon-DDB1 bound to CC-92480 and Ikaros ZF1-2-3 Deposited 2022-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 2 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.10 Å
8D80 Cereblon~DDB1 bound to Iberdomide and Ikaros ZF1-2-3 Deposited 2022-06-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 2 8W7 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.60 Å
8D81 Cereblon~DDB1 bound to Pomalidomide Deposited 2022-06-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–395（395 aa） Fragment：residues 396 through 706 deleted, substituted with GNGNSG,residues 396 through 706 deleted, substituted with GNGNSG
Chain A 706–1140（435 aa） Fragment：residues 396 through 706 deleted, substituted with GNGNSG,residues 396 through 706 deleted, substituted with GNGNSG
Not recorded ZN ZINC ION × 1 Y70 S-Pomalidomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.90 Å
8DEY Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2,3) and the molecular glue DKY709 Deposited 2022-06-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–395（395 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140
Chain B 706–1140（435 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140
Not recorded ZN ZINC ION × 3 LWK (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5
Resolution 3.70 Å R-free 0.348
8DEY Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2,3) and the molecular glue DKY709 Deposited 2022-06-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–395（395 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140
Chain E 706–1140（435 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5
Resolution 3.70 Å R-free 0.348
8G46 Cryo-EM structure of DDB1deltaB-DDA1-DCAF16-BRD4(BD2)-MMH2 Deposited 2023-02-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–395（395 aa） Fragment：UNP residues 1-395 + GNGNSG linker + UNP residues 706-1140
Chain A 706–1140（435 aa） Fragment：UNP residues 1-395 + GNGNSG linker + UNP residues 706-1140
Not recorded ZN ZINC ION × 1 YK3 tert-butyl [(6S,10P)-4-{4-[(ethanesulfonyl)amino]phenyl}-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50 mM HEPES pH 7.4, 200 mM NaCl, 2 mM TCEP, 0.011% LMNG
cryo-EM vitrification conditions Cryogen ETHANE；detergent added directly before grid application
Resolution 2.20 Å
8G66 Structure with SJ3149 Deposited 2023-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded ZN ZINC ION × 1 YOT (3S)-3-{5-[(1,2-benzoxazol-3-yl)amino]-1-oxo-1,3-dihydro-2H-isoindol-2-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；70 MM TRIS PH 7.0, 140 MM MGCL2, 7% W/V PEG 8000
Resolution 3.45 Å R-free 0.272
8G66 Structure with SJ3149 Deposited 2023-02-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–395（395 aa）
Chain D 706–1140（435 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；70 MM TRIS PH 7.0, 140 MM MGCL2, 7% W/V PEG 8000
Resolution 3.45 Å R-free 0.272
8OIZ Crystal structure of human CRBN-DDB1 in complex with Pomalidomide Deposited 2023-03-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded EDO 1,2-ETHANEDIOL × 6 ZN ZINC ION × 1 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；291 K；0.8 microliter of CRBN-DDB1 complex at 25 mg/mL (including 1 mM compound and 2 % DMSO final) plus 0.8 microliter of a crystallisation solution consisting of 0.1 M Hepes pH 8.2, 0.2 M NaCl and 10-16 % PEG Smear Medium, plus 0.2 microliter of seeds (established from the same conditions), against 500 microliter of crystallisation solution.
Resolution 2.50 Å R-free 0.262
8OJH Crystal structure of human CRBN-DDB1 in complex with compound 4 Deposited 2023-03-24 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded EDO 1,2-ETHANEDIOL × 9 ZN ZINC ION × 1 VP9 4-azanyl-2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-7-methoxy-isoindole-1,3-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；291 K；0.8 microliter of CRBN-DDB1 complex at 25 mg/mL (including 1 mM compound and 2 % DMSO final) plus 0.8 microliter of a crystallisation solution consisting of 0.1 M Hepes pH 8.2, 0.2 M NaCl and 10-16 % PEG Smear Medium, plus 0.2 microliter of seeds (established from the same conditions), against 500 microliter of crystallisation solution.
Resolution 2.72 Å R-free 0.254
8QH5 CryoEM structure of UVSSA(VHS)-CSA-DDB1-DDA1 Deposited 2023-09-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8ROX Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to compound furan 12 Deposited 2024-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–395（395 aa）
Chain B 706–1140（435 aa）
Not recorded A1H17 5-[[3,4-bis(chloranyl)-1~{H}-indol-7-yl]sulfamoyl]-~{N},~{N},3-trimethyl-furan-2-carboxamide;ethane × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8ROY Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to compound furan 24 Deposited 2024-01-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–395（395 aa）
Chain B 706–1140（435 aa）
Not recorded A1H18 1-[5-[[3,4-bis(chloranyl)-1~{H}-indol-7-yl]sulfamoyl]-3-methyl-furan-2-yl]carbonyl-~{N}-methyl-piperidine-4-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8T9A CryoEM structure of human DDB1-DCAF12 in complex with MAGEA3 Deposited 2023-06-23 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.17 Å
8TL6 Cryo-EM structure of DDB1deltaB-DDA1-DCAF5 Deposited 2023-07-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；25mM HEPES, pH 7.4, 200mM NaCl, 4mM TCEP
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 2.63 Å
8TNP Cryo-EM structure of DDB1dB:CRBN:Pomalidomide:SD40 Deposited 2023-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Mutation：residues 396-705 deleted Mutation：residues 396-705 deleted ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM HEPES/NaOH pH 7.0, 150 mM NaCl, and 3 mM TCEP. DMSO concentrations were kept below 2% (v/v)
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.
Resolution 3.30 Å
8TNQ Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 1 Deposited 2023-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Mutation：residues 396-705 deleted Mutation：residues 396-705 deleted ZN ZINC ION × 2 MIQ 2-[(3S)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1H-isoindole-1,3(2H)-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM HEPES/NaOH pH 7.0, 150 mM NaCl, and 3 mM TCEP. DMSO concentrations were kept below 2% (v/v)
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.
Resolution 2.41 Å
8TNR Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 2 Deposited 2023-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Mutation：residues 396-705 deleted Mutation：residues 396-705 deleted ZN ZINC ION × 2 MIQ 2-[(3S)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1H-isoindole-1,3(2H)-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM HEPES/NaOH pH 7.0, 150 mM NaCl, and 3 mM TCEP. DMSO concentrations were kept below 2% (v/v)
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.
Resolution 2.50 Å
8TZX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue dWIZ-1 Deposited 2023-08-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–395（395 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140
Chain B 706–1140（435 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140
Not recorded ZN ZINC ION × 2 U3I (3S)-3-(5-{(1R)-1-[(2R)-1-ethylpiperidin-2-yl]ethoxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350
Resolution 3.15 Å R-free 0.252
8TZX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue dWIZ-1 Deposited 2023-08-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–395（395 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140
Chain E 706–1140（435 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140
Not recorded ZN ZINC ION × 2 U3I (3S)-3-(5-{(1R)-1-[(2R)-1-ethylpiperidin-2-yl]ethoxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350
Resolution 3.15 Å R-free 0.252
8U16 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to Pomalidomide Deposited 2023-08-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–395（395 aa）
Chain B 706–1140（435 aa）
Not recorded ZN ZINC ION × 3 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
Resolution 2.90 Å R-free 0.273
8U16 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to Pomalidomide Deposited 2023-08-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–395（395 aa）
Chain E 706–1140（435 aa）
Not recorded ZN ZINC ION × 3 Y70 S-Pomalidomide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
Resolution 2.90 Å R-free 0.273
8U17 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-long bound to Pomalidomide Deposited 2023-08-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–395（395 aa）
Chain B 706–1140（435 aa）
Not recorded ZN ZINC ION × 3 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
Resolution 3.10 Å R-free 0.346
8U17 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-long bound to Pomalidomide Deposited 2023-08-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–395（395 aa）
Chain E 706–1140（435 aa）
Not recorded ZN ZINC ION × 3 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
Resolution 3.10 Å R-free 0.346
8UH6 Degrader-induced complex between PTPN2 and CRBN-DDB1 Deposited 2023-10-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded WO8 (5P)-3-(carboxymethoxy)-4-chloro-5-(3-{[(4S)-1-({3-[(4-{1-[(3R)-2,6-dioxopiperidin-3-yl]-3-methyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl}piperidine-1-carbonyl)amino]phenyl}methanesulfonyl)-2,2-dimethylpiperidin-4-yl]amino}phenyl)thiophene-2-carboxylic acid × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8WQR Structure of the DDB1-AMBRA1 E3 ligase receptor complex linked to cell cycle regulation Deposited 2023-10-12 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
8ZSW Crystal Structure of Human DDB1, a Component of the E3 Ubiquitin Ligase Complex Deposited 2024-06-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1140（1140 aa）
Not recorded ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；287 K；0.1M MES (pH 6.5), 0.1M sodium acetate, 27%(w/v) PEG 400
Resolution 2.25 Å R-free 0.229
9BBE Co-crystal structure of human DDB1 bound to fragment UB028668 Deposited 2024-04-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1140（1140 aa）
Not recorded TLA L(+)-TARTARIC ACID × 2 A1AK9 5-(4-methoxyphenyl)-3-[(3S)-pyrrolidin-3-yl]-1,2,4-oxadiazole × 1 UNX UNKNOWN LIGAND × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% (v/w) PEG 3350, 0.2 M di-NH4tart
Resolution 2.00 Å R-free 0.239
9BBG Co-crystal structure of human DDB1 bound to fragment UB028671 Deposited 2024-04-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1140（1140 aa）
Not recorded TLA L(+)-TARTARIC ACID × 2 A1ALA 1H-indol-6-amine × 1 EDO 1,2-ETHANEDIOL × 6 UNX UNKNOWN LIGAND × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% (v/w) PEG 3350, 0.2 M di-NH4tart
Resolution 1.70 Å R-free 0.218
9BBH Co-crystal structure of human DDB1 bound to fragment UB028670 Deposited 2024-04-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1140（1140 aa）
Not recorded TLA L(+)-TARTARIC ACID × 2 VVP 4-methoxy-1H-indole × 2 EDO 1,2-ETHANEDIOL × 2 UNX UNKNOWN LIGAND × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% (v/w) PEG 3350, 0.2 M di-NH4tart
Resolution 2.00 Å R-free 0.232
9BBI Co-crystal structure of human DDB1 bound to fragment UB028669 Deposited 2024-04-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1140（1140 aa）
Not recorded TLA L(+)-TARTARIC ACID × 2 A1ALB 3-([1,3]oxazolo[4,5-b]pyridin-2-yl)aniline × 1 UNX UNKNOWN LIGAND × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% (v/w) PEG 3350, 0.2 M di-NH4tart
Resolution 1.90 Å R-free 0.221
9BJZ Structure of the human DDD-Ube2e2 complex Deposited 2024-04-26 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Mutation：residues 396-705 replaced with GNGNSG Mutation：residues 396-705 replaced with GNGNSG No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.83 Å
9BZ0 Structure of an STK19-containing TC-NER complex Deposited 2024-05-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: 22-meric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
9C5T Cryo EM structure of DCAF2 Deposited 2024-06-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å
9C5U Cryo EM structure of DCAF2:Compound 1 complex Deposited 2024-06-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–1140（1140 aa）
Not recorded A1AUM 1'-acetyl-1',4'-dihydro-3'H-spiro[cyclopentane-1,2'-quinoxalin]-3'-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
9C5V Cryo EM structure of a DCAF2:degrader:BRD4 ternary complex Deposited 2024-06-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–1140（1140 aa）
Not recorded A1AUO N-({4-[(4-{[1'-(chloroacetyl)-3'-oxo-3',4'-dihydro-1'H-spiro[cyclopentane-1,2'-quinoxalin]-6'-yl]oxy}piperidin-1-yl)methyl]phenyl}methyl)-2-[(6S,10P)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å
9D0W Cryo-EM structure of CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 4 Deposited 2024-08-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 A1A1I (3R)-3-(5-{4-[(2-{4-[(8-cyclopentyl-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl)amino]-3-methylbenzene-1-sulfonyl}-7-azaspiro[3.5]nonan-7-yl)methyl]piperidin-1-yl}-4-fluoro-3-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-1-yl)piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9DHD The ternary complex of DDB1, DDA1, DET1 Deposited 2024-09-03 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–1140（1139 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9DJT Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-5 Deposited 2024-09-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–395（395 aa）
Chain B 706–1140（435 aa）
Not recorded ZN ZINC ION × 2 SO4 SULFATE ION × 1 A1A5H (3S)-3-(5-{[(4R)-6-ethyl-6-azaspiro[2.5]octan-4-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350
Resolution 2.95 Å R-free 0.260
9DJT Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-5 Deposited 2024-09-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–395（395 aa）
Chain E 706–1140（435 aa）
Not recorded ZN ZINC ION × 2 SO4 SULFATE ION × 1 A1A5H (3S)-3-(5-{[(4R)-6-ethyl-6-azaspiro[2.5]octan-4-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350
Resolution 2.95 Å R-free 0.260
9DJX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-6 Deposited 2024-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–395（395 aa）
Chain B 706–1140（435 aa）
Not recorded ZN ZINC ION × 2 SO4 SULFATE ION × 1 A1A5I (3S)-3-(5-{[(3R,6S)-1-ethyl-6-methylpiperidin-3-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1M BIS-TRIS Propane pH 7.5, 20% PEG3350 (Qiagen PACT G8)
Resolution 3.35 Å R-free 0.271
9DJX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-6 Deposited 2024-09-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–395（395 aa）
Chain E 706–1140（435 aa）
Not recorded ZN ZINC ION × 2 SO4 SULFATE ION × 2 A1A5I (3S)-3-(5-{[(3R,6S)-1-ethyl-6-methylpiperidin-3-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1M BIS-TRIS Propane pH 7.5, 20% PEG3350 (Qiagen PACT G8)
Resolution 3.35 Å R-free 0.271
9DQD cryo-EM structure of human Cereblon/DDB1 in complex with a non-traditional CRBN binder Deposited 2024-09-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–395（395 aa）
Chain B 706–1140（435 aa）
Mutation：deletion of residues 396-705 Mutation：deletion of residues 396-705 ZN ZINC ION × 1 A1BEP (3R)-3-{1-methyl-6-[(piperidin-4-yl)amino]-1H-indazol-3-yl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9DWV Ternary complex of CRBN-DDB1-PPIL4 RRM domain with FPFT-2216 Deposited 2024-10-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 A1BC8 (3S)-3-[(4M)-4-(4-methoxythiophen-3-yl)-1H-1,2,3-triazol-1-yl]piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9DWW Ternary complex of CRBN-DDB1-PDE6D with FPFT-2216 Deposited 2024-10-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 A1BC8 (3S)-3-[(4M)-4-(4-methoxythiophen-3-yl)-1H-1,2,3-triazol-1-yl]piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Chain I 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Chain A 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Chain C 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Chain E 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Chain G 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Chain K 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain M 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Chain M 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain O 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Chain O 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9EJQ Crystal structure of DDB1 in complex with XS381952 Deposited 2024-11-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1140（1140 aa）
Not recorded TLA L(+)-TARTARIC ACID × 2 GOL GLYCEROL × 6 A1BIX (4S)-4-(3-ethoxyphenyl)-3-methyl-1-[(4R)-[1,2,4]triazolo[4,3-b]pyridazin-6-yl]-1,4,5,7-tetrahydro-6H-pyrazolo[3,4-b]pyridin-6-one × 1 EDO 1,2-ETHANEDIOL × 5 SO4 SULFATE ION × 7 UNX UNKNOWN LIGAND × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20.0 P3350, 0.2 di-NH4tart
Resolution 1.87 Å R-free 0.220
9ER2 PolII-TCR-STK19 structure. Deposited 2024-03-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: 22-meric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 11 MG MAGNESIUM ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9FD2 Structure of Pol II-TC-NER-STK19 complex Deposited 2024-05-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: 22-meric
Chain b 1–1140（1140 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9FJX Crystal structure of human CRBN-DDB1 in complex with Lenalidomide Deposited 2024-05-31 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded EDO 1,2-ETHANEDIOL × 5 DMS DIMETHYL SULFOXIDE × 3 ZN ZINC ION × 1 LVY S-Lenalidomide × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；291 K；0.8 microliter of CRBN-DDB1 complex at 25 mg/mL (including 1 mM compound and 2 % DMSO final) plus 0.8 microliter of a crystallisation solution consisting of 0.1 M Hepes pH 8.2, 0.2 M NaCl and 10-16 % PEG Smear Medium, plus 0.2 microliter of seeds (established from the same conditions), against 500 microliter of crystallisation solution.
Resolution 2.00 Å R-free 0.232
9FMR Structure of DDB1/Cdk12/Cyclin K with molecular glue SR-4835 Deposited 2024-06-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 1–391（391 aa）
Chain A 708–1140（433 aa）
Chain D 1–391（391 aa）
Chain D 708–1140（433 aa）
Chain G 1–391（391 aa）
Chain G 708–1140（433 aa）
Not recorded RMF ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；283 K；1 M potassium citrate and 15% glycerol
Resolution 3.90 Å R-free 0.250
9H59 Cryo-EM structure of DDB1-CRBN in complex with NK7-902 and NEK7 Deposited 2024-10-22 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded A1ISP 2-[(3S)-2,6-bis(oxidanylidene)piperidin-3-yl]-5-[(1S,2R,5S)-2-(ethylamino)-8-azabicyclo[3.2.1]octan-8-yl]isoindole-1,3-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9HNE Cereblon in complex with DDB1, GSPT1 and Compound-1 Deposited 2024-12-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 A1IWG 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1-oxidanylidene-3~{H}-isoindole-5-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Sodium citrate, 0.1 M Bis-Tris propane pH 7.5, 20% w/v PEG 3350
Resolution 3.90 Å R-free 0.336
9HNE Cereblon in complex with DDB1, GSPT1 and Compound-1 Deposited 2024-12-10 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 A1IWG 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1-oxidanylidene-3~{H}-isoindole-5-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Sodium citrate, 0.1 M Bis-Tris propane pH 7.5, 20% w/v PEG 3350
Resolution 3.90 Å R-free 0.336
9HPI Cryo-EM structure of DDB1dB-CRBN-MRT-0031619, conformation 1 Deposited 2024-12-13 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Mutation：aa396-705 replaced with GNGNSG ZN ZINC ION × 2 A1IW1 (3~{S})-3-[3-oxidanylidene-5-[8-(phenylcarbonyl)-2,8-diazaspiro[4.5]decan-2-yl]-1~{H}-isoindol-2-yl]piperidine-2,6-dione × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Sample supplemented with DDM directly before vitrification
cryo-EM vitrification conditions Cryogen ETHANE；LEICA EMGP2
Resolution 2.93 Å
9HPJ Cryo-EM structure of DDB1dB-CRBN-MRT-0031619, conformation 2 Deposited 2024-12-13 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Mutation：aa396-705 replaced with GNGNSG ZN ZINC ION × 2 A1IW1 (3~{S})-3-[3-oxidanylidene-5-[8-(phenylcarbonyl)-2,8-diazaspiro[4.5]decan-2-yl]-1~{H}-isoindol-2-yl]piperidine-2,6-dione × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Sample supplemented with DDM directly before vitrification
cryo-EM vitrification conditions Cryogen ETHANE；LEICA EMGP2
Resolution 3.10 Å
9HWG Structure of the transcribing Pol II-TCR-RECQL5 complex Deposited 2025-01-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 18 PDB declaration: 21-meric
Chain d 1–1140（1140 aa）
Not recorded ZN ZINC ION × 10 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES pH 7.5, 50 mM KCl, 4 mM MgCl2, 1 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9IVD Cryo-EM structure of CyclinD1 bound AMBRA1-DDB1 Deposited 2024-07-23 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.55 Å
9J6J HBx fused DDB1 4M mutant Deposited 2024-08-16 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–1140（1140 aa）
Mutation：A583D,W774K,I770D,R772E No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.86 Å
9J6K HBx complexed with DDB1 Deposited 2024-08-16 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.68 Å
9LTJ Cryo-EM structure of DDB1-DDA1-DET1 complex Deposited 2025-02-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
9LTL Cryo-EM structure of DDB1-DDA1-DET1 complex Deposited 2025-02-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
9LTO Cryo-EM structure of DDB1-DDA1-DET1-Ube2e2 complex Deposited 2025-02-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain S 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.92 Å
9LTR Cryo-EM structure of dimeric DDB1-DDA1-DET1-Ube2e2-COP1 complex Deposited 2025-02-06 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 1–1140（1140 aa）
Chain E 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
9LTW protein structure of DDB1-DDA1-DET1 Deposited 2025-02-06 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.25 Å
9LTZ protein structure of DDB1-DDA1-DET1-Ube2e2 complex Deposited 2025-02-07 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain S 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.26 Å
9LU1 protein structure of DDB1-DDA1-DET1-Ube2e2 bound to COP1 dimer Deposited 2025-02-07 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain S 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.62 Å
9LUL Local refinement of stacked like DDB1-DDA1-DET1-Ube2e2-COP1 complex (layer 1) Deposited 2025-02-09 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain c 1–1140（1140 aa）
Chain f 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.99 Å
9LWI The head region of HBx-Smc5/6 ubiquitination complex Deposited 2025-02-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain B 1–1140（1140 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9LWJ The head-arm region of HBx-Smc5/6 ubiquitination complex Deposited 2025-02-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 1–1140（1140 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.19 Å
9LWL HBx-Smc5/6 ubiquitination complex Deposited 2025-02-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 1–1140（1140 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.25 Å
9M0Y Local refinement of stacked like DDB1-DDA1-DET1-Ube2e2-COP1 complex (layer 2) Deposited 2025-02-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain S 1–1140（1140 aa）
Chain V 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.25 Å
9NFQ Crystal structure of CRBN-DDB1 and MRT-3486 in complex with NEK7 Deposited 2025-02-21 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded A1BX6 (3S)-N-{[(4R)-3-(2,4-dioxo-1,3-diazinan-1-yl)imidazo[1,2-a]pyridin-7-yl]methyl}-2-(phenylmethanesulfonyl)-1,2,3,4-tetrahydroisoquinoline-3-carboxamide × 1 ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.029 M HEPES salt, 0.071 M MOPS acid, 0.06 M NaNO3, 0.06 M Na2HPO4, 0.06 M (NH4)2SO4, 11 % (w/v) PEG 8,000 and 25 % (v/v) ethylene glycol.
Resolution 3.25 Å R-free 0.261
9NFR Crystal structure of CRBN-DDB1 and MRT-23227 in complex with VAV1 Deposited 2025-02-21 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 A1BYX (3R)-3-{2-chloro-4'-[(1-methyl-1H-pyrazol-3-yl)methoxy][1,1'-biphenyl]-3-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.6 % PEG Smear Low, 6.1 % PEG Smear Medium, 4.3 % PEG Smear High, 5 % glycerol, 0.1 M CaCl2, and 0.1 M MES pH 5.8
Resolution 3.40 Å R-free 0.271
9NGT Crystal structure of CRBN-DDB1 and FPFT-2216 in complex with mTOR Deposited 2025-02-22 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 A1BC8 (3S)-3-[(4M)-4-(4-methoxythiophen-3-yl)-1H-1,2,3-triazol-1-yl]piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；70 mM MES pH 6.0, 1.8-3.2 % (w/v) PEG 3,000, and 13-24 % (w/v) PEG 200
Resolution 2.95 Å R-free 0.260
9NR3 CRBN-DDB1 in complex with GLUL-cN Deposited 2025-03-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–393（393 aa）
Chain A 709–1140（432 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；8% v/v TacsimateTM pH 6.0, 20% w/v Polyethylene glycol 3,350
Resolution 2.93 Å R-free 0.278
9NWS Cryo-EM structure of DDB1dB:CRBN:mezigdomide:SALL4(392-449) Deposited 2025-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded ZN ZINC ION × 2 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50 mM HEPES/NaOH pH 7.4, 150 mM NaCl, 3 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；UltrAuFoil R 0.6/1 300 mesh grids were glow-discharged for 2 min at 20 mA and 39 Pa, pre-incubated with 4 uL of 10 uM FLAG-IKZF1(140-196;Q146A/G151N) for 1 min, and blotted from behind for 4 s. 4 uL of the sample was then applied to the grid. Grids were vitrified using an EM GP plunge freezer operated at 90% humidity and 10 C with 0 s pre-blot, 4 s blot, and 0 s post-blot.
Resolution 2.70 Å
9NWT Cryo-EM structure of DDB1dB:CRBN:mezigdomide:SALL4(392-449;G416A) Deposited 2025-03-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded ZN ZINC ION × 2 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50 mM HEPES/NaOH pH 7.4, 150 mM NaCl, 3 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；UltrAuFoil R 0.6/1 300 mesh grids were glow-discharged for 2 min at 20 mA and 39 Pa, pre-incubated with 4 uL of 10 uM FLAG-IKZF1(140-196;Q146A/G151N) for 1 min, and blotted from behind for 4 s. 4 uL of the sample was then applied to the grid. Grids were vitrified using an EM GP plunge freezer operated at 90% humidity and 10 C with 0 s pre-blot, 4 s blot, and 0 s post-blot.
Resolution 2.70 Å
9NYR Cryo-EM structure of CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 24 Deposited 2025-03-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Not recorded A1B7G N-{(1R,4S)-4-[(4-{3-chloro-4-[(3R)-2,6-dioxo-1,2,3,6-tetrahydropyridin-3-yl]phenyl}piperazin-1-yl)methyl]cyclohexyl}-4-({4-[(3S)-3-hydroxy-3-methylpiperidin-1-yl]-5-(trifluoromethyl)pyrimidin-2-yl}amino)-3-methylbenzene-1-sulfonamide × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50mM HEPES, pH 7.5, 150mM NaCl, 2mM TCEP, 2 mM FFC8, protein = 13.4 mg/ml
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9OS2 Cryo-EM structure of the DDB1/CRBN-MRT-5702-G3BP2 ternary complex Deposited 2025-05-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 A1CED (1S,3S)-2-[(2-chlorophenyl)methanesulfonyl]-N-{[(4R)-3-(2,4-dioxo-1,3-diazinan-1-yl)imidazo[1,2-a]pyridin-7-yl]methyl}-1-methyl-1,2,3,4-tetrahydroisoquinoline-3-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
9OTY DDB1-CRBN with CK1 alpha, SB-405483, and DEG-47: composite map and model submission Deposited 2025-05-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–391（391 aa）
Chain A 710–1140（431 aa）
Not recorded ZN ZINC ION × 1 A1CEH N-{2-[(3R)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide × 1 A1CEG N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；10mM HEPES, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9OUK DDB1-CRBN with Ikaros(ZF2) and DEG-47: composite map and model submission Deposited 2025-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded ZN ZINC ION × 2 A1CEK N-{2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；10mM HEPES, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.69 Å
9OUL DDB1-CRBN with Ikaros(ZF2), SB-405483, and DEG-47: composite map and model submission Deposited 2025-05-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded ZN ZINC ION × 1 A1CEG N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea × 1 A1CEK N-{2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；10mM HEPES, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.97 Å
9Q22 Crystal structure of ternary complex Helios-ZF2:I-19:CRBN:DDB1 Deposited 2025-08-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–381（381 aa） Fragment：UNP residues 1-381,706-1140
Chain A 706–1140（435 aa） Fragment：UNP residues 1-381,706-1140
Not recorded A1CNP (3S)-3-[5-(1-benzyl-4-hydroxypiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.148 M lithium citrate, 0.1 M Tris, pH 7.5, 19.4% PEG3350
Resolution 3.41 Å R-free 0.252
9Q2D Cryo-EM structure of ternary complex Ikaros-ZF2:CC-885:CRBN:DDB1 (molecular glue degrader) Deposited 2025-08-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–395（395 aa） Fragment：UNP residues 1-395,706-1140
Chain C 706–1140（435 aa） Fragment：UNP residues 1-395,706-1140
Not recorded ZN ZINC ION × 2 85C 1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE；blot time 4 sec blot force 4
Resolution 2.94 Å
9S3R Ternary complex structure of compound 1 bound to SMARCA2 bromodomain and DCAF16:DDB1deltaBPB Deposited 2025-07-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 A1JLV 2-[6-azanyl-5-[(1~{S},5~{R})-8-[2-[(~{E})-3-(azepan-1-yl)prop-1-enyl]pyridin-4-yl]-3,8-diazabicyclo[3.2.1]octan-3-yl]pyridazin-3-yl]phenol × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Applied 3.5 uL of sample to grid. wait = 10 sec, drain = 0 sec, blot = 4 sec, blotForce = 4
Resolution 3.30 Å
9SAF Ternary PROTAC-mediated complex of BRD4-BD1/CRBN/DDB1 and JQ1-AcQ bifunctional degrader Deposited 2025-08-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 A1JM8 ~{N}-[(2~{S})-1-[[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]amino]-1-oxidanylidene-propan-2-yl]-9-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,10,12-tetraen-9-yl]ethanoylamino]nonanamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.55 Å
9SAI Ternary PROTAC-mediated complex consisting of Cereblon, DDB1 and BRD4-BD1, non-covalently linked by JQ1-AcN Deposited 2025-08-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–395（395 aa）
Chain A 706–1140（435 aa）
Not recorded ZN ZINC ION × 1 A1JM3 N-[(2S)-1-[[(3S)-2,5-bis(oxidanylidene)pyrrolidin-3-yl]amino]-1-oxidanylidene-propan-2-yl]-9-[2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]nonanamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES, 100 mM NaCl, 0.25 mM TCEP, pH: 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å
9SFM Crystal structure of Cereblon-DDB1 in complex with SB-405483 and Lenalidomide Deposited 2025-08-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded EDO 1,2-ETHANEDIOL × 6 ZN ZINC ION × 1 LVY S-Lenalidomide × 1 A1CEG N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；20% w/v PEG 4000 0.1 M TRIS pH 8.2, 0.2 M
Resolution 2.39 Å R-free 0.244
9U7T Structure of the human DCAF8-DDB1 complex Deposited 2025-03-25 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9UUM Cryo-EM structure of mezigdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-07 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.41 Å
9UWG Structure of the human DCAF2-DDB1 complex Deposited 2025-05-12 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.21 Å
9V0A Cryo-EM structure of pomalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.69 Å
9V0F Cryo-EM structure of cemsidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.71 Å
9W2F Cryo-EM structure of DDB1-CRBN in complex with dHuR-2 and HuR Deposited 2025-07-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–1140（1140 aa）
Not recorded ZN ZINC ION × 1 A1EUN (3S)-3-[6-[1-[(4-methoxyphenyl)methyl]pyrazol-4-yl]-1-benzofuran-3-yl]piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9W90 DDB1-DDA1-DET1-Ube2e2-COP1-c-Jun-STK40 complex Deposited 2025-08-08 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 1–1140（1140 aa）
Chain E 1–1140（1140 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9ZXM DDB1 delta with compound 6 Deposited 2026-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–393（393 aa）
Chain A 706–1140（435 aa）
Not recorded A1C4E (3S,5S)-1-{(4P)-4-(2,2-difluoro-2H-1,3-benzodioxol-4-yl)-3-[(propan-2-yl)oxy]benzene-1-carbonyl}-N-methyl-5-phenylpiperidine-3-carboxamide × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M ammonium acetate, 0.1M Bis Tris pH 5.5-6.5, and 25% PEG 3350
Resolution 2.19 Å R-free 0.246
9ZXN DDB1 delta with compound 26 Deposited 2026-01-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–393（393 aa）
Chain A 706–1140（435 aa）
Not recorded A1C4F (3S,5S)-1-{(4P)-4-(2,2-difluoro-2H-1,3-benzodioxol-4-yl)-1-methyl-5-[(propan-2-yl)oxy]-1H-1,3-benzimidazole-7-carbonyl}-N-methyl-5-phenylpiperidine-3-carboxamide × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M ammonium acetate, 0.1M Bis Tris pH 5.5-6.5, and 25% PEG 3350
Resolution 2.07 Å R-free 0.235

202 other PDB entries and 290 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name DDB1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–1140； UniProt 1–1140

Protein cereblon

Homo sapiens

UniProt Q96SW2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain C； UniProt 41–442 Not recorded Cullin-4A × 1 （Q13619） DNA damage-binding protein 1 × 1 （Q16531） Ubiquitin-conjugating enzyme E2 D1 × 1 （P51668） Zinc finger protein Aiolos × 1 （Q9UKT9） NEDD8 × 1 （Q15843） E3 ubiquitin-protein ligase RBX1, N-terminally processed × 1 （P62877） Ubiquitin × 1 （P62979） ZINC ION × 6 (3S)-3-(5-azanyl-2-methyl-4-oxidanylidene-quinazolin-3-yl)piperidine-2,6-dione × 1 ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 3.54 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9V0B Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
10AY Cryo-EM structure of CRBN-DDB1 in complex with HBS1L and TNG961 Deposited 2026-01-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 40–442（403 aa）
Chain E 40–442（403 aa）
Not recorded A1C4S N-{6-[(3R)-2,6-dioxopiperidin-3-yl]naphthalen-1-yl}-N'-{2-[6-(trifluoromethyl)-1-benzothiophen-2-yl]propan-2-yl}urea × 2 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；0.1 M HEPES (pH 7.5), 0.24 M sodium chloride, 3 mM TCEP, 0.2 % n-octylglucoside
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
11MR Cryo-EM structure of CRBN in complex with HBS1L and TNG-4857 (focused refinement) Deposited 2026-03-05 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 40–442（403 aa）
Chain D 40–442（403 aa）
Not recorded ZN ZINC ION × 2 A1C9W N-[(3S)-2,6-dioxopiperidin-3-yl]-2-fluoro-3-[(2-{4-[1-(trifluoromethyl)cyclopropyl]phenyl}propan-2-yl)carbamamido]benzamide × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；10 mM HEPES (pH 7.5), 240 mM NaCl, 3 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
4M91 crystal structure of hN33/Tusc3-peptide 1 Deposited 2013-08-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 229–240（12 aa） Fragment：unp residues 229-240
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；0.2 M KSCN, 10.5% PEG 8K, 10% PEG 1K in 100 mM cacodylic acid-NaOH, pH 6.5, VAPOR DIFFUSION, SITTING DROP
Resolution 1.10 Å R-free 0.160
4TZ4 Crystal Structure of Human Cereblon in Complex with DDB1 and Lenalidomide Deposited 2014-07-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 47–427（381 aa）
Not recorded ZN ZINC ION × 1 LVY S-Lenalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；100mM HEPES pH 7.5, 18% PEG 10K
Resolution 3.01 Å R-free 0.271
5FQD Structural basis of Lenalidomide induced CK1a degradation by the crl4crbn ubiquitin ligase Deposited 2015-12-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 41–442（402 aa）
Not recorded ZN ZINC ION × 1 LVY S-Lenalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 70 MM TRIS PH 7.0 140 MM MGCL2 7% W/V PEG 8000
Resolution 2.45 Å R-free 0.210
5FQD Structural basis of Lenalidomide induced CK1a degradation by the crl4crbn ubiquitin ligase Deposited 2015-12-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 41–442（402 aa）
Not recorded ZN ZINC ION × 1 LVY S-Lenalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 70 MM TRIS PH 7.0 140 MM MGCL2 7% W/V PEG 8000
Resolution 2.45 Å R-free 0.210
5HXB Cereblon in complex with DDB1, CC-885, and GSPT1 Deposited 2016-01-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Z 39–441（403 aa）
Not recorded ZN ZINC ION × 1 85C 1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；280 K；200mM Sodium Citrate, Tris pH 8.5, 18% PEG 3350
Resolution 3.60 Å R-free 0.273
5HXB Cereblon in complex with DDB1, CC-885, and GSPT1 Deposited 2016-01-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 39–441（403 aa）
Not recorded ZN ZINC ION × 1 85C 1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；280 K；200mM Sodium Citrate, Tris pH 8.5, 18% PEG 3350
Resolution 3.60 Å R-free 0.273
5V3O Cereblon in complex with DDB1 and CC-220 Deposited 2017-03-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 40–442（403 aa） Fragment：residues 40-442
Not recorded 8W7 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；200mM NaCl, 20% PEG 3350
Resolution 3.20 Å R-free 0.267
6BN7 Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET23 PROTAC. Deposited 2017-11-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–441（441 aa）
Not recorded ZN ZINC ION × 1 RN3 methyl {(6S)-4-(4-chlorophenyl)-2-[(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl)carbamoyl]-3,9-dimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl}acetate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9% (w/v) PEG20K, 18% (v/v) PEG MME 550, 0.09M BICINE pH8.5, 9% Silver bullet B5 (0.33% w/v 2,7-Naphthalenedisulfonic acid disodium salt, 0.33% w/v Azelaic acid, 0.33% w/v trans-Cinnamic acid, 0.02 M HEPES sodium pH 6.8)
Resolution 3.50 Å R-free 0.256
6BN8 Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET55 PROTAC. Deposited 2017-11-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–441（441 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9% PEG20K, 18% PEG MME 550, 0.09M BICINE pH8.5, 9% Silver bullet G4 (0.16% w/v 3-Indolebutyric acid, 0.16% w/v Hexadecanedioic acid, 0.16% w/v Oxamic acid, 0.16% w/v Pyromellitic acid, 0.16% w/v Sebacic acid, 0.16% w/v Suberic acid, 0.02 M HEPES sodium pH 6.8)
Resolution 3.99 Å R-free 0.333
6BN9 Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET70 PROTAC Deposited 2017-11-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–441（441 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；10% (w/v) PEG20K, 20% (v/v) PEG MME 550, 0.1M BICINE pH8.5, Silver Bullet F2 (0.2% w/v D-Fructose 1,6-bisphosphate trisodium salt hydrate, 0.2% w/v Glycerol phosphate disodium salt hydrate, 0.2% w/v L-O-Phosphoserine, 0.2% w/v O-Phospho-L-tyrosine, 0.2% w/v Phytic acid sodium salt hydrate, 0.02 M HEPES sodium pH 6.8)
Resolution 4.38 Å R-free 0.301
6BNB Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET57 PROTAC Deposited 2017-11-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–441（441 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.34M NaH2PO4, 0.33M K2HPO4
Resolution 6.34 Å R-free 0.381
6BOY Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET6 PROTAC. Deposited 2017-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–441（441 aa）
Not recorded ZN ZINC ION × 1 RN6 2-[(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]-N-(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl)acetamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9% (w/v) PEG20K, 18% (v/v) PEG MME 550, 0.09M BICINE pH8.5, 9% (v/v) Silver bullet D11 (0.25% w/v 2,6-Naphthalenedisulfonic acid disodium salt, 0.25% w/v 4-Aminobenzoic acid, 0.25% w/v 5-Sulfosalicylic acid dihydrate, 0.25% w/v Naphthalene-1,3,6-trisulfonic acid trisodium salt hydrate, 0.02 M HEPES sodium pH 6.8)
Resolution 3.33 Å R-free 0.234
6H0F Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2) Deposited 2018-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 36–442（407 aa）
Mutation：N-terminally truncated (1-40 aa deleted) ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；Protein solution: 350 uM IKZF1-ZF2, 70 uM DDB1/CRBN, 80 uM pomalidomide in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP Crystallisation solution: (Morpheus HT condition) 100 mM Morpheus buffer system 1 pH 6.5, 10% (v/v) Morpheus NPS solution, 15% (v/v) ethylene glycol and 9.5% (w/v) poly(ethylene glycol) 5000 monomethyl ether.
Resolution 3.25 Å R-free 0.234
6H0F Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2) Deposited 2018-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 36–442（407 aa）
Mutation：N-terminally truncated (1-40 aa deleted) ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；Protein solution: 350 uM IKZF1-ZF2, 70 uM DDB1/CRBN, 80 uM pomalidomide in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP Crystallisation solution: (Morpheus HT condition) 100 mM Morpheus buffer system 1 pH 6.5, 10% (v/v) Morpheus NPS solution, 15% (v/v) ethylene glycol and 9.5% (w/v) poly(ethylene glycol) 5000 monomethyl ether.
Resolution 3.25 Å R-free 0.234
6H0F Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2) Deposited 2018-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 36–442（407 aa）
Mutation：N-terminally truncated (1-40 aa deleted) ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；Protein solution: 350 uM IKZF1-ZF2, 70 uM DDB1/CRBN, 80 uM pomalidomide in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP Crystallisation solution: (Morpheus HT condition) 100 mM Morpheus buffer system 1 pH 6.5, 10% (v/v) Morpheus NPS solution, 15% (v/v) ethylene glycol and 9.5% (w/v) poly(ethylene glycol) 5000 monomethyl ether.
Resolution 3.25 Å R-free 0.234
6H0F Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2) Deposited 2018-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 36–442（407 aa）
Mutation：N-terminally truncated (1-40 aa deleted) ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；Protein solution: 350 uM IKZF1-ZF2, 70 uM DDB1/CRBN, 80 uM pomalidomide in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP Crystallisation solution: (Morpheus HT condition) 100 mM Morpheus buffer system 1 pH 6.5, 10% (v/v) Morpheus NPS solution, 15% (v/v) ethylene glycol and 9.5% (w/v) poly(ethylene glycol) 5000 monomethyl ether.
Resolution 3.25 Å R-free 0.234
6H0G Structure of the DDB1-CRBN-pomalidomide complex bound to ZNF692(ZF4) Deposited 2018-07-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 41–442（402 aa）
Mutation：N-terminally truncated (1-40 aa deleted) ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；Protein-drug solution: 350 uM ZNF692-ZF4, 70 uM DDB1/CRBN, 80 uM pomalidomide and in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP Crystallisation solution: 14.1% (w/v) PEG 5K MME and 70 mM Tris-HCl pH 7.5
Resolution 4.25 Å R-free 0.256
6H0G Structure of the DDB1-CRBN-pomalidomide complex bound to ZNF692(ZF4) Deposited 2018-07-09 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 41–442（402 aa）
Mutation：N-terminally truncated (1-40 aa deleted) ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；Protein-drug solution: 350 uM ZNF692-ZF4, 70 uM DDB1/CRBN, 80 uM pomalidomide and in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP Crystallisation solution: 14.1% (w/v) PEG 5K MME and 70 mM Tris-HCl pH 7.5
Resolution 4.25 Å R-free 0.256
6UML Structural Basis for Thalidomide Teratogenicity Revealed by the Cereblon-DDB1-SALL4-Pomalidomide Complex Deposited 2019-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 40–442（403 aa）
Not recorded ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；10% PEG MME 500, 8% PEG 20K, 210mM calcium acetate, 100mM tris pH 7.5
Resolution 3.58 Å R-free 0.267
6XK9 Cereblon in complex with DDB1, CC-90009, and GSPT1 Deposited 2020-06-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Z 40–442（403 aa）
Not recorded V4M 2-(4-chlorophenyl)-N-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)-2,2-difluoroacetamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 100mM Tris-HCl (pH 7.5), 300mM sodium citrate
Resolution 3.64 Å R-free 0.245
6XK9 Cereblon in complex with DDB1, CC-90009, and GSPT1 Deposited 2020-06-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 40–442（403 aa）
Not recorded V4M 2-(4-chlorophenyl)-N-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)-2,2-difluoroacetamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 100mM Tris-HCl (pH 7.5), 300mM sodium citrate
Resolution 3.64 Å R-free 0.245
7BQU Cereblon in complex with SALL4 and (S)-thalidomide Deposited 2020-03-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 318–426（109 aa）
Not recorded EF2 S-Thalidomide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；27% PEG 4000, 0.1 M sodium acetate (pH 5.5), 0.1 M magnesium chloride
Resolution 1.90 Å R-free 0.236
7BQV Cereblon in complex with SALL4 and (S)-5-hydroxythalidomide Deposited 2020-03-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 318–426（109 aa）
Mutation：C366S F4U 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-5-oxidanyl-isoindole-1,3-dione × 1 ZN ZINC ION × 2 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；22% PEG 4000, 0.1 M MES (pH 6.0), 0.2 M lithium sulfate
Resolution 1.80 Å R-free 0.223
7LPS Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) Deposited 2021-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 47–436（390 aa）
Not recorded ZN ZINC ION × 2 RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.57；293 K；30% (w/v) PEG3350, 0.1 M Tris pH 8.57
Resolution 3.78 Å R-free 0.303
7LPS Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) Deposited 2021-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 47–436（390 aa）
Not recorded ZN ZINC ION × 2 RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.57；293 K；30% (w/v) PEG3350, 0.1 M Tris pH 8.57
Resolution 3.78 Å R-free 0.303
7LPS Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) Deposited 2021-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 47–436（390 aa）
Not recorded ZN ZINC ION × 2 RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.57；293 K；30% (w/v) PEG3350, 0.1 M Tris pH 8.57
Resolution 3.78 Å R-free 0.303
7LPS Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) Deposited 2021-02-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 47–436（390 aa）
Not recorded ZN ZINC ION × 2 RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.57；293 K；30% (w/v) PEG3350, 0.1 M Tris pH 8.57
Resolution 3.78 Å R-free 0.303
7U8F Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2) and the molecular glue DKY709 Deposited 2022-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 40–442（403 aa）
Not recorded ZN ZINC ION × 2 LWK (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5
Resolution 3.15 Å R-free 0.243
7U8F Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2) and the molecular glue DKY709 Deposited 2022-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 40–442（403 aa）
Not recorded ZN ZINC ION × 2 LWK (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 SO4 SULFATE ION × 4 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5
Resolution 3.15 Å R-free 0.243
8CVP Cereblon-DDB1 in the Apo form Deposited 2022-05-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4? coldroom
Resolution 3.40 Å
8D7U Cereblon~DDB1 bound to CC-92480 with DDB1 in the linear conformation Deposited 2022-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.10 Å
8D7V Cereblon~DDB1 bound to CC-92480 with DDB1 in the twisted conformation Deposited 2022-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.20 Å
8D7W Cereblon~DDB1 bound to CC-92480 with DDB1 in the hinged conformation Deposited 2022-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.10 Å
8D7X Cereblon~DDB1 in the Apo form with DDB1 in the hinged conformation Deposited 2022-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.40 Å
8D7Y Cereblon-DDB1 in the Apo form with DDB1 in the twisted conformation Deposited 2022-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.40 Å
8D7Z Cereblon-DDB1 bound to CC-92480 and Ikaros ZF1-2-3 Deposited 2022-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 2 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.10 Å
8D80 Cereblon~DDB1 bound to Iberdomide and Ikaros ZF1-2-3 Deposited 2022-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 2 8W7 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.60 Å
8D81 Cereblon~DDB1 bound to Pomalidomide Deposited 2022-06-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 Y70 S-Pomalidomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20mM HEPES pH 7, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room
Resolution 3.90 Å
8DEY Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2,3) and the molecular glue DKY709 Deposited 2022-06-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 70–442（373 aa）
Not recorded ZN ZINC ION × 3 LWK (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5
Resolution 3.70 Å R-free 0.348
8DEY Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2,3) and the molecular glue DKY709 Deposited 2022-06-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 70–442（373 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5
Resolution 3.70 Å R-free 0.348
8G66 Structure with SJ3149 Deposited 2023-02-14 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 41–442（402 aa）
Not recorded ZN ZINC ION × 1 YOT (3S)-3-{5-[(1,2-benzoxazol-3-yl)amino]-1-oxo-1,3-dihydro-2H-isoindol-2-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；70 MM TRIS PH 7.0, 140 MM MGCL2, 7% W/V PEG 8000
Resolution 3.45 Å R-free 0.272
8G66 Structure with SJ3149 Deposited 2023-02-14 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 41–442（402 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；70 MM TRIS PH 7.0, 140 MM MGCL2, 7% W/V PEG 8000
Resolution 3.45 Å R-free 0.272
8OIZ Crystal structure of human CRBN-DDB1 in complex with Pomalidomide Deposited 2023-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 40–442（403 aa）
Not recorded EDO 1,2-ETHANEDIOL × 6 ZN ZINC ION × 1 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；291 K；0.8 microliter of CRBN-DDB1 complex at 25 mg/mL (including 1 mM compound and 2 % DMSO final) plus 0.8 microliter of a crystallisation solution consisting of 0.1 M Hepes pH 8.2, 0.2 M NaCl and 10-16 % PEG Smear Medium, plus 0.2 microliter of seeds (established from the same conditions), against 500 microliter of crystallisation solution.
Resolution 2.50 Å R-free 0.262
8OJH Crystal structure of human CRBN-DDB1 in complex with compound 4 Deposited 2023-03-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 40–442（403 aa）
Not recorded EDO 1,2-ETHANEDIOL × 9 ZN ZINC ION × 1 VP9 4-azanyl-2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-7-methoxy-isoindole-1,3-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；291 K；0.8 microliter of CRBN-DDB1 complex at 25 mg/mL (including 1 mM compound and 2 % DMSO final) plus 0.8 microliter of a crystallisation solution consisting of 0.1 M Hepes pH 8.2, 0.2 M NaCl and 10-16 % PEG Smear Medium, plus 0.2 microliter of seeds (established from the same conditions), against 500 microliter of crystallisation solution.
Resolution 2.72 Å R-free 0.254
8RQ1 Crystal structure of CRBN-midi Deposited 2024-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 41–187（147 aa）
Chain A 249–426（178 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M sodium citrate, 20% (w/v) PEG 3350, and 0.1 M BIS-TRIS propane pH 6.5
Resolution 3.11 Å R-free 0.300
8RQ8 Crystal structure of CRBN-midi in complex with mezigdomide Deposited 2024-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 41–187（147 aa）
Chain A 249–426（178 aa）
Not recorded ZN ZINC ION × 1 QFC Mezigdomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；214 uM mezigdomide 0.2 M sodium acetate, 25% (w/v) PEG 3350, and 0.1 M BIS-TRIS pH 6.5
Resolution 2.19 Å R-free 0.285
8RQ9 Crystal structure of PROTAC CFT-1297 in complex with CRBN-midi and BRD4(BD2) Deposited 2024-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 41–187（147 aa）
Chain A 249–426（178 aa）
Not recorded A1H2F (3~{S})-3-[7-[1-[7-[4-[6-(4-chlorophenyl)-1-methyl-spiro[[1,2,4]triazolo[4,3-a][1,4]benzodiazepine-4,1'-cyclopropane]-8-yl]pyrazol-1-yl]heptyl]piperidin-4-yl]-3-oxidanylidene-1~{H}-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG 3350, 0.2 M sodium citrate and 0.1 M Bis-Tris Propane pH 7.5
Resolution 2.91 Å R-free 0.293
8RQ9 Crystal structure of PROTAC CFT-1297 in complex with CRBN-midi and BRD4(BD2) Deposited 2024-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 41–187（147 aa）
Chain C 249–426（178 aa）
Not recorded A1H2F (3~{S})-3-[7-[1-[7-[4-[6-(4-chlorophenyl)-1-methyl-spiro[[1,2,4]triazolo[4,3-a][1,4]benzodiazepine-4,1'-cyclopropane]-8-yl]pyrazol-1-yl]heptyl]piperidin-4-yl]-3-oxidanylidene-1~{H}-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG 3350, 0.2 M sodium citrate and 0.1 M Bis-Tris Propane pH 7.5
Resolution 2.91 Å R-free 0.293
8RQA Crystal structure of CRBN-midi in complex with Lenalidomide Deposited 2024-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 41–187（147 aa）
Chain A 249–426（178 aa）
Not recorded LVY S-Lenalidomide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M Tris pH 8, 20 % w/v PEG 4000, 1.2 % myo-inositol
Resolution 2.50 Å R-free 0.342
8RQC Crystal structure of CRBN-midi in complex with mezigdomide and IKZF1 ZF2 Deposited 2024-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 41–187（147 aa）
Chain A 249–426（178 aa）
Chain D 41–187（147 aa）
Chain D 249–426（178 aa）
Not recorded ZN ZINC ION × 4 QFC Mezigdomide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium sulphate, 25% (w/v) PEG 3350, and 0.1 M HEPES pH 7.5
Resolution 2.15 Å R-free 0.286
8TNP Cryo-EM structure of DDB1dB:CRBN:Pomalidomide:SD40 Deposited 2023-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM HEPES/NaOH pH 7.0, 150 mM NaCl, and 3 mM TCEP. DMSO concentrations were kept below 2% (v/v)
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.
Resolution 3.30 Å
8TNQ Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 1 Deposited 2023-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 2 MIQ 2-[(3S)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1H-isoindole-1,3(2H)-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM HEPES/NaOH pH 7.0, 150 mM NaCl, and 3 mM TCEP. DMSO concentrations were kept below 2% (v/v)
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.
Resolution 2.41 Å
8TNR Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 2 Deposited 2023-08-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 2 MIQ 2-[(3S)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1H-isoindole-1,3(2H)-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；20 mM HEPES/NaOH pH 7.0, 150 mM NaCl, and 3 mM TCEP. DMSO concentrations were kept below 2% (v/v)
cryo-EM vitrification conditions Cryogen ETHANE；Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.
Resolution 2.50 Å
8TZX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue dWIZ-1 Deposited 2023-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 70–442（373 aa）
Not recorded ZN ZINC ION × 2 U3I (3S)-3-(5-{(1R)-1-[(2R)-1-ethylpiperidin-2-yl]ethoxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350
Resolution 3.15 Å R-free 0.252
8TZX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue dWIZ-1 Deposited 2023-08-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 70–442（373 aa）
Not recorded ZN ZINC ION × 2 U3I (3S)-3-(5-{(1R)-1-[(2R)-1-ethylpiperidin-2-yl]ethoxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 SO4 SULFATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350
Resolution 3.15 Å R-free 0.252
8U15 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to CC-220 Deposited 2023-08-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 70–442（373 aa）
Not recorded ZN ZINC ION × 3 8W7 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
Resolution 2.95 Å R-free 0.272
8U15 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to CC-220 Deposited 2023-08-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 70–442（373 aa）
Not recorded ZN ZINC ION × 3 8W7 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 SO4 SULFATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
Resolution 2.95 Å R-free 0.272
8U16 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to Pomalidomide Deposited 2023-08-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 70–442（373 aa）
Not recorded ZN ZINC ION × 3 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
Resolution 2.90 Å R-free 0.273
8U16 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to Pomalidomide Deposited 2023-08-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 70–442（373 aa）
Not recorded ZN ZINC ION × 3 Y70 S-Pomalidomide × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
Resolution 2.90 Å R-free 0.273
8U17 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-long bound to Pomalidomide Deposited 2023-08-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 70–442（373 aa）
Not recorded ZN ZINC ION × 3 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
Resolution 3.10 Å R-free 0.346
8U17 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-long bound to Pomalidomide Deposited 2023-08-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 70–442（373 aa）
Not recorded ZN ZINC ION × 3 Y70 S-Pomalidomide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
Resolution 3.10 Å R-free 0.346
8UH6 Degrader-induced complex between PTPN2 and CRBN-DDB1 Deposited 2023-10-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded WO8 (5P)-3-(carboxymethoxy)-4-chloro-5-(3-{[(4S)-1-({3-[(4-{1-[(3R)-2,6-dioxopiperidin-3-yl]-3-methyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl}piperidine-1-carbonyl)amino]phenyl}methanesulfonyl)-2,2-dimethylpiperidin-4-yl]amino}phenyl)thiophene-2-carboxylic acid × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9CUO Crystal structure of CRBN with compound 3 Deposited 2024-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain A 319–427（109 aa）
Chain B 319–427（109 aa）
Chain C 319–427（109 aa）
Not recorded ZN ZINC ION × 3 A1A0J (3S)-3-(3-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-1-yl)piperidine-2,6-dione × 3 SO4 SULFATE ION × 8 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；291 K；0.1M Acetate, pH4.7, 0.2M sodium chloride, 1.1M ammonium sulfate
Resolution 1.60 Å R-free 0.205
9CUO Crystal structure of CRBN with compound 3 Deposited 2024-07-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric
Chain D 319–427（109 aa）
Chain E 319–427（109 aa）
Chain F 319–427（109 aa）
Not recorded ZN ZINC ION × 3 A1A0J (3S)-3-(3-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-1-yl)piperidine-2,6-dione × 3 SO4 SULFATE ION × 5 EDO 1,2-ETHANEDIOL × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.7；291 K；0.1M Acetate, pH4.7, 0.2M sodium chloride, 1.1M ammonium sulfate
Resolution 1.60 Å R-free 0.205
9D0W Cryo-EM structure of CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 4 Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 40–442（403 aa）
Not recorded ZN ZINC ION × 1 A1A1I (3R)-3-(5-{4-[(2-{4-[(8-cyclopentyl-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl)amino]-3-methylbenzene-1-sulfonyl}-7-azaspiro[3.5]nonan-7-yl)methyl]piperidin-1-yl}-4-fluoro-3-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-1-yl)piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9D0X Cryo-EM structure of CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 4 (local mask) Deposited 2024-08-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 40–442（403 aa）
Not recorded ZN ZINC ION × 1 A1A1I (3R)-3-(5-{4-[(2-{4-[(8-cyclopentyl-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl)amino]-3-methylbenzene-1-sulfonyl}-7-azaspiro[3.5]nonan-7-yl)methyl]piperidin-1-yl}-4-fluoro-3-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-1-yl)piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.84 Å
9DJT Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-5 Deposited 2024-09-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 70–442（373 aa）
Not recorded ZN ZINC ION × 2 SO4 SULFATE ION × 1 A1A5H (3S)-3-(5-{[(4R)-6-ethyl-6-azaspiro[2.5]octan-4-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350
Resolution 2.95 Å R-free 0.260
9DJT Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-5 Deposited 2024-09-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 70–442（373 aa）
Not recorded ZN ZINC ION × 2 SO4 SULFATE ION × 1 A1A5H (3S)-3-(5-{[(4R)-6-ethyl-6-azaspiro[2.5]octan-4-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350
Resolution 2.95 Å R-free 0.260
9DJX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-6 Deposited 2024-09-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 70–442（373 aa）
Not recorded ZN ZINC ION × 2 SO4 SULFATE ION × 1 A1A5I (3S)-3-(5-{[(3R,6S)-1-ethyl-6-methylpiperidin-3-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1M BIS-TRIS Propane pH 7.5, 20% PEG3350 (Qiagen PACT G8)
Resolution 3.35 Å R-free 0.271
9DJX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-6 Deposited 2024-09-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 70–442（373 aa）
Not recorded ZN ZINC ION × 2 SO4 SULFATE ION × 2 A1A5I (3S)-3-(5-{[(3R,6S)-1-ethyl-6-methylpiperidin-3-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1M BIS-TRIS Propane pH 7.5, 20% PEG3350 (Qiagen PACT G8)
Resolution 3.35 Å R-free 0.271
9DOM PVTX-405: A Potent, Highly Selective, and Orally Efficacious Molecular Glue Degrader of IKZF2 for Cancer Immunotherapy Deposited 2024-09-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 319–426（108 aa）
Not recorded A1A8N (3S)-3-(1'-benzyl-6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.4 M Magnesium chloride 0.1 M TRIS pH 7.5 27% w/v PEG 4000
Resolution 1.69 Å R-free 0.234
9DOM PVTX-405: A Potent, Highly Selective, and Orally Efficacious Molecular Glue Degrader of IKZF2 for Cancer Immunotherapy Deposited 2024-09-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 319–426（108 aa）
Not recorded A1A8N (3S)-3-(1'-benzyl-6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.4 M Magnesium chloride 0.1 M TRIS pH 7.5 27% w/v PEG 4000
Resolution 1.69 Å R-free 0.234
9DOM PVTX-405: A Potent, Highly Selective, and Orally Efficacious Molecular Glue Degrader of IKZF2 for Cancer Immunotherapy Deposited 2024-09-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 319–426（108 aa）
Not recorded A1A8N (3S)-3-(1'-benzyl-6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.4 M Magnesium chloride 0.1 M TRIS pH 7.5 27% w/v PEG 4000
Resolution 1.69 Å R-free 0.234
9DOM PVTX-405: A Potent, Highly Selective, and Orally Efficacious Molecular Glue Degrader of IKZF2 for Cancer Immunotherapy Deposited 2024-09-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 319–426（108 aa）
Not recorded A1A8N (3S)-3-(1'-benzyl-6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.4 M Magnesium chloride 0.1 M TRIS pH 7.5 27% w/v PEG 4000
Resolution 1.69 Å R-free 0.234
9DQD cryo-EM structure of human Cereblon/DDB1 in complex with a non-traditional CRBN binder Deposited 2024-09-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–442（442 aa）
Not recorded ZN ZINC ION × 1 A1BEP (3R)-3-{1-methyl-6-[(piperidin-4-yl)amino]-1H-indazol-3-yl}piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9DUR Cryo-EM Structure of CRBN:dHTC1:ENL YEATS Deposited 2024-10-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 A1IQT 2-[3-[2-[4-[[(5~{S})-1,3-bis(oxidanylidene)-2,7-diazaspiro[4.4]nonan-7-yl]sulfonylamino]piperidin-1-yl]ethylcarbamoyl]phenyl]-~{N}-cyclobutyl-imidazo[1,2-a]pyridine-6-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；30 mM HEPES/NaOH pH7.4, 150 mM NaCl. DMSO concentrations were kept below 2% (v/v)
cryo-EM vitrification conditions Cryogen ETHANE；Grids were vitrified using a Leica EM GP plunge freezer operated at 90% humidity and 10 C. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixturewas applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C
Resolution 2.90 Å
9DWV Ternary complex of CRBN-DDB1-PPIL4 RRM domain with FPFT-2216 Deposited 2024-10-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 A1BC8 (3S)-3-[(4M)-4-(4-methoxythiophen-3-yl)-1H-1,2,3-triazol-1-yl]piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
9DWW Ternary complex of CRBN-DDB1-PDE6D with FPFT-2216 Deposited 2024-10-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–442（442 aa）
Not recorded ZN ZINC ION × 1 A1BC8 (3S)-3-[(4M)-4-(4-methoxythiophen-3-yl)-1H-1,2,3-triazol-1-yl]piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–441（441 aa）
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–441（441 aa）
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–441（441 aa）
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 1–441（441 aa）
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 1–441（441 aa）
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain L 1–441（441 aa）
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain N 1–441（441 aa）
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain P 1–441（441 aa）
Not recorded RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
Resolution 4.11 Å R-free 0.289
9FJX Crystal structure of human CRBN-DDB1 in complex with Lenalidomide Deposited 2024-05-31 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 40–442（403 aa）
Not recorded EDO 1,2-ETHANEDIOL × 5 DMS DIMETHYL SULFOXIDE × 3 ZN ZINC ION × 1 LVY S-Lenalidomide × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；291 K；0.8 microliter of CRBN-DDB1 complex at 25 mg/mL (including 1 mM compound and 2 % DMSO final) plus 0.8 microliter of a crystallisation solution consisting of 0.1 M Hepes pH 8.2, 0.2 M NaCl and 10-16 % PEG Smear Medium, plus 0.2 microliter of seeds (established from the same conditions), against 500 microliter of crystallisation solution.
Resolution 2.00 Å R-free 0.232
9GAO Crystal structure of CRBNmidi in complex with 2-(4-(2,6-dioxopiperidin-3-yl)phenoxy)-N-methylacetamide Deposited 2024-07-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 41–187（147 aa）
Chain A 249–426（178 aa）
Chain C 41–187（147 aa）
Chain C 249–426（178 aa）
Not recorded A1IJM 2-[4-[(3~{R})-2,6-bis(oxidanylidene)piperidin-3-yl]phenoxy]-~{N}-methyl-ethanamide × 2 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Buffer system I (Molecular Dimensions), 15.45% v/v Precipitant mix 2 (MD), 180 mM Monosaccharides (MD)
Resolution 1.95 Å R-free 0.286
9GY3 Crystal structure of CRBNmidi in complex with (S)-dHTC1 Deposited 2024-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 41–187（147 aa）
Chain A 249–426（178 aa）
Not recorded A1IQT 2-[3-[2-[4-[[(5~{S})-1,3-bis(oxidanylidene)-2,7-diazaspiro[4.4]nonan-7-yl]sulfonylamino]piperidin-1-yl]ethylcarbamoyl]phenyl]-~{N}-cyclobutyl-imidazo[1,2-a]pyridine-6-carboxamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus H10 (0.1 M Buffer System 3 pH 8.5, 0.12 M Alcohols, 30 % Precipitant Mix 2) (Molecular Dimensions)
Resolution 2.50 Å R-free 0.303
9GY3 Crystal structure of CRBNmidi in complex with (S)-dHTC1 Deposited 2024-10-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 41–187（147 aa）
Chain C 249–426（178 aa）
Not recorded A1IQT 2-[3-[2-[4-[[(5~{S})-1,3-bis(oxidanylidene)-2,7-diazaspiro[4.4]nonan-7-yl]sulfonylamino]piperidin-1-yl]ethylcarbamoyl]phenyl]-~{N}-cyclobutyl-imidazo[1,2-a]pyridine-6-carboxamide × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus H10 (0.1 M Buffer System 3 pH 8.5, 0.12 M Alcohols, 30 % Precipitant Mix 2) (Molecular Dimensions)
Resolution 2.50 Å R-free 0.303
9H59 Cryo-EM structure of DDB1-CRBN in complex with NK7-902 and NEK7 Deposited 2024-10-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–442（441 aa）
Not recorded A1ISP 2-[(3S)-2,6-bis(oxidanylidene)piperidin-3-yl]-5-[(1S,2R,5S)-2-(ethylamino)-8-azabicyclo[3.2.1]octan-8-yl]isoindole-1,3-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9HNE Cereblon in complex with DDB1, GSPT1 and Compound-1 Deposited 2024-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 40–442（403 aa）
Not recorded ZN ZINC ION × 1 A1IWG 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1-oxidanylidene-3~{H}-isoindole-5-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Sodium citrate, 0.1 M Bis-Tris propane pH 7.5, 20% w/v PEG 3350
Resolution 3.90 Å R-free 0.336
9HNE Cereblon in complex with DDB1, GSPT1 and Compound-1 Deposited 2024-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain F 40–442（403 aa）
Not recorded ZN ZINC ION × 1 A1IWG 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1-oxidanylidene-3~{H}-isoindole-5-carboxylic acid × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Sodium citrate, 0.1 M Bis-Tris propane pH 7.5, 20% w/v PEG 3350
Resolution 3.90 Å R-free 0.336
9HPI Cryo-EM structure of DDB1dB-CRBN-MRT-0031619, conformation 1 Deposited 2024-12-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 41–442（402 aa）
Chain C 41–442（402 aa）
Not recorded ZN ZINC ION × 2 A1IW1 (3~{S})-3-[3-oxidanylidene-5-[8-(phenylcarbonyl)-2,8-diazaspiro[4.5]decan-2-yl]-1~{H}-isoindol-2-yl]piperidine-2,6-dione × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Sample supplemented with DDM directly before vitrification
cryo-EM vitrification conditions Cryogen ETHANE；LEICA EMGP2
Resolution 2.93 Å
9HPJ Cryo-EM structure of DDB1dB-CRBN-MRT-0031619, conformation 2 Deposited 2024-12-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 41–442（402 aa）
Chain C 41–442（402 aa）
Not recorded ZN ZINC ION × 2 A1IW1 (3~{S})-3-[3-oxidanylidene-5-[8-(phenylcarbonyl)-2,8-diazaspiro[4.5]decan-2-yl]-1~{H}-isoindol-2-yl]piperidine-2,6-dione × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；Sample supplemented with DDM directly before vitrification
cryo-EM vitrification conditions Cryogen ETHANE；LEICA EMGP2
Resolution 3.10 Å
9NFQ Crystal structure of CRBN-DDB1 and MRT-3486 in complex with NEK7 Deposited 2025-02-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded A1BX6 (3S)-N-{[(4R)-3-(2,4-dioxo-1,3-diazinan-1-yl)imidazo[1,2-a]pyridin-7-yl]methyl}-2-(phenylmethanesulfonyl)-1,2,3,4-tetrahydroisoquinoline-3-carboxamide × 1 ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.029 M HEPES salt, 0.071 M MOPS acid, 0.06 M NaNO3, 0.06 M Na2HPO4, 0.06 M (NH4)2SO4, 11 % (w/v) PEG 8,000 and 25 % (v/v) ethylene glycol.
Resolution 3.25 Å R-free 0.261
9NFR Crystal structure of CRBN-DDB1 and MRT-23227 in complex with VAV1 Deposited 2025-02-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 A1BYX (3R)-3-{2-chloro-4'-[(1-methyl-1H-pyrazol-3-yl)methoxy][1,1'-biphenyl]-3-yl}piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；2.6 % PEG Smear Low, 6.1 % PEG Smear Medium, 4.3 % PEG Smear High, 5 % glycerol, 0.1 M CaCl2, and 0.1 M MES pH 5.8
Resolution 3.40 Å R-free 0.271
9NGT Crystal structure of CRBN-DDB1 and FPFT-2216 in complex with mTOR Deposited 2025-02-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 A1BC8 (3S)-3-[(4M)-4-(4-methoxythiophen-3-yl)-1H-1,2,3-triazol-1-yl]piperidine-2,6-dione × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；70 mM MES pH 6.0, 1.8-3.2 % (w/v) PEG 3,000, and 13-24 % (w/v) PEG 200
Resolution 2.95 Å R-free 0.260
9NR3 CRBN-DDB1 in complex with GLUL-cN Deposited 2025-03-13 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 41–442（402 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；8% v/v TacsimateTM pH 6.0, 20% w/v Polyethylene glycol 3,350
Resolution 2.93 Å R-free 0.278
9NWS Cryo-EM structure of DDB1dB:CRBN:mezigdomide:SALL4(392-449) Deposited 2025-03-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 2 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50 mM HEPES/NaOH pH 7.4, 150 mM NaCl, 3 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；UltrAuFoil R 0.6/1 300 mesh grids were glow-discharged for 2 min at 20 mA and 39 Pa, pre-incubated with 4 uL of 10 uM FLAG-IKZF1(140-196;Q146A/G151N) for 1 min, and blotted from behind for 4 s. 4 uL of the sample was then applied to the grid. Grids were vitrified using an EM GP plunge freezer operated at 90% humidity and 10 C with 0 s pre-blot, 4 s blot, and 0 s post-blot.
Resolution 2.70 Å
9NWT Cryo-EM structure of DDB1dB:CRBN:mezigdomide:SALL4(392-449;G416A) Deposited 2025-03-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 2 QFC Mezigdomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4；50 mM HEPES/NaOH pH 7.4, 150 mM NaCl, 3 mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE；UltrAuFoil R 0.6/1 300 mesh grids were glow-discharged for 2 min at 20 mA and 39 Pa, pre-incubated with 4 uL of 10 uM FLAG-IKZF1(140-196;Q146A/G151N) for 1 min, and blotted from behind for 4 s. 4 uL of the sample was then applied to the grid. Grids were vitrified using an EM GP plunge freezer operated at 90% humidity and 10 C with 0 s pre-blot, 4 s blot, and 0 s post-blot.
Resolution 2.70 Å
9NYR Cryo-EM structure of CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 24 Deposited 2025-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 40–442（403 aa）
Not recorded A1B7G N-{(1R,4S)-4-[(4-{3-chloro-4-[(3R)-2,6-dioxo-1,2,3,6-tetrahydropyridin-3-yl]phenyl}piperazin-1-yl)methyl]cyclohexyl}-4-({4-[(3S)-3-hydroxy-3-methylpiperidin-1-yl]-5-(trifluoromethyl)pyrimidin-2-yl}amino)-3-methylbenzene-1-sulfonamide × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；50mM HEPES, pH 7.5, 150mM NaCl, 2mM TCEP, 2 mM FFC8, protein = 13.4 mg/ml
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9O91 Structure of IKZF2:CRBN:Compound 5 ternary structure Deposited 2025-04-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 318–426（109 aa） Fragment：CULT domain
Not recorded A1CAC (3S)-3-[(5M)-1-oxo-5-{4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2 M Magnesium chloride 0.1 M TRIS pH 8.5 33 % w/v PEG 4000
Resolution 1.86 Å R-free 0.218
9O91 Structure of IKZF2:CRBN:Compound 5 ternary structure Deposited 2025-04-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 318–426（109 aa） Fragment：CULT domain
Not recorded A1CAC (3S)-3-[(5M)-1-oxo-5-{4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2 M Magnesium chloride 0.1 M TRIS pH 8.5 33 % w/v PEG 4000
Resolution 1.86 Å R-free 0.218
9O91 Structure of IKZF2:CRBN:Compound 5 ternary structure Deposited 2025-04-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 318–426（109 aa） Fragment：CULT domain
Not recorded A1CAC (3S)-3-[(5M)-1-oxo-5-{4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2 M Magnesium chloride 0.1 M TRIS pH 8.5 33 % w/v PEG 4000
Resolution 1.86 Å R-free 0.218
9O91 Structure of IKZF2:CRBN:Compound 5 ternary structure Deposited 2025-04-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 318–426（109 aa） Fragment：CULT domain
Not recorded A1CAC (3S)-3-[(5M)-1-oxo-5-{4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2 M Magnesium chloride 0.1 M TRIS pH 8.5 33 % w/v PEG 4000
Resolution 1.86 Å R-free 0.218
9ODR Structure of CRBN TBD bound to compound C1 Deposited 2025-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 319–426（108 aa） Fragment：TBD domain
Not recorded A1CAV (3S)-3-(6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；277 K；0.2M tri-Sodium citrate 18 % w/v PEG 3,350
Resolution 2.42 Å R-free 0.228
9ODR Structure of CRBN TBD bound to compound C1 Deposited 2025-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 319–426（108 aa） Fragment：TBD domain
Not recorded A1CAV (3S)-3-(6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；277 K；0.2M tri-Sodium citrate 18 % w/v PEG 3,350
Resolution 2.42 Å R-free 0.228
9ODR Structure of CRBN TBD bound to compound C1 Deposited 2025-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 319–426（108 aa） Fragment：TBD domain
Not recorded A1CAV (3S)-3-(6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；277 K；0.2M tri-Sodium citrate 18 % w/v PEG 3,350
Resolution 2.42 Å R-free 0.228
9ODR Structure of CRBN TBD bound to compound C1 Deposited 2025-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 319–426（108 aa） Fragment：TBD domain
Not recorded A1CAV (3S)-3-(6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；277 K；0.2M tri-Sodium citrate 18 % w/v PEG 3,350
Resolution 2.42 Å R-free 0.228
9ODS Structure of CRBN TBD bound to compound C3 Deposited 2025-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 319–426（108 aa） Fragment：TBD domain
Not recorded A1CAW (1P)-1-[(4S)-8H-spiro[furo[2,3-c]imidazo[1,2-a]pyridine-7,4'-piperidin]-3-yl]pyrimidine-2,4(1H,3H)-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291 K；0.2M tri-Sodium citrate 18 % w/v PEG 3,350
Resolution 2.61 Å R-free 0.248
9ODS Structure of CRBN TBD bound to compound C3 Deposited 2025-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 319–426（108 aa） Fragment：TBD domain
Not recorded A1CAW (1P)-1-[(4S)-8H-spiro[furo[2,3-c]imidazo[1,2-a]pyridine-7,4'-piperidin]-3-yl]pyrimidine-2,4(1H,3H)-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291 K；0.2M tri-Sodium citrate 18 % w/v PEG 3,350
Resolution 2.61 Å R-free 0.248
9ODS Structure of CRBN TBD bound to compound C3 Deposited 2025-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 319–426（108 aa） Fragment：TBD domain
Not recorded A1CAW (1P)-1-[(4S)-8H-spiro[furo[2,3-c]imidazo[1,2-a]pyridine-7,4'-piperidin]-3-yl]pyrimidine-2,4(1H,3H)-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291 K；0.2M tri-Sodium citrate 18 % w/v PEG 3,350
Resolution 2.61 Å R-free 0.248
9ODS Structure of CRBN TBD bound to compound C3 Deposited 2025-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 319–426（108 aa） Fragment：TBD domain
Not recorded A1CAW (1P)-1-[(4S)-8H-spiro[furo[2,3-c]imidazo[1,2-a]pyridine-7,4'-piperidin]-3-yl]pyrimidine-2,4(1H,3H)-dione × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；291 K；0.2M tri-Sodium citrate 18 % w/v PEG 3,350
Resolution 2.61 Å R-free 0.248
9OHQ Structure of CRBN:IKZF2:Compound 15 Deposited 2025-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 319–426（108 aa）
Not recorded A1CBH (3S)-3-[(5M)-5-{1-methyl-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2M Magnesium Chloride, 0.5M Sodium Chloride, 0.1M Tris-HCl pH 8.5, 32.5% w/v PEG 3350
Resolution 1.60 Å R-free 0.201
9OHQ Structure of CRBN:IKZF2:Compound 15 Deposited 2025-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 319–426（108 aa）
Not recorded A1CBH (3S)-3-[(5M)-5-{1-methyl-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2M Magnesium Chloride, 0.5M Sodium Chloride, 0.1M Tris-HCl pH 8.5, 32.5% w/v PEG 3350
Resolution 1.60 Å R-free 0.201
9OHQ Structure of CRBN:IKZF2:Compound 15 Deposited 2025-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 319–426（108 aa）
Not recorded A1CBH (3S)-3-[(5M)-5-{1-methyl-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2M Magnesium Chloride, 0.5M Sodium Chloride, 0.1M Tris-HCl pH 8.5, 32.5% w/v PEG 3350
Resolution 1.60 Å R-free 0.201
9OHQ Structure of CRBN:IKZF2:Compound 15 Deposited 2025-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 319–426（108 aa）
Not recorded A1CBH (3S)-3-[(5M)-5-{1-methyl-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2M Magnesium Chloride, 0.5M Sodium Chloride, 0.1M Tris-HCl pH 8.5, 32.5% w/v PEG 3350
Resolution 1.60 Å R-free 0.201
9OHR Structure of CRBN:IKZF2:Compound 35 Deposited 2025-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 319–426（108 aa）
Not recorded A1CBG (3S)-3-[(5M)-5-{1-(oxetan-3-yl)-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2 M Magnesium Chloride, 0.5 M Sodium Chloride, 0.1 M Tris-HCl pH 8.1, 32.5% w/v PEG 3350
Resolution 2.34 Å R-free 0.290
9OHR Structure of CRBN:IKZF2:Compound 35 Deposited 2025-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 319–426（108 aa）
Not recorded A1CBG (3S)-3-[(5M)-5-{1-(oxetan-3-yl)-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2 M Magnesium Chloride, 0.5 M Sodium Chloride, 0.1 M Tris-HCl pH 8.1, 32.5% w/v PEG 3350
Resolution 2.34 Å R-free 0.290
9OHR Structure of CRBN:IKZF2:Compound 35 Deposited 2025-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 319–426（108 aa）
Not recorded A1CBG (3S)-3-[(5M)-5-{1-(oxetan-3-yl)-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2 M Magnesium Chloride, 0.5 M Sodium Chloride, 0.1 M Tris-HCl pH 8.1, 32.5% w/v PEG 3350
Resolution 2.34 Å R-free 0.290
9OHR Structure of CRBN:IKZF2:Compound 35 Deposited 2025-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 319–426（108 aa）
Not recorded A1CBG (3S)-3-[(5M)-5-{1-(oxetan-3-yl)-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.2 M Magnesium Chloride, 0.5 M Sodium Chloride, 0.1 M Tris-HCl pH 8.1, 32.5% w/v PEG 3350
Resolution 2.34 Å R-free 0.290
9OS2 Cryo-EM structure of the DDB1/CRBN-MRT-5702-G3BP2 ternary complex Deposited 2025-05-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 47–424（378 aa）
Not recorded ZN ZINC ION × 1 A1CED (1S,3S)-2-[(2-chlorophenyl)methanesulfonyl]-N-{[(4R)-3-(2,4-dioxo-1,3-diazinan-1-yl)imidazo[1,2-a]pyridin-7-yl]methyl}-1-methyl-1,2,3,4-tetrahydroisoquinoline-3-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
9OTY DDB1-CRBN with CK1 alpha, SB-405483, and DEG-47: composite map and model submission Deposited 2025-05-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 46–427（382 aa）
Not recorded ZN ZINC ION × 1 A1CEH N-{2-[(3R)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide × 1 A1CEG N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；10mM HEPES, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9OUK DDB1-CRBN with Ikaros(ZF2) and DEG-47: composite map and model submission Deposited 2025-05-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 2 A1CEK N-{2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；10mM HEPES, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.69 Å
9OUL DDB1-CRBN with Ikaros(ZF2), SB-405483, and DEG-47: composite map and model submission Deposited 2025-05-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–427（427 aa）
Not recorded ZN ZINC ION × 1 A1CEG N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea × 1 A1CEK N-{2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7；10mM HEPES, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.97 Å
9Q03 Cryo-EM structure of ternary complex BCL6-CRBN-DDB1 with BCL6-760 (LDD, local refined) Deposited 2025-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–442（442 aa）
Not recorded ZN ZINC ION × 1 A1CM7 (3R)-3-(6-{4-[(5-chloro-4-{[3-(3-hydroxy-3-methylbutyl)-1-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-5-yl]amino}pyrimidin-2-yl)(methyl)amino]piperidin-1-yl}-1-methyl-1H-indazol-3-yl)piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
9Q22 Crystal structure of ternary complex Helios-ZF2:I-19:CRBN:DDB1 Deposited 2025-08-14 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 41–442（402 aa）
Not recorded A1CNP (3S)-3-[5-(1-benzyl-4-hydroxypiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.148 M lithium citrate, 0.1 M Tris, pH 7.5, 19.4% PEG3350
Resolution 3.41 Å R-free 0.252
9Q2D Cryo-EM structure of ternary complex Ikaros-ZF2:CC-885:CRBN:DDB1 (molecular glue degrader) Deposited 2025-08-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 2 85C 1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE；blot time 4 sec blot force 4
Resolution 2.94 Å
9Q33 Cereblon Ternary Complex with Blimp1 and compound 5 Deposited 2025-08-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–442（442 aa）
Not recorded ZN ZINC ION × 1 A1CN1 N-({(4R)-7-[(1S)-2-amino-1-(4-bromo-2-methylphenyl)-2-oxoethyl]-5,6,7,8-tetrahydroimidazo[1,2-a]pyrazin-3-yl}methyl)-13-{4-[(3R)-2,6-dioxopiperidin-3-yl]anilino}tridecanamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.20 Å
9SAF Ternary PROTAC-mediated complex of BRD4-BD1/CRBN/DDB1 and JQ1-AcQ bifunctional degrader Deposited 2025-08-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–442（441 aa）
Not recorded ZN ZINC ION × 1 A1JM8 ~{N}-[(2~{S})-1-[[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]amino]-1-oxidanylidene-propan-2-yl]-9-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,10,12-tetraen-9-yl]ethanoylamino]nonanamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.55 Å
9SAI Ternary PROTAC-mediated complex consisting of Cereblon, DDB1 and BRD4-BD1, non-covalently linked by JQ1-AcN Deposited 2025-08-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–442（441 aa）
Not recorded ZN ZINC ION × 1 A1JM3 N-[(2S)-1-[[(3S)-2,5-bis(oxidanylidene)pyrrolidin-3-yl]amino]-1-oxidanylidene-propan-2-yl]-9-[2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]nonanamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM HEPES, 100 mM NaCl, 0.25 mM TCEP, pH: 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å
9SFM Crystal structure of Cereblon-DDB1 in complex with SB-405483 and Lenalidomide Deposited 2025-08-19 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 46–427（382 aa）
Not recorded EDO 1,2-ETHANEDIOL × 6 ZN ZINC ION × 1 LVY S-Lenalidomide × 1 A1CEG N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；20% w/v PEG 4000 0.1 M TRIS pH 8.2, 0.2 M
Resolution 2.39 Å R-free 0.244
9UUM Cryo-EM structure of mezigdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-07 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 41–442（402 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.41 Å
9V0A Cryo-EM structure of pomalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 41–442（402 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.69 Å
9V0F Cryo-EM structure of cemsidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 41–442（402 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.71 Å
9W2F Cryo-EM structure of DDB1-CRBN in complex with dHuR-2 and HuR Deposited 2025-07-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 45–425（381 aa）
Not recorded ZN ZINC ION × 1 A1EUN (3S)-3-[6-[1-[(4-methoxyphenyl)methyl]pyrazol-4-yl]-1-benzofuran-3-yl]piperidine-2,6-dione × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9Y7D Cereblon with Golcadomide and Ikaros ZF1-2-3 Deposited 2025-09-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 40–442（403 aa）
Not recorded ZN ZINC ION × 2 A1AF4 Golcadomide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 3.26 Å
9YA9 Cryo-EM structure of ternary complex BCL6-CRBN-DDB1 with BMS-986458 (local refined), a potent and selective BCL6 ligand directed degrader (LDD) Deposited 2025-09-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–442（442 aa）
Not recorded A1CTU (3R)-3-(6-{[(3R,4R)-1-{5-chloro-4-[(1-methyl-2-oxo-2,3-dihydro-1H-indol-5-yl)amino]pyrimidin-2-yl}-3-methylpiperidin-4-yl]amino}-1-methyl-1H-indazol-3-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.09 Å

93 other PDB entries and 141 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CRBN_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 26–427； UniProt 41–442

Ubiquitin-conjugating enzyme E2 D1

Homo sapiens

UniProt P51668

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain D； UniProt 2–147 Not recorded Cullin-4A × 1 （Q13619） DNA damage-binding protein 1 × 1 （Q16531） Protein cereblon × 1 （Q96SW2） Zinc finger protein Aiolos × 1 （Q9UKT9） NEDD8 × 1 （Q15843） E3 ubiquitin-protein ligase RBX1, N-terminally processed × 1 （P62877） Ubiquitin × 1 （P62979） ZINC ION × 6 (3S)-3-(5-azanyl-2-methyl-4-oxidanylidene-quinazolin-3-yl)piperidine-2,6-dione × 1 ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 3.54 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9V0B Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2C4P Crystal structure of human ubiquitin-conjugating enzyme UbcH5A Deposited 2005-10-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–147（147 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；200 MM AMMONIUM SULPHATE, 100 MM SODIUM ACETATE TRIHYDRATE [PH 4.6], 25% W/V PEG MME 2000
Resolution 2.35 Å R-free 0.272
2C4P Crystal structure of human ubiquitin-conjugating enzyme UbcH5A Deposited 2005-10-21 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–147（147 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.6；200 MM AMMONIUM SULPHATE, 100 MM SODIUM ACETATE TRIHYDRATE [PH 4.6], 25% W/V PEG MME 2000
Resolution 2.35 Å R-free 0.272
2YHO The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor Deposited 2011-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–147（147 aa）
Not recorded ZN ZINC ION × 2 ACT ACETATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；0.1 M SODIUM CITRATE PH 5.5, 0.2 M SODIUM ACETATE, 10% PEG 4000
Resolution 2.10 Å R-free 0.233
2YHO The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor Deposited 2011-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–147（147 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；0.1 M SODIUM CITRATE PH 5.5, 0.2 M SODIUM ACETATE, 10% PEG 4000
Resolution 2.10 Å R-free 0.233
2YHO The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor Deposited 2011-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–147（147 aa）
Not recorded ZN ZINC ION × 2 ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；0.1 M SODIUM CITRATE PH 5.5, 0.2 M SODIUM ACETATE, 10% PEG 4000
Resolution 2.10 Å R-free 0.233
2YHO The IDOL-UBE2D complex mediates sterol-dependent degradation of the LDL receptor Deposited 2011-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–147（147 aa）
Not recorded ZN ZINC ION × 2 ACT ACETATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；0.1 M SODIUM CITRATE PH 5.5, 0.2 M SODIUM ACETATE, 10% PEG 4000
Resolution 2.10 Å R-free 0.233
3OJ4 Crystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex Deposited 2010-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–147（147 aa） Fragment：Ubiquitin-conjugating enzyme E2 D1
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.1；292 K；0.1 M HEPES pH 7.1 and 1.85 M Na Malonate pH 7.0, VAPOR DIFFUSION, temperature 292K
Resolution 3.40 Å R-free 0.319
3OJ4 Crystal structure of the A20 ZnF4, ubiquitin and UbcH5A complex Deposited 2010-08-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–147（147 aa） Fragment：Ubiquitin-conjugating enzyme E2 D1
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.1；292 K；0.1 M HEPES pH 7.1 and 1.85 M Na Malonate pH 7.0, VAPOR DIFFUSION, temperature 292K
Resolution 3.40 Å R-free 0.319
3PTF X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin Deposited 2010-12-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–147（147 aa） Fragment：E2
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；Crystals of the complex were grown by hanging-drop vapor diffusion at 19 C by combining 1.5 ul of protein solution (20 mM MES pH 6.0, 150 mM NaCl and 0.5 mM TCEP) at 20 mg/ml with 1.5 ul of reservoir solution (0.1 M Tris pH 8.5 and 24% PEG 10,000), VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.70 Å R-free 0.275
3PTF X-ray structure of the non-covalent complex between UbcH5A and Ubiquitin Deposited 2010-12-02 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–147（147 aa） Fragment：E2
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；Crystals of the complex were grown by hanging-drop vapor diffusion at 19 C by combining 1.5 ul of protein solution (20 mM MES pH 6.0, 150 mM NaCl and 0.5 mM TCEP) at 20 mg/ml with 1.5 ul of reservoir solution (0.1 M Tris pH 8.5 and 24% PEG 10,000), VAPOR DIFFUSION, HANGING DROP, temperature 292K
Resolution 2.70 Å R-free 0.275
4AP4 Rnf4 - ubch5a - ubiquitin heterotrimeric complex Deposited 2012-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–147（147 aa）
Chain E 1–147（147 aa）
Mutation：YES Mutation：YES ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.2；pH 7.2
Resolution 2.21 Å R-free 0.242
4QPL Crystal structure of RNF146(RING-WWE)/UbcH5a/iso-ADPr complex Deposited 2014-06-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–147（147 aa）
Not recorded V3L 2'-O-(5-O-phosphono-alpha-D-ribofuranosyl)adenosine 5'-(dihydrogen phosphate) × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.8 M sodium citrate, 80 mM Tris HCl pH7.0, 160 mM NaCl, 4 mMDTT, 20 mM trimethylamin HCl, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.90 Å R-free 0.222
4QPL Crystal structure of RNF146(RING-WWE)/UbcH5a/iso-ADPr complex Deposited 2014-06-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–147（147 aa）
Not recorded V3L 2'-O-(5-O-phosphono-alpha-D-ribofuranosyl)adenosine 5'-(dihydrogen phosphate) × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；0.8 M sodium citrate, 80 mM Tris HCl pH7.0, 160 mM NaCl, 4 mMDTT, 20 mM trimethylamin HCl, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Resolution 1.90 Å R-free 0.222
5FER Complex of TRIM25 RING with UbcH5-Ub Deposited 2015-12-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–147（147 aa）
Chain E 1–147（147 aa）
Not recorded ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；10% PEG 20000 and 100 mM Tris pH 8.5
Resolution 2.34 Å R-free 0.273
5TUT UbcH5a-Ub isopeptide conjugate Deposited 2016-11-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–147（147 aa）
Mutation：C85K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；Hampton PEG/Ion F10
Resolution 2.60 Å R-free 0.243
6D4P Ube2D1 in complex with ubiquitin variant Ubv.D1.1 Deposited 2018-04-18 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–147（147 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；24% PEG2000-MME, 0.2M trimethylamine N-oxide, 0.1M Tris-HCl
Resolution 2.11 Å R-free 0.231
7ZJ3 Structure of TRIM2 RING domain in complex with UBE2D1~Ub conjugate Deposited 2022-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 2–146（145 aa）
Chain K 2–146（145 aa）
Mutation：S22R C85K Mutation：S22R C85K ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5 10% (w/v) PEG 8K
Resolution 2.53 Å R-free 0.258
7ZJ3 Structure of TRIM2 RING domain in complex with UBE2D1~Ub conjugate Deposited 2022-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 2–146（145 aa）
Chain H 2–146（145 aa）
Mutation：S22R C85K Mutation：S22R C85K ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES pH 7.5 10% (w/v) PEG 8K
Resolution 2.53 Å R-free 0.258
9UUM Cryo-EM structure of mezigdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-07 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 2–147（146 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.41 Å
9V0A Cryo-EM structure of pomalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 2–147（146 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.69 Å
9V0F Cryo-EM structure of cemsidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 2–147（146 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.71 Å

13 other PDB entries and 21 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name UB2D1_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 1–146； UniProt 2–147

Zinc finger protein Aiolos

Homo sapiens

UniProt Q9UKT9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain I； UniProt 142–197 Not recorded Cullin-4A × 1 （Q13619） DNA damage-binding protein 1 × 1 （Q16531） Protein cereblon × 1 （Q96SW2） Ubiquitin-conjugating enzyme E2 D1 × 1 （P51668） NEDD8 × 1 （Q15843） E3 ubiquitin-protein ligase RBX1, N-terminally processed × 1 （P62877） Ubiquitin × 1 （P62979） ZINC ION × 6 (3S)-3-(5-azanyl-2-methyl-4-oxidanylidene-quinazolin-3-yl)piperidine-2,6-dione × 1 ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 3.54 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9V0B Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9UUM Cryo-EM structure of mezigdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-07 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain I 142–197（56 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.41 Å
9V0A Cryo-EM structure of pomalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain I 142–197（56 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.69 Å
9V0F Cryo-EM structure of cemsidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain I 142–197（56 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.71 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name IKZF3_HUMAN
Isoform —
PDB entities 5
Chains and sequence ranges Author chain I； PDBConstruct 3–58； UniProt 142–197

NEDD8

Homo sapiens

UniProt Q15843

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain N； UniProt 1–76 Not recorded Cullin-4A × 1 （Q13619） DNA damage-binding protein 1 × 1 （Q16531） Protein cereblon × 1 （Q96SW2） Ubiquitin-conjugating enzyme E2 D1 × 1 （P51668） Zinc finger protein Aiolos × 1 （Q9UKT9） E3 ubiquitin-protein ligase RBX1, N-terminally processed × 1 （P62877） Ubiquitin × 1 （P62979） ZINC ION × 6 (3S)-3-(5-azanyl-2-methyl-4-oxidanylidene-quinazolin-3-yl)piperidine-2,6-dione × 1 ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 3.54 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9V0B Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NDD STRUCTURE OF NEDD8 Deposited 1998-08-21 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.8；pH 4.8
Resolution 1.60 Å R-free 0.300
1NDD STRUCTURE OF NEDD8 Deposited 1998-08-21 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.8；pH 4.8
Resolution 1.60 Å R-free 0.300
1NDD STRUCTURE OF NEDD8 Deposited 1998-08-21 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 1–76（76 aa）
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.8；pH 4.8
Resolution 1.60 Å R-free 0.300
1NDD STRUCTURE OF NEDD8 Deposited 1998-08-21 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 1–76（76 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.8；pH 4.8
Resolution 1.60 Å R-free 0.300
1NDD STRUCTURE OF NEDD8 Deposited 1998-08-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Not recorded CL CHLORIDE ION × 2 SO4 SULFATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.8；pH 4.8
Resolution 1.60 Å R-free 0.300
1R4M APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex Deposited 2003-10-07 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；PEG10K, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.00 Å R-free 0.280
1R4M APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex Deposited 2003-10-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–76（76 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；PEG10K, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.00 Å R-free 0.280
1R4M APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex Deposited 2003-10-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 1–76（76 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；PEG10K, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.00 Å R-free 0.280
1R4M APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex Deposited 2003-10-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain L 1–76（76 aa）
Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；PEG10K, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.00 Å R-free 0.280
1R4N APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP Deposited 2003-10-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；peg10k, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.60 Å R-free 0.290
1R4N APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP Deposited 2003-10-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；peg10k, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.60 Å R-free 0.290
1R4N APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP Deposited 2003-10-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；peg10k, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.60 Å R-free 0.290
1R4N APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex with ATP Deposited 2003-10-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain L 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；peg10k, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.60 Å R-free 0.290
1XT9 Crystal Structure of Den1 in complex with Nedd8 Deposited 2004-10-21 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；291 K；2M ammonium sulfate, 0.1M bicine, 4% tert-butanol, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.20 Å R-free 0.259
2BKR NEDD8 NEDP1 complex Deposited 2005-02-18 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；CRYSTALS WERE GROWN BY SETTING-DROP METHOD BY MIXING THE NEDP1-NEDD8 COMPLEX (20MG/ML) WITH EQUAL VOLUME OF RESERVOIR SOLUTION CONTAINING 20%PEG8000, 200MM NACL, 100MM PHOSPHATE CITRATE PH4.5, pH 4.50
Resolution 1.90 Å R-free 0.209
2KO3 Nedd8 solution structure Deposited 2009-09-09 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 200；Pressure ambient
NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Nedd8-1, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2N7K Unveiling the structural determinants of KIAA0323 binding preference for NEDD8 Deposited 2015-09-14 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–81（81 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 5.8；298 K；Ionic strength (raw mmCIF value) 0.02；Pressure ambient
NMR sample composition 0.15-1.5 mM [U-100% 15N] protein, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
2NVU Structure of APPBP1-UBA3~NEDD8-NEDD8-MgATP-Ubc12(C111A), a trapped ubiquitin-like protein activation complex Deposited 2006-11-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain I 1–76（76 aa）
Chain J 1–76（76 aa）
Not recorded MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7；291 K；17% v/v PEG 3350, 0.1 M HEPES pH 7.0, 0.2 M Disodium tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 7.00
Resolution 2.80 Å R-free 0.274
3DBH Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Ala-NEDD8Ala72Arg) Deposited 2008-05-31 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–76（76 aa）
Mutation：A172R ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M Tris, 0.4 M ammonium acetate, 9-10% PEG 10K, 5 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.85 Å R-free 0.274
3DBH Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Ala-NEDD8Ala72Arg) Deposited 2008-05-31 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–76（76 aa）
Mutation：A172R ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M Tris, 0.4 M ammonium acetate, 9-10% PEG 10K, 5 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.85 Å R-free 0.274
3DBH Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Ala-NEDD8Ala72Arg) Deposited 2008-05-31 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain L 1–76（76 aa）
Mutation：A172R ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M Tris, 0.4 M ammonium acetate, 9-10% PEG 10K, 5 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.85 Å R-free 0.274
3DBH Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Ala-NEDD8Ala72Arg) Deposited 2008-05-31 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 1–76（76 aa）
Mutation：A172R ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M Tris, 0.4 M ammonium acetate, 9-10% PEG 10K, 5 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.85 Å R-free 0.274
3DBL Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190wt-NEDD8Ala72Gln) Deposited 2008-06-01 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain L 1–76（76 aa）
Mutation：A172Q ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M Tris, 0.4 M ammonium acetate, 9-10% PEG 10K, 5 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.90 Å R-free 0.274
3DBL Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190wt-NEDD8Ala72Gln) Deposited 2008-06-01 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–76（76 aa）
Mutation：A172Q ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M Tris, 0.4 M ammonium acetate, 9-10% PEG 10K, 5 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.90 Å R-free 0.274
3DBL Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190wt-NEDD8Ala72Gln) Deposited 2008-06-01 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 1–76（76 aa）
Mutation：A172Q ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M Tris, 0.4 M ammonium acetate, 9-10% PEG 10K, 5 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.90 Å R-free 0.274
3DBL Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190wt-NEDD8Ala72Gln) Deposited 2008-06-01 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–76（76 aa）
Mutation：A172Q ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.1 M Tris, 0.4 M ammonium acetate, 9-10% PEG 10K, 5 mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.90 Å R-free 0.274
3DBR Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Gln-NEDD8Ala72Arg) Deposited 2008-06-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain K 1–76（76 aa）
Mutation：A172R ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.1 M Tris, 0.2 M NaCl, 10% PEG 10K, 8% PEG400, 5 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.05 Å R-free 0.280
3DBR Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Gln-NEDD8Ala72Arg) Deposited 2008-06-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain L 1–76（76 aa）
Mutation：A172R ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.1 M Tris, 0.2 M NaCl, 10% PEG 10K, 8% PEG400, 5 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.05 Å R-free 0.280
3DBR Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Gln-NEDD8Ala72Arg) Deposited 2008-06-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–76（76 aa）
Mutation：A172R ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.1 M Tris, 0.2 M NaCl, 10% PEG 10K, 8% PEG400, 5 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.05 Å R-free 0.280
3DBR Structural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Gln-NEDD8Ala72Arg) Deposited 2008-06-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–76（76 aa）
Mutation：A172R ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.1 M Tris, 0.2 M NaCl, 10% PEG 10K, 8% PEG400, 5 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.05 Å R-free 0.280
3DQV Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation Deposited 2008-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–76（76 aa） Fragment：NEDD8 C-terminus covalently linked to Cul5 Lys724
Mutation：L162M Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；with ~19% PEG3350, 275mM (NH4)2PO4, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.299
3DQV Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation Deposited 2008-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa） Fragment：NEDD8 C-terminus covalently linked to Cul5 Lys724
Mutation：L162M Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；with ~19% PEG3350, 275mM (NH4)2PO4, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.299
3DQV Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation Deposited 2008-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–76（76 aa） Fragment：NEDD8 C-terminus covalently linked to Cul5 Lys724
Chain B 1–76（76 aa） Fragment：NEDD8 C-terminus covalently linked to Cul5 Lys724
Mutation：L162M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：L162M Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；with ~19% PEG3350, 275mM (NH4)2PO4, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.299
3GZN Structure of NEDD8-activating enzyme in complex with NEDD8 and MLN4924 Deposited 2009-04-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–76（76 aa）
Not recorded ZN ZINC ION × 1 B39 [(1S,2S,4R)-4-{4-[(1S)-2,3-dihydro-1H-inden-1-ylamino]-7H-pyrrolo[2,3-d]pyrimidin-7-yl}-2-hydroxycyclopentyl]methyl sulfamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 293 K；1.8 M tri-ammonium citrate pH 7.0, 4% (v/v) 1,3 butanediol, temperature 293K
Resolution 3.00 Å R-free 0.287
3GZN Structure of NEDD8-activating enzyme in complex with NEDD8 and MLN4924 Deposited 2009-04-07 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain J 1–76（76 aa）
Not recorded ZN ZINC ION × 1 B39 [(1S,2S,4R)-4-{4-[(1S)-2,3-dihydro-1H-inden-1-ylamino]-7H-pyrrolo[2,3-d]pyrimidin-7-yl}-2-hydroxycyclopentyl]methyl sulfamate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 293 K；1.8 M tri-ammonium citrate pH 7.0, 4% (v/v) 1,3 butanediol, temperature 293K
Resolution 3.00 Å R-free 0.287
4F8C Structure of the Cif:Nedd8 complex - Yersinia pseudotuberculosis Cycle Inhibiting Factor in complex with human Nedd8 Deposited 2012-05-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–81（81 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；2.2M sodium malonate, 44mM bis-tris propane (pH 7.0), 66mM bis-tris propane (pH 8.0), VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 1.95 Å R-free 0.235
4F8C Structure of the Cif:Nedd8 complex - Yersinia pseudotuberculosis Cycle Inhibiting Factor in complex with human Nedd8 Deposited 2012-05-17 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–81（81 aa）
Not recorded EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；2.2M sodium malonate, 44mM bis-tris propane (pH 7.0), 66mM bis-tris propane (pH 8.0), VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 1.95 Å R-free 0.235
4FBJ Structure of the Cif:Nedd8 complex - Photorhabdus luminescens Cycle Inhibiting Factor in complex with human Nedd8 Deposited 2012-05-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–81（81 aa）
Not recorded CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.7；289 K；20% PEG 4000, 200mM sodium acetate, 100mM MES pH 6.7, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 1.60 Å R-free 0.236
4HCP crystal structure of Burkholderia pseudomallei effector protein chbp in complex with nedd8 Deposited 2012-10-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa） Fragment：unp residues 1-76
Not recorded SO4 SULFATE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；pH 5.5；293 K；1.5 M ammonium sulfate and 100 mM citrate, pH 5.5, EVAPORATION, temperature 293K
Resolution 2.52 Å R-free 0.267
4P5O Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action Deposited 2014-03-18 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain K 1–76（76 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；11% PEG3350, 0.2M ammonium citrate, 10mM ATP
Resolution 3.11 Å R-free 0.284
4P5O Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action Deposited 2014-03-18 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain H 1–76（76 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；11% PEG3350, 0.2M ammonium citrate, 10mM ATP
Resolution 3.11 Å R-free 0.284
6R7F Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain N 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCL 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.20 Å
6TTU Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 Deposited 2019-12-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain N 1–76（76 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.70 Å
7B5L Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27-UBE2L3~Ub~ARIH1. Transition State 1 Deposited 2020-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain N 1–76（76 aa）
Not recorded ZN ZINC ION × 9 SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7B5N Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1. Deposited 2020-12-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain N 1–81（81 aa）
Not recorded ZN ZINC ION × 9 SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7ONI Structure of Neddylated CUL5 C-terminal region-RBX2-ARIH2* Deposited 2021-05-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain N 1–81（81 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8B3G C(N)RL4CSA-UVSSA-E2-ubiquitin complex. Deposited 2022-09-16 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain N 1–76（76 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8B3I CRL4CSA-E2-Ub (state 2) Deposited 2022-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain N 1–76（76 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8CAF N8C_Fab3b in complex with NEDD8-CUL1(WHB) Deposited 2023-01-24 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain F 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2.0-2.1M Ammonium Sulfate, 0.1M Citrate pH 6.0, 10mM TCEP
Resolution 2.66 Å R-free 0.263
8CAF N8C_Fab3b in complex with NEDD8-CUL1(WHB) Deposited 2023-01-24 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain G 1–76（76 aa） Fragment：UNP residues 1-76
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2.0-2.1M Ammonium Sulfate, 0.1M Citrate pH 6.0, 10mM TCEP
Resolution 2.66 Å R-free 0.263
8H38 Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(mutate) complex Deposited 2022-10-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain N 1–76（76 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
Resolution 4.25 Å
8Q7H Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylated and neddylated conformation - focused cullin dimer Deposited 2023-08-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain N 1–81（81 aa）
Not recorded ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8RX0 (NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub Deposited 2024-02-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain N 1–76（76 aa）
Not recorded 759 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8WQC cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CDK5R1 Deposited 2023-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain K 1–76（76 aa）
Chain N 1–76（76 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
8WQG cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89 (conformation 1) Deposited 2023-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain K 1–76（76 aa）
Chain N 1–76（76 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.09 Å
8WZN ParkinK211N in complex with phospho NEDD8 Deposited 2023-11-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 PEG DI(HYDROXYETHYL)ETHER × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；291 K；0.1 M, MMT, 7.0, 25% w/v, PEG 1500
Resolution 1.80 Å R-free 0.212
8WZO Parkin in complex with phospho NEDD8 Deposited 2023-11-02 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；277 K；0.02 M Sodium/potassium phosphate, 0.1 M Bis-Tris propane, 7.5, 20% w/v PEG 3350
Resolution 2.25 Å R-free 0.248
9E77 Cryo-EM structure of CSN-N8 in complex with CSN5i-3 Deposited 2024-11-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain I 1–81（81 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9EFM Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-1 Deposited 2024-11-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain I 1–81（81 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9EFQ Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-2 Deposited 2024-11-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain I 1–81（81 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.96 Å
9EFV Cryo-EM structure of CSN-N8CUL1 in complex with CSN5i-3 Deposited 2024-11-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain I 1–81（81 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
9EG1 COP9 signalosome deneddylation complex with cullin-5 Deposited 2024-11-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain I 1–81（81 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.52 Å
9EG8 Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-4A Deposited 2024-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain I 1–81（81 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9EGL Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-3 Deposited 2024-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain I 1–81（81 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
9QO0 Pre-activated 9-subunit COP9 signalosome and neddylated SCF (Skp1-Skp2-Cks1) complex structure Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: 15-meric
Chain K 1–76（76 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.26 Å
9QO1 Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain K 1–76（76 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
9SDX Structure of RBR binding E2 variant crosslinked with NEDD8-CUL5-RBX2 bound ARIH2 and Ub Deposited 2025-08-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain N 1–81（81 aa）
Not recorded ZN ZINC ION × 7 SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.97 Å
9T7V Structure of LRRC58-EloB/C-CDO1 in complex with NEDD8-CUL5-RBX2-ARIH2-Ub Deposited 2025-11-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain N 1–76（76 aa）
Not recorded FE FE (III) ION × 1 SY8 5-azanylpentan-2-one × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9UUM Cryo-EM structure of mezigdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-07 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain N 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.41 Å
9V0A Cryo-EM structure of pomalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain N 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.69 Å
9V0F Cryo-EM structure of cemsidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain N 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.71 Å

46 other PDB entries and 71 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NEDD8_HUMAN
Isoform —
PDB entities 6
Chains and sequence ranges Author chain N； PDBConstruct 1–76； UniProt 1–76

E3 ubiquitin-protein ligase RBX1, N-terminally processed

Homo sapiens

UniProt P62877

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain R； UniProt 2–108 Not recorded Cullin-4A × 1 （Q13619） DNA damage-binding protein 1 × 1 （Q16531） Protein cereblon × 1 （Q96SW2） Ubiquitin-conjugating enzyme E2 D1 × 1 （P51668） Zinc finger protein Aiolos × 1 （Q9UKT9） NEDD8 × 1 （Q15843） Ubiquitin × 1 （P62979） ZINC ION × 6 (3S)-3-(5-azanyl-2-methyl-4-oxidanylidene-quinazolin-3-yl)piperidine-2,6-dione × 1 ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 3.54 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9V0B Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1LDJ Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex Deposited 2002-04-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 19–108（90 aa） Fragment：Residues 19-108
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；10% Ethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.288
1LDK Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex Deposited 2002-04-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 19–108（90 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；peg4k, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.331
1LDK Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex Deposited 2002-04-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain C 19–108（90 aa）
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；peg4k, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.331
1U6G Crystal Structure of The Cand1-Cul1-Roc1 Complex Deposited 2004-07-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–108（108 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；PEG 8000, sodium chloride, DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.317
29HG Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO22 SCF ubiquition ligase in complex with NSD2 via UNC10088 Deposited 2026-03-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–108（108 aa）
Not recorded A1J20 ~{N}-cyclopropyl-~{N}-[[4-[[2-(6-oxidanylhexanoyl)-1~{H}-isoquinolin-6-yl]carbamoyl]phenyl]methyl]-3-oxidanylidene-4~{H}-1,4-benzoxazine-7-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
29HH Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO22 SCF ubiquition ligase in complex with NSD2, UNC10088 and Bach1 Deposited 2026-03-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain E 1–108（108 aa）
Not recorded A1J20 ~{N}-cyclopropyl-~{N}-[[4-[[2-(6-oxidanylhexanoyl)-1~{H}-isoquinolin-6-yl]carbamoyl]phenyl]methyl]-3-oxidanylidene-4~{H}-1,4-benzoxazine-7-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
29HI Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO22 SCF ubiquition ligase in complex with NSD2 via UNC10415667 Deposited 2026-03-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–108（108 aa）
Not recorded A1J21 4-[[cyclopropyl-[(~{Z})-2-methyl-4-(5-oxidanylidene-2~{H}-1,4-oxazin-3-yl)but-3-enoyl]amino]methyl]-~{N}-[3-[2-[[4-(hydroxymethyl)phenyl]carbonyl-methyl-amino]ethyl]phenyl]benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
2HYE Crystal Structure of the DDB1-Cul4A-Rbx1-SV5V Complex Deposited 2006-08-05 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–108（108 aa）
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；100mM NaHEPES, 7-9% PEG4000, 10% iso-propanol, 5mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.316
2LGV Rbx1 Deposited 2011-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 12–108（97 aa） Fragment：sequence database residues 12-108
Mutation：W27S, V30S, L32Q, W33S ZN ZINC ION × 3 SOLUTION NMR
NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 0.120；Pressure ambient
NMR sample composition 20 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 700 uM [U-98% 15N] protein, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 20 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 700 uM [U-98% 13C; U-98% 15N] protein, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 20 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 700 uM [U-98% 13C; U-98% 15N] protein, 100% D2O | 100% D2O
Resolution not provided
3DPL Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation. Deposited 2008-07-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain R 5–108（104 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；277 K；2% PEG 3350, 0.1M HEPES, 0.2M L-proline, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.60 Å R-free 0.277
3DQV Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation Deposited 2008-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain R 5–108（104 aa） Fragment：Rbx1 residues 5-108
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；with ~19% PEG3350, 275mM (NH4)2PO4, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.299
3DQV Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation Deposited 2008-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Y 5–108（104 aa） Fragment：Rbx1 residues 5-108
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；with ~19% PEG3350, 275mM (NH4)2PO4, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.299
3DQV Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation Deposited 2008-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 5–108（104 aa） Fragment：Rbx1 residues 5-108
Chain Y 5–108（104 aa） Fragment：Rbx1 residues 5-108
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；with ~19% PEG3350, 275mM (NH4)2PO4, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.299
3RTR A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases Deposited 2011-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 5–108（104 aa） Fragment：UNP residues 5-108
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；17% PEG 3350, 100 mM Tris pH 7.5, 200 mM Sodium/Postassium Tartrate, 2% Benzamidine Hydrochloride, 1% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.21 Å R-free 0.282
3RTR A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases Deposited 2011-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 5–108（104 aa） Fragment：UNP residues 5-108
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；17% PEG 3350, 100 mM Tris pH 7.5, 200 mM Sodium/Postassium Tartrate, 2% Benzamidine Hydrochloride, 1% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.21 Å R-free 0.282
3RTR A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases Deposited 2011-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 5–108（104 aa） Fragment：UNP residues 5-108
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；17% PEG 3350, 100 mM Tris pH 7.5, 200 mM Sodium/Postassium Tartrate, 2% Benzamidine Hydrochloride, 1% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.21 Å R-free 0.282
3RTR A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases Deposited 2011-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 5–108（104 aa） Fragment：UNP residues 5-108
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；17% PEG 3350, 100 mM Tris pH 7.5, 200 mM Sodium/Postassium Tartrate, 2% Benzamidine Hydrochloride, 1% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.21 Å R-free 0.282
4F52 Structure of a Glomulin-RBX1-CUL1 complex Deposited 2012-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 5–108（104 aa） Fragment：UNP residues 5-108
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；18-21% PEG3350, 0.3-0.45M ammonium citrate, 10mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.00 Å R-free 0.289
4F52 Structure of a Glomulin-RBX1-CUL1 complex Deposited 2012-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 5–108（104 aa） Fragment：UNP residues 5-108
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；18-21% PEG3350, 0.3-0.45M ammonium citrate, 10mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.00 Å R-free 0.289
4P5O Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action Deposited 2014-03-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 3–108（106 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；11% PEG3350, 0.2M ammonium citrate, 10mM ATP
Resolution 3.11 Å R-free 0.284
4P5O Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action Deposited 2014-03-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 3–108（106 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；11% PEG3350, 0.2M ammonium citrate, 10mM ATP
Resolution 3.11 Å R-free 0.284
5N4W Crystal structure of the Cul2-Rbx1-EloBC-VHL ubiquitin ligase complex Deposited 2017-02-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 1–102（102 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.1 M Tris pH 7.6, 0.15 M ammonium sulphate, 15% polyethyleneglycol 4000 and 3% 1,4-dioxane or 4% acetonitrile. The sample was crystallised in the presence of a 19-mer peptide mimicking the substrate HIF-1alpha - residues 559-577 (DEALAPYIPMDDDFQLRSF, with the mutations L559D and M561A and P564 is hydroxyproline).
Resolution 3.90 Å R-free 0.346
6TTU Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 Deposited 2019-12-30 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.70 Å
7B5L Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27-UBE2L3~Ub~ARIH1. Transition State 1 Deposited 2020-12-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 9 SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7B5M Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1. Transition State 2 Deposited 2020-12-05 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.91 Å
7B5N Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1. Deposited 2020-12-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 9 SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7B5S Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-ARIH1 Ariadne. Transition State 1 Deposited 2020-12-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7OKQ Cryo-EM Structure of the DDB1-DCAF1-CUL4A-RBX1 Complex Deposited 2021-05-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: Hexadecameric
Chain D 1–108（108 aa）
Chain H 1–108（108 aa）
Chain L 1–108（108 aa）
Chain P 1–108（108 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.40 Å
7PLO H. sapiens replisome-CUL2/LRR1 complex Deposited 2021-09-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain T 1–108（108 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 3 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3 SO4 SULFATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7Z8B Structure of CRL7FBXW8 reveals coupling with CUL1-RBX1/ROC1 for multi-cullin-RING E3-catalyzed ubiquitin ligation Deposited 2022-03-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7Z8R CAND1-CUL1-RBX1 Deposited 2022-03-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain R 5–108（104 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7Z8T CAND1-SCF-SKP2 CAND1 engaged SCF rocked Deposited 2022-03-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 5–108（104 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7Z8V CAND1-SCF-SKP2 (SKP1deldel) CAND1 engaged SCF rocked Deposited 2022-03-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 5–108（104 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7ZBW CAND1-SCF-SKP2 CAND1 rolling-2 SCF engaged Deposited 2022-03-24 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 5–108（104 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8B3G C(N)RL4CSA-UVSSA-E2-ubiquitin complex. Deposited 2022-09-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8B3I CRL4CSA-E2-Ub (state 2) Deposited 2022-09-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8CDJ CAND1 b-hairpin++-SCF-SKP2 CAND1 rolling SCF engaged Deposited 2023-01-31 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 5–108（104 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8CDK CAND1 b-hairpin++-SCF-SKP2 CAND1 partly engaged SCF partly rocked Deposited 2023-01-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 5–108（104 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
8GQ6 Cryo-EM Structure of the KBTBD2-CUL3-Rbx1 dimeric complex Deposited 2022-08-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 1–108（108 aa）
Chain E 1–108（108 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.96 Å
8H33 Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 tetrameric complex Deposited 2022-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain D 1–108（108 aa）
Chain E 1–108（108 aa）
Chain K 1–108（108 aa）
Chain L 1–108（108 aa）
Not recorded ZN ZINC ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.86 Å
8H34 Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 hexameric complex Deposited 2022-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain D 1–108（108 aa）
Chain E 1–108（108 aa）
Chain K 1–108（108 aa）
Chain L 1–108（108 aa）
Chain Q 1–108（108 aa）
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.99 Å
8H35 Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 octameric complex Deposited 2022-10-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain D 1–108（108 aa）
Chain E 1–108（108 aa）
Chain K 1–108（108 aa）
Chain L 1–108（108 aa）
Chain Q 1–108（108 aa）
Chain R 1–108（108 aa）
Chain W 1–108（108 aa）
Chain X 1–108（108 aa）
Not recorded ZN ZINC ION × 24 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.41 Å
8H36 Cryo-EM Structure of the KBTBD2-CUL3-Rbx1-p85a dimeric complex Deposited 2022-10-08 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 1–108（108 aa）
Chain E 1–108（108 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8H37 Cryo-EM Structure of the KBTBD2-CUL3-Rbx1-p85a tetrameric complex Deposited 2022-10-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain D 1–108（108 aa）
Chain E 1–108（108 aa）
Chain Q 1–108（108 aa）
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.52 Å
8H38 Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(mutate) complex Deposited 2022-10-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
Resolution 4.25 Å
8H3A Cryo-EM Structure of the KBTBD2-CRL3~N8(removed)-CSN complex Deposited 2022-10-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.51 Å
8H3F Cryo-EM Structure of the KBTBD2-CRL3-CSN complex Deposited 2022-10-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.73 Å
8H3Q Cryo-EM Structure of the CAND1-Cul3-Rbx1 complex Deposited 2022-10-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.76 Å
8H3R Cryo-EM Structure of the KBTBD2-CRL3~N8 dimeric complex Deposited 2022-10-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 1–108（108 aa）
Chain E 1–108（108 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.36 Å
8IJ1 Protomer 1 and 2 of the asymmetry trimer of the Cul2-Rbx1-EloBC-FEM1B ubiquitin ligase complex Deposited 2023-02-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8JAQ Structure of CRL2APPBP2 bound with RxxGP degron (tetramer) Deposited 2023-05-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric
Chain R 1–108（108 aa）
Chain V 1–108（108 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.26 Å
8JAS Structure of CRL2APPBP2 bound with RxxGPAA degron (tetramer) Deposited 2023-05-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric
Chain R 1–108（108 aa）
Chain V 1–108（108 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
8JAV Structure of CRL2APPBP2 bound with the C-degron of MRPL28 (tetramer) Deposited 2023-05-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric
Chain R 1–108（108 aa）
Chain V 1–108（108 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å
8JE1 An asymmetry dimer of the Cul2-Rbx1-EloBC-FEM1B ubiquitin ligase complexed with BEX2 Deposited 2023-05-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.95 Å
8K9I Structure of CUL3-RBX1-KLHL22 complex without CUL3 NA motif Deposited 2023-08-01 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 1–108（108 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8KHP CULLIN3-KLHL22-RBX1 E3 ligase Deposited 2023-08-22 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–108（108 aa）
Chain F 1–108（108 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.67 Å
8OR0 CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2 Deposited 2023-04-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain B 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8OR2 CAND1-CUL1-RBX1-DCNL1 Deposited 2023-04-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8OR3 CAND1-CUL1-RBX1-SKP1-SKP2-DCNL1 Deposited 2023-04-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8OR4 Partially dissociated CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2 Deposited 2023-04-13 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain B 1–108（108 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8PQL K48-linked ubiquitin chain formation with a cullin-RING E3 ligase and Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2-donor UB-acceptor UB-SIL1 peptide Deposited 2023-07-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: nonameric
Chain K 1–108（108 aa）
Not recorded SY8 5-azanylpentan-2-one × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.76 Å
8Q7E Structure of CUL9-RBX1 ubiquitin E3 ligase complex - hexameric assembly Deposited 2023-08-16 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain C 1–108（108 aa）
Chain D 1–108（108 aa）
Chain G 1–108（108 aa）
Chain H 1–108（108 aa）
Chain K 1–108（108 aa）
Chain L 1–108（108 aa）
Mutation：p.M1_A4del Mutation：p.M1_A4del Mutation：p.M1_A4del Mutation：p.M1_A4del Mutation：p.M1_A4del Mutation：p.M1_A4del No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8Q7H Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylated and neddylated conformation - focused cullin dimer Deposited 2023-08-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–108（108 aa）
Chain D 1–108（108 aa）
Mutation：p.M1_A4del Mutation：p.M1_A4del ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8Q7R Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB-Sil1 peptide Deposited 2023-08-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain R 1–108（108 aa）
Not recorded U9O 5-azanyl-1-oxidanyl-pentan-2-one × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.71 Å
8QU8 PROTAC-mediated complex of KRAS with VHL/Elongin-B/Elongin-C/Cullin-2/Rbx1 Deposited 2023-10-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 2–108（107 aa）
Not recorded ZN ZINC ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 WYL (2S,4R)-1-[(2S)-2-[4-[4-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butoxy]-1,2,3-triazol-1-yl]-3-methyl-butanoyl]-N-[(1R)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-2-oxidanyl-ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8R5H Ubiquitin ligation to neosubstrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-VHL-MZ1 with trapped UBE2R2~donor UB-BRD4 BD2 Deposited 2023-11-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain R 5–108（104 aa）
Not recorded ZN ZINC ION × 3 SY8 5-azanylpentan-2-one × 1 759 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.44 Å
8RHZ Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylated conformation - symmetry expanded unneddylated dimer Deposited 2023-12-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–108（108 aa）
Chain D 1–108（108 aa）
Mutation：p.M1_A4del Mutation：p.M1_A4del ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.37 Å
8RWZ Open non-crosslinked structure Brd4BD2-MZ1-(NEDD8)-CRL2VHL Deposited 2024-02-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 16–108（93 aa）
Not recorded 759 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8RX0 (NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub Deposited 2024-02-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain R 16–108（93 aa）
Not recorded 759 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8UBU Cryo-EM structure of dimeric SCF-FBXL17-BACH1BTB E3 ligase complex close conformation Deposited 2023-09-25 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 16–108（93 aa）
Chain I 16–108（93 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8WDK The complex structure of Cul2-VCB-Protac-Wee1 Deposited 2023-09-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 21–102（82 aa）
Not recorded W6U (2S,4R)-1-[(2S)-3,3-dimethyl-2-[3-[4-[4-[4-[[3-oxidanylidene-1-[6-(2-oxidanylpropan-2-yl)pyridin-2-yl]-2-prop-2-enyl-pyrazolo[3,4-d]pyrimidin-6-yl]amino]phenyl]piperazin-1-yl]butoxy]propanoylamino]butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.64 Å
8WQA Cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89 (conformation 1) Deposited 2023-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain I 16–108（93 aa）
Chain J 16–108（93 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
8WQB Cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89 (conformation 2) Deposited 2023-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain E 16–108（93 aa）
Chain I 16–108（93 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.37 Å
8WQC cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CDK5R1 Deposited 2023-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 16–108（93 aa）
Chain J 16–108（93 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
8WQE Cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CUX1 (conformation 1) Deposited 2023-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain I 16–108（93 aa）
Chain J 16–108（93 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å
8WQF cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CUX1 (conformation 2) Deposited 2023-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain E 16–108（93 aa）
Chain I 16–108（93 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
8WQG cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89 (conformation 1) Deposited 2023-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 16–108（93 aa）
Chain J 16–108（93 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.09 Å
8WQH cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89 (conformation 2) Deposited 2023-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 16–108（93 aa）
Chain J 16–108（93 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å
9BJ8 human CRL2-ZYG11B complex Deposited 2024-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.78 Å
9BJ9 Human CRL-2 ZYG11B binding to human NLRP1 Gly/N degron Deposited 2024-04-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9EFM Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-1 Deposited 2024-11-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain K 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9EFQ Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-2 Deposited 2024-11-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain K 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.96 Å
9EFV Cryo-EM structure of CSN-N8CUL1 in complex with CSN5i-3 Deposited 2024-11-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain K 1–108（108 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
9EG8 Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-4A Deposited 2024-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain K 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9EGL Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-3 Deposited 2024-11-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain K 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
9J63 Cryo-EM structure of neddylated Cul2-Rbx1-EloBC-FEM1B homodimer Deposited 2024-08-14 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 1–108（108 aa）
Chain H 1–108（108 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
9J64 Cryo-EM structure of neddylated Cul2-Rbx1-EloBC-FEM1B homodimer complexed with FNIP1 degron Deposited 2024-08-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain E 1–108（108 aa）
Chain H 1–108（108 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.28 Å
9J77 Cryo-EM structure of CRL2-FEM1B (dimer 1) Deposited 2024-08-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain E 16–108（93 aa）
Chain I 16–108（93 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.56 Å
9J78 Cryo-EM structure of CRL2-FEM1B (dimer 2) Deposited 2024-08-18 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain E 16–108（93 aa）
Chain I 16–108（93 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.88 Å
9J79 Cryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer) Deposited 2024-08-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: 19-meric
Chain I 16–108（93 aa）
Chain N 16–108（93 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.08 Å
9JKB Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO4 SCF ubiquition ligase complex Deposited 2024-09-15 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 16–108（93 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
9KBD Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO3 SCF ubiquition ligase complex Deposited 2024-10-30 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 1–108（108 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9LKY Dimer of CRL2-FEM1B bound with PLD6 Deposited 2025-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: 11-meric
Chain E 16–108（93 aa）
Chain I 16–108（93 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
9LWI The head region of HBx-Smc5/6 ubiquitination complex Deposited 2025-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain H 1–108（108 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9LWJ The head-arm region of HBx-Smc5/6 ubiquitination complex Deposited 2025-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain H 1–108（108 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.19 Å
9LWL HBx-Smc5/6 ubiquitination complex Deposited 2025-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain H 1–108（108 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.25 Å
9QO0 Pre-activated 9-subunit COP9 signalosome and neddylated SCF (Skp1-Skp2-Cks1) complex structure Deposited 2025-03-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: 15-meric
Chain J 1–108（108 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.26 Å
9QO1 Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure Deposited 2025-03-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain J 1–108（108 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
9QO2 Dissociation-state-1 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain J 1–108（108 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9QO4 Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain J 1–108（108 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9QO5 Dissociation-state-4 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain J 1–108（108 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9T32 The Cullin 2 RING VHL E3 ligase dimerised by the homoPROTAC CM11 Deposited 2025-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain R 20–108（89 aa）
Chain S 20–108（89 aa）
Not recorded A1JTC (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[2-[2-[[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-2-oxidanylidene-ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
9UUM Cryo-EM structure of mezigdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-07 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain R 2–108（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.41 Å
9V0A Cryo-EM structure of pomalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain R 2–108（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.69 Å
9V0F Cryo-EM structure of cemsidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain R 2–108（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.71 Å
9XZJ Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex and a 3-way DNA fork (consensus structure) Deposited 2025-08-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain R 1–108（108 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
9XZK Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex and a 3-way DNA fork (head structure) Deposited 2025-08-27 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain R 1–108（108 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.91 Å

99 other PDB entries and 107 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RBX1_HUMAN
Isoform —
PDB entities 7
Chains and sequence ranges Author chain R； PDBConstruct 5–111； UniProt 2–108

Ubiquitin

Homo sapiens

UniProt P62979

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain U； UniProt 1–76 Not recorded Cullin-4A × 1 （Q13619） DNA damage-binding protein 1 × 1 （Q16531） Protein cereblon × 1 （Q96SW2） Ubiquitin-conjugating enzyme E2 D1 × 1 （P51668） Zinc finger protein Aiolos × 1 （Q9UKT9） NEDD8 × 1 （Q15843） E3 ubiquitin-protein ligase RBX1, N-terminally processed × 1 （P62877） ZINC ION × 6 (3S)-3-(5-azanyl-2-methyl-4-oxidanylidene-quinazolin-3-yl)piperidine-2,6-dione × 1 ELECTRON MICROSCOPY mmCIF provides none of the parsed experimental conditions Resolution 3.54 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 9V0B Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
22TU Human 80S ribosome in complex with DHX29 Deposited 2026-01-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 191 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
28LN XBP1u-stalled RPL4 RNC in complex with NAC Deposited 2026-02-05 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 86-meric
Chain Af 1–156（156 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.70 Å
28ZU human 48S PIC with Kozak mRNA and eIF1A W70A mutant Deposited 2026-03-03 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 38 PDB declaration: 41-meric
Chain Sf 1–156（156 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.20 Å
28ZV human 48S PIC with mRNA (non-Kozak) Deposited 2026-03-03 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 38 PDB declaration: 41-meric
Chain Sf 1–156（156 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.90 Å
28ZX human 48S PIC with mRNA (Kozak_1) Deposited 2026-03-03 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain Sf 1–156（156 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.80 Å
28ZY human 48S PIC with mRNA (Kozak_2) Deposited 2026-03-03 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain Sf 1–156（156 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.00 Å
3AXC Crystal structure of linear diubiquitin Deposited 2011-04-01 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；289 K；30% PEG 4000, 0.1M Tris-HCl, 0.1M MgCl2, 30% Dioxane, 30% Isopropanol , pH 7.5, VAPOR DIFFUSION, temperature 289K
Resolution 2.19 Å R-free 0.278
3PHW OTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex with Ubiquitin Deposited 2010-11-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa） Fragment：UNP residues 1-75
Not recorded NEH ETHANAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.27 M sodium phosphate dihydrogen, 1.53 M di-potassium phosphate hydrogen, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.278
3PHW OTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex with Ubiquitin Deposited 2010-11-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa） Fragment：UNP residues 1-75
Not recorded NEH ETHANAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.27 M sodium phosphate dihydrogen, 1.53 M di-potassium phosphate hydrogen, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.278
3PHW OTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex with Ubiquitin Deposited 2010-11-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–75（75 aa） Fragment：UNP residues 1-75
Not recorded NEH ETHANAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.27 M sodium phosphate dihydrogen, 1.53 M di-potassium phosphate hydrogen, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.278
3PHW OTU Domain of Crimean Congo Hemorrhagic Fever Virus in complex with Ubiquitin Deposited 2010-11-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–75（75 aa） Fragment：UNP residues 1-75
Not recorded NEH ETHANAMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.27 M sodium phosphate dihydrogen, 1.53 M di-potassium phosphate hydrogen, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.278
3TBL Structure of Mono-ubiquitinated PCNA: Implications for DNA Polymerase Switching and Okazaki Fragment Maturation Deposited 2011-08-07 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–76（76 aa）
Chain E 1–76（76 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；0.9 to 1.3 M sodium citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.90 Å R-free 0.293
4R62 Structure of Rad6~Ub Deposited 2014-08-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa） Fragment：Ubiquitin
Not recorded ACT ACETATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.4；293 K；24% PEG 300, 50 mM sodium acetate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.28 Å R-free 0.265
4UG0 STRUCTURE OF THE HUMAN 80S RIBOSOME Deposited 2015-03-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 89-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 239 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
4V6X Structure of the human 80S ribosome Deposited 2013-02-27 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 84 PDB declaration: 89-meric
Chain Af 77–156（80 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Blot for 3 seconds using two pieces of filter paper, then plunge into liquid ethane (FEI VITROBOT MARK IV).
Resolution 5.00 Å
5AJ0 Cryo electron microscopy of actively translating human polysomes (POST state). Deposited 2015-02-19 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain Bf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 326 ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer 20 MM HEPES-KOH, PH 7.5, 100 MM KCL, 1.5 MM MGCL2, 0.5 MM SPERMIDINE, 0.04 MM SPERMINE, 1 MM DTT；pH 7.5；20 MM HEPES-KOH, PH 7.5, 100 MM KCL, 1.5 MM MGCL2, 0.5 MM SPERMIDINE, 0.04 MM SPERMINE, 1 MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 93, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT FOR 2-4 SECONDS BEFORE PLUNGING,
Resolution 3.50 Å
5FLX Mammalian 40S HCV-IRES complex Deposited 2015-10-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 35-meric
Chain f 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 74 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer 20MM TRIS-HCL, 7.5MM MGCL2, 100MM KCL, 0.2MM SPERMIDINE, 2MM DTT；pH 7.6；20MM TRIS-HCL, 7.5MM MGCL2, 100MM KCL, 0.2MM SPERMIDINE, 2MM DTT
cryo-EM vitrification conditions Cryogen ETHANE；VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 93, INSTRUMENT- FEI VITROBOT MARK I, METHOD- BLOT FOR 2-4 SECONDS BEFORE PLUNGING,
Resolution 3.90 Å
5LKS Structure-function insights reveal the human ribosome as a cancer target for antibiotics Deposited 2016-07-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain Sf 1–156（156 aa）
Not recorded 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 MG MAGNESIUM ION × 224 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
5T2C CryoEM structure of the human ribosome at 3.6 Angstrom resolution Deposited 2016-08-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain AH 1–156（156 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
5WVO Crystal structure of DNMT1 RFTS domain in complex with K18/K23 mono-ubiquitylated histone H3 Deposited 2016-12-28 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–76（76 aa）
Chain B 1–76（76 aa）
Mutation：G76C Mutation：G76C ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；100mM Bis-Tris (pH 6.0), 200mM lithium sulfate monohydrate, 20% PEG 10000
Resolution 2.00 Å R-free 0.239
5YDK Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form Deposited 2017-09-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa） Fragment：UNP residues 1-76
Chain D 1–77（77 aa） Fragment：UNP residues 1-76
Mutation：K63R Mutation：D77 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 7.6 21% PEG3350
Resolution 2.50 Å R-free 0.260
5YDK Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form Deposited 2017-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 1–76（76 aa） Fragment：UNP residues 1-76
Chain J 1–77（77 aa） Fragment：UNP residues 1-76
Mutation：K63R Mutation：D77 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 7.6 21% PEG3350
Resolution 2.50 Å R-free 0.260
5YDK Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form Deposited 2017-09-13 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–77（77 aa） Fragment：UNP residues 1-76
Chain E 1–76（76 aa） Fragment：UNP residues 1-76
Mutation：D77 Mutation：K63R GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 7.6 21% PEG3350
Resolution 2.50 Å R-free 0.260
5YDK Crystal structure of RNF168 UDM1 in complex with Lys63-linked diubiquitin, tetrameric form Deposited 2017-09-13 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain I 1–77（77 aa） Fragment：UNP residues 1-76
Chain K 1–76（76 aa） Fragment：UNP residues 1-76
Mutation：D77 Mutation：K63R No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris pH 7.6 21% PEG3350
Resolution 2.50 Å R-free 0.260
6DC6 Crystal structure of human ubiquitin activating enzyme E1 (Uba1) in complex with ubiquitin Deposited 2018-05-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded MG MAGNESIUM ION × 2 POP PYROPHOSPHATE 2- × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；285 K；0.1 M MgCl2, 0.2 M Tris HCl pH 8.0, 20% PEG 4000
Resolution 3.14 Å R-free 0.250
6DC6 Crystal structure of human ubiquitin activating enzyme E1 (Uba1) in complex with ubiquitin Deposited 2018-05-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–76（76 aa）
Not recorded MG MAGNESIUM ION × 2 POP PYROPHOSPHATE 2- × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；285 K；0.1 M MgCl2, 0.2 M Tris HCl pH 8.0, 20% PEG 4000
Resolution 3.14 Å R-free 0.250
6FEC Human cap-dependent 48S pre-initiation complex Deposited 2017-12-31 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain p 82–152（71 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Tris HCl, 50 mM KOAc, 2.5 mM MgCl2, 2 mM DTT, 0.25 mM spermidine 0.25 mM GMPPNP
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.30 Å
6G18 Cryo-EM structure of a late human pre-40S ribosomal subunit - State C Deposited 2018-03-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 35-meric
Chain f 1–156（156 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
6G51 Cryo-EM structure of a late human pre-40S ribosomal subunit - State D Deposited 2018-03-28 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 38-meric
Chain f 1–156（156 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6G53 Cryo-EM structure of a late human pre-40S ribosomal subunit - State E Deposited 2018-03-28 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain f 1–156（156 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6IP5 Cryo-EM structure of the CMV-stalled human 80S ribosome (Structure ii) Deposited 2018-11-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain 3R 1–156（156 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6IP6 Cryo-EM structure of the CMV-stalled human 80S ribosome with HCV IRES (Structure iii) Deposited 2018-11-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain 3R 1–156（156 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6IP8 Cryo-EM structure of the HCV IRES dependently initiated CMV-stalled 80S ribosome (Structure iv) Deposited 2018-11-02 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain 3R 1–156（156 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6J99 Cryo-EM structure of human DOT1L in complex with an H2B-monoubiquitinated nucleosome Deposited 2019-01-22 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric
Chain L 1–76（76 aa）
Mutation：G76C SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
6KIU Cryo-EM structure of human MLL1-ubNCP complex (3.2 angstrom) Deposited 2019-07-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain O 1–76（76 aa）
Mutation：G76C SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 LYS LYSINE × 1 GLN GLUTAMINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6KIV Cryo-EM structure of human MLL1-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain O 1–76（76 aa）
Mutation：G76C SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6KIW Cryo-EM structure of human MLL3-ubNCP complex (4.0 angstrom) Deposited 2019-07-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain O 1–76（76 aa）
Mutation：G76C ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6OLE Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AP and PE tRNAs Deposited 2019-04-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 31 ZN ZINC ION × 6 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6OLF Human ribosome nascent chain complex (CDH1-RNC) stalled by a drug-like molecule with AA and PE tRNAs Deposited 2019-04-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain Sf 85–151（67 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 31 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6OLG Human ribosome nascent chain complex stalled by a drug-like small molecule (CDH1_RNC with PP tRNA) Deposited 2019-04-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain Bf 79–151（73 aa）
Not recorded MG MAGNESIUM ION × 326 ZN ZINC ION × 5 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
6OLI Structure of human ribosome nascent chain complex selectively stalled by a drug-like small molecule (USO1-RNC) Deposited 2019-04-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 31 ZN ZINC ION × 6 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6OLZ Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like molecule with PP tRNA Deposited 2019-04-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain Bf 79–151（73 aa）
Not recorded MG MAGNESIUM ION × 326 ZN ZINC ION × 5 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6OM0 Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like molecule with AP and PE tRNAs Deposited 2019-04-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 31 ZN ZINC ION × 6 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6OM7 Human ribosome nascent chain complex (PCSK9-RNC) stalled by a drug-like small molecule with AA and PE tRNAs Deposited 2019-04-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain Sf 85–151（67 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 31 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6QZP High-resolution cryo-EM structure of the human 80S ribosome Deposited 2019-03-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 81-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 438 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 ZN ZINC ION × 8 HYG HYGROMYCIN B × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6XA1 Structure of a drug-like compound stalled human translation termination complex Deposited 2020-06-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain Sf 89–151（63 aa）
Not recorded MG MAGNESIUM ION × 190 MVM N-(3-chloropyridin-2-yl)-N-[(3R)-piperidin-3-yl]-4-(3H-[1,2,3]triazolo[4,5-b]pyridin-3-yl)benzamide × 1 ZN ZINC ION × 8 K POTASSIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
6Y0G Structure of human ribosome in classical-PRE state Deposited 2020-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 83-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 72 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6Y57 Structure of human ribosome in hybrid-PRE state Deposited 2020-02-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain sh 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 160 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6YBS Structure of a human 48S translational initiation complex - head Deposited 2020-03-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 17 PDB declaration: octadecameric
Chain k 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 29 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6Z6L Cryo-EM structure of human CCDC124 bound to 80S ribosomes Deposited 2020-05-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6Z6M Cryo-EM structure of human 80S ribosomes bound to EBP1, eEF2 and SERBP1 Deposited 2020-05-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6Z6N Cryo-EM structure of human EBP1-80S ribosomes (focus on EBP1) Deposited 2020-05-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6ZLW SARS-CoV-2 Nsp1 bound to the human 40S ribosomal subunit Deposited 2020-07-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain g 1–156（156 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6ZM7 SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-EBP1 ribosome complex Deposited 2020-07-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
6ZME SARS-CoV-2 Nsp1 bound to the human CCDC124-80S-eERF1 ribosome complex Deposited 2020-07-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 83 PDB declaration: 88-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 8 SF4 IRON/SULFUR CLUSTER × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6ZMI SARS-CoV-2 Nsp1 bound to the human LYAR-80S ribosome complex Deposited 2020-07-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6ZMO SARS-CoV-2 Nsp1 bound to the human LYAR-80S-eEF1a ribosome complex Deposited 2020-07-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 88-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6ZMT SARS-CoV-2 Nsp1 bound to a pre-40S-like ribosome complex Deposited 2020-07-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 35-meric
Chain g 1–156（156 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6ZMW Structure of a human 48S translational initiation complex Deposited 2020-07-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain k 1–156（156 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 89 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6ZON SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 1 Deposited 2020-07-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 48-meric
Chain U 1–156（156 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6ZP4 SARS-CoV-2 Nsp1 bound to a human 43S preinitiation ribosome complex - state 2 Deposited 2020-07-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 54-meric
Chain U 1–156（156 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6ZUO Human RIO1(kd)-StHA late pre-40S particle, structural state A (pre 18S rRNA cleavage) Deposited 2020-07-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 35-meric
Chain f 1–156（156 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
6ZV6 Human RIO1(kd)-StHA late pre-40S particle, structural state B (post 18S rRNA cleavage) Deposited 2020-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 35-meric
Chain f 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 3 ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6ZVH EDF1-ribosome complex Deposited 2020-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 37-meric
Chain f 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 30 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
6ZVJ Structure of a human ABCE1-bound 43S pre-initiation complex - State II Deposited 2020-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 51-meric
Chain U 88–149（62 aa）
Not recorded ZN ZINC ION × 3 SF4 IRON/SULFUR CLUSTER × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
6ZXD Cryo-EM structure of a late human pre-40S ribosomal subunit - State F1 Deposited 2020-07-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 37-meric
Chain f 1–156（156 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
6ZXE Cryo-EM structure of a late human pre-40S ribosomal subunit - State F2 Deposited 2020-07-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 37-meric
Chain f 1–156（156 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6ZXF Cryo-EM structure of a late human pre-40S ribosomal subunit - State G Deposited 2020-07-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 37-meric
Chain f 1–156（156 aa）
Not recorded ZN ZINC ION × 3 MG MAGNESIUM ION × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6ZXG Cryo-EM structure of a late human pre-40S ribosomal subunit - State H1 Deposited 2020-07-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 37-meric
Chain f 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 131 ZN ZINC ION × 3 ASP ASPARTIC ACID × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
6ZXH Cryo-EM structure of a late human pre-40S ribosomal subunit - State H2 Deposited 2020-07-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain f 1–156（156 aa）
Not recorded ASP ASPARTIC ACID × 1 MG MAGNESIUM ION × 131 ZN ZINC ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7A09 Structure of a human ABCE1-bound 43S pre-initiation complex - State III Deposited 2020-08-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 54-meric
Chain U 1–156（156 aa）
Not recorded ZN ZINC ION × 4 SF4 IRON/SULFUR CLUSTER × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MET METHIONINE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7BWD Structure of Dot1L-H2BK34ub Nucleosome Complex Deposited 2020-04-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain L 1–76（76 aa）
Chain M 1–76（76 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 4.32 Å
7MQ9 Cryo-EM structure of the human SSU processome, state pre-A1* Deposited 2021-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 70 PDB declaration: 74-meric
Chain NT 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 22 ZN ZINC ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.87 Å
7MQA Cryo-EM structure of the human SSU processome, state post-A1 Deposited 2021-05-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 72-meric
Chain NT 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 64 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7OOJ Structure of D-Thr53 Ubiquitin Deposited 2021-05-27 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–76（76 aa）
Mutation：Gly53D-Thr Non-standard monomer：Yes (specific site not provided by mmCIF) CD CADMIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M Bis-Tris, pH 7.5, 20 % polyethylene glycol monomethyl ether 2000, 50 mM CdCl2
Resolution 2.60 Å R-free 0.269
7OOJ Structure of D-Thr53 Ubiquitin Deposited 2021-05-27 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–76（76 aa）
Mutation：Gly53D-Thr Non-standard monomer：Yes (specific site not provided by mmCIF) CD CADMIUM ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M Bis-Tris, pH 7.5, 20 % polyethylene glycol monomethyl ether 2000, 50 mM CdCl2
Resolution 2.60 Å R-free 0.269
7QP6 Structure of the human 48S initiation complex in open state (h48S AUG open) Deposited 2022-01-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric
Chain k 1–156（156 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 95 mM KOAc, 3.75 mM Mg(OAc)2, 1 mM ATP, 0.5 mM GTP, 0.25 mM spermidine, 2 mM DTT, 0.4 U/uL RiboLock RNase inhibitor
cryo-EM vitrification conditions Cryogen ETHANE；Cryo-EM grids were prepared by floating home-made continuous carbon on 40 ul sample in the wells of teflon block (custom-made). The sample-covered carbon was then adsorbed to an EM grid.
Resolution 4.70 Å
7QP7 Structure of the human 48S initiation complex in closed state (h48S AUG closed) Deposited 2022-01-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain k 1–156（156 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20 mM Hepes, pH 7.5, 95 mM KOAc, 3.75 mM Mg(OAc)2, 1 mM ATP, 0.5 mM GTP, 0.25 mM spermidine, 2 mM DTT, 0.4 U/uL RiboLock RNase inhibitor
cryo-EM vitrification conditions Cryogen ETHANE；Cryo-EM grids were prepared by floating home-made continuous carbon on 40 ul sample in the wells of teflon block (custom-made). The sample-covered carbon was then adsorbed to an EM grid.
Resolution 3.70 Å
7R4X Cryo-EM reconstruction of the human 40S ribosomal subunit - Full map Deposited 2022-02-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 35-meric
Chain f 1–156（156 aa）
Not recorded K POTASSIUM ION × 82 MG MAGNESIUM ION × 88 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.15 Å
7TQL CryoEM structure of the human 40S small ribosomal subunit in complex with translation initiation factors eIF1A and eIF5B. Deposited 2022-01-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 38-meric
Chain g 85–149（65 aa）
Not recorded GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 5GP GUANOSINE-5'-MONOPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7WTT Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A1 (with CK1) Deposited 2022-02-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 34-meric
Chain f 1–156（156 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7WTU Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A1 (without CK1) Deposited 2022-02-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 32 PDB declaration: 33-meric
Chain f 1–156（156 aa）
Not recorded SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7WTV Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A2 Deposited 2022-02-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 35-meric
Chain f 1–156（156 aa）
Not recorded ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7WTW Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-A3 Deposited 2022-02-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 37-meric
Chain f 1–156（156 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7WTX Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-B1 Deposited 2022-02-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 34-meric
Chain f 1–156（156 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7WTZ Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-B2 Deposited 2022-02-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 33 PDB declaration: 34-meric
Chain f 1–156（156 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7WU0 Cryo-EM structure of a human pre-40S ribosomal subunit - State RRP12-B3 Deposited 2022-02-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 35-meric
Chain f 1–156（156 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7XNY High resolution cry-EM structure of the human 80S ribosome from SNORD127+/- Kasumi-1 cells Deposited 2022-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 421 K POTASSIUM ION × 12 ZN ZINC ION × 9 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
8G5Y mRNA decoding in human is kinetically and structurally distinct from bacteria (IC state) Deposited 2023-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain Sf 1–156（156 aa）
Not recorded SPD SPERMIDINE × 13 PUT 1,4-DIAMINOBUTANE × 11 K POTASSIUM ION × 77 MG MAGNESIUM ION × 524 ANM ANISOMYCIN × 1 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 ZN ZINC ION × 8 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.29 Å
8G60 mRNA decoding in human is kinetically and structurally distinct from bacteria (CR state) Deposited 2023-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain Sf 1–156（156 aa）
Not recorded SPD SPERMIDINE × 8 PUT 1,4-DIAMINOBUTANE × 10 MG MAGNESIUM ION × 461 ANM ANISOMYCIN × 1 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 K POTASSIUM ION × 10 ZN ZINC ION × 7 PHE PHENYLALANINE × 1 MET METHIONINE × 1 GSP 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 1 ZIY plitidepsin × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.54 Å
8G61 mRNA decoding in human is kinetically and structurally distinct from bacteria (AC state) Deposited 2023-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 84-meric
Chain Sf 1–156（156 aa）
Not recorded PUT 1,4-DIAMINOBUTANE × 4 K POTASSIUM ION × 16 MG MAGNESIUM ION × 326 ANM ANISOMYCIN × 1 SPD SPERMIDINE × 5 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 ZN ZINC ION × 8 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.94 Å
8G6J mRNA decoding in human is kinetically and structurally distinct from bacteria (GA state 2) Deposited 2023-02-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain Sf 1–156（156 aa）
Not recorded SPD SPERMIDINE × 10 K POTASSIUM ION × 34 MG MAGNESIUM ION × 337 PUT 1,4-DIAMINOBUTANE × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 ZN ZINC ION × 8 PHE PHENYLALANINE × 1 MET METHIONINE × 1 GSP 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE × 1 YRB (3R,6R,9S,12S,15S,18S,20R,24aR)-6-[(2S)-butan-2-yl]-3,12-bis[(1R)-1-hydroxy-2-methylpropyl]-8,9,11,17,18-pentamethyl-15-[(2S)-2-methylbutyl]hexadecahydropyrido[1,2-a][1,4,7,10,13,16,19]heptaazacyclohenicosine-1,4,7,10,13,16,19(21H)-heptone × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8GLP mRNA decoding in human is kinetically and structurally distinct from bacteria (Consensus LSU focused refined structure) Deposited 2023-03-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 81-meric
Chain Sf 1–156（156 aa）
Not recorded SPD SPERMIDINE × 15 PUT 1,4-DIAMINOBUTANE × 9 K POTASSIUM ION × 152 MG MAGNESIUM ION × 671 ANM ANISOMYCIN × 1 3H3 4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 ZN ZINC ION × 8 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.67 Å
8IFD Dibekacin-added human 80S ribosome Deposited 2023-02-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain 3R 1–156（156 aa）
Not recorded 84D Dibekacin × 24 MG MAGNESIUM ION × 397 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.59 Å
8IFE Arbekacin-added human 80S ribosome Deposited 2023-02-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 80-meric
Chain 3R 1–156（156 aa）
Not recorded 84G Arbekacin × 23 MG MAGNESIUM ION × 410 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
8IVB K113-Ubiquitinated BAK Deposited 2023-03-26 Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–76（76 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；310 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 20 mM sodium phosphate, 0.1 M sodium chloride, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
8K2C Cryo-EM structure of the human 80S ribosome with Tigecycline Deposited 2023-07-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 259 T1C TIGECYCLINE × 9 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8OZ0 Structure of a human 48S translation initiation complex with eIF4F and eIF4A Deposited 2023-05-06 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 57-meric
Chain p 1–156（156 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 89 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8PJ1 Structure of human 48S translation initiation complex in open codon scanning state (48S-1) Deposited 2023-06-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain k 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 90 ZN ZINC ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 3.40 Å
8PJ2 Structure of human 48S translation initiation complex in AUG recognition state after eIF5-induced GTP hydrolysis by eIF2 (48S-2) Deposited 2023-06-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 49-meric
Chain k 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 87 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 3.40 Å
8PJ3 Structure of human 48S translation initiation complex upon transfer of initiator tRNA to eIF5B (48S-3) Deposited 2023-06-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 54-meric
Chain k 1–156（156 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 NA SODIUM ION × 1 MG MAGNESIUM ION × 89 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 3.70 Å
8PJ4 Structure of human 48S translation initiation complex after eIF5 release (48S-4) Deposited 2023-06-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 53-meric
Chain k 1–156（156 aa）
Not recorded GTP GUANOSINE-5'-TRIPHOSPHATE × 1 NA SODIUM ION × 1 MG MAGNESIUM ION × 89 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 3.20 Å
8PJ5 Structure of human 48S translation initiation complex after eIF2 release prior 60S subunit joining (48S-5) Deposited 2023-06-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 48 PDB declaration: 51-meric
Chain k 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 91 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 2.90 Å
8PJ6 Structure of human 48S translation initiation complex with initiator tRNA, eIF1A and eIF3 (off-pathway) Deposited 2023-06-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 50-meric
Chain k 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 87 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE；Manual blotting & plunge-freezing
Resolution 2.90 Å
8PPK Bat-Hp-CoV Nsp1 and eIF1 bound to the human 40S small ribosomal subunit Deposited 2023-07-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 37-meric
Chain f 1–156（156 aa）
Not recorded UNX UNKNOWN LIGAND × 117 MG MAGNESIUM ION × 111 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.98 Å
8PPL MERS-CoV Nsp1 bound to the human 43S pre-initiation complex Deposited 2023-07-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 52-meric
Chain Af 1–156（156 aa）
Not recorded ZN ZINC ION × 4 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 116 MET METHIONINE × 1 UNX UNKNOWN LIGAND × 129 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.65 Å
8QOI Structure of the human 80S ribosome at 1.9 A resolution - the molecular role of chemical modifications and ions in RNA Deposited 2023-09-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 79-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 292 K POTASSIUM ION × 108 SPD SPERMIDINE × 2 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6；Titan Krios sample is prepared with Sodium cacodylate buffer. CryoARM 300 sample is prepared with Hepes buffer.
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
8T4S MERS-CoV Nsp1 protein bound to the Human 40S Ribosomal subunit Deposited 2023-06-09 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain f 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 97 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
8UKB In situ HHT and CHX treated human hibernating state without E-tRNA 80S ribosome Deposited 2023-10-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 84-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 255 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 WV3 4-{(2R)-2-[(1R,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.05 Å
8X7I Cryo-EM structures of RNF168/UbcH5c-Ub in complex with H2AK13Ub nucleosomes determined by intein-based E2-Ub-NCP conjugation strategy Deposited 2023-11-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 1–75（75 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
8X7J Cryo-EM structures of RNF168/UbcH5c-Ub/nucleosomes complex determined by activity-based chemical trapping strategy Deposited 2023-11-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 11 PDB declaration: tridecameric
Chain M 1–75（75 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
8XP2 Cryo-EM structure of the human 40S ribosome with LARP1 Deposited 2024-01-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain Sf 1–156（156 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8XP3 Cryo-EM structure of the human 40S ribosome with LARP1 and LRRC47 Deposited 2024-01-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 37-meric
Chain Sf 1–156（156 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8XSX Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA, SERBP1 and eEF2 Deposited 2024-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 259 T1C TIGECYCLINE × 7 ZN ZINC ION × 8 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8XSY Cryo-EM structure of the human 80S ribosome with Tigecycline, e-tRNA and CCDC124 (40S head Swivelled) Deposited 2024-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 255 T1C TIGECYCLINE × 8 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8XSZ Cryo-EM structure of the human 80S ribosome with Tigecycline, E-tRNA and P-tRNA Deposited 2024-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 248 T1C TIGECYCLINE × 5 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8XXL Cryo-EM structure of the human 40S ribosome with PDCD4 Deposited 2024-01-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 22 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8XXM Cryo-EM structure of the human 40S ribosome with PDCD4 and eIF3G Deposited 2024-01-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 37-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 23 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8XXN Cryo-EM structure of the human 43S ribosome with PDCD4 Deposited 2024-01-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 50-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 23 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8YOO Cryo-EM structure of the human 80S ribosome with 100 um Tigecycline Deposited 2024-03-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 81-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 257 T1C TIGECYCLINE × 6 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.00 Å
8YOP Cryo-EM structure of the human 80S ribosome with 4 um Tigecycline Deposited 2024-03-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 82-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 255 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
8ZDB Cryo-EM structure of the human ubiquitylated 40S ribosome with RIOK3 Deposited 2024-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 38-meric
Chain f 1–156（156 aa）
Chain i 1–156（156 aa）
Chain j 1–156（156 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8ZDC Cryo-EM structure of the human ubiquitylated pre-40S ribosome with RIOK3 Deposited 2024-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 37 PDB declaration: 38-meric
Chain i 1–76（76 aa）
Chain j 1–76（76 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8ZDD Cryo-EM structure of the human ubiquitylated pre-40S ribosome with RIOK3 (without NOB1) Deposited 2024-05-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 37-meric
Chain i 1–76（76 aa）
Chain j 1–76（76 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9B0P In situ human Hibernating class1 80S ribosome Deposited 2024-03-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 85-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 255 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.82 Å
9B0Q In situ human top-back di-ribosome structure (Composite map) Deposited 2024-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 160 PDB declaration: 172-meric
Chain Sf 85–151（67 aa）
Chain sf 85–151（67 aa）
Not recorded ZN ZINC ION × 12 MG MAGNESIUM ION × 510 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9B0S In situ human top-top di-ribosome structure (Composite map) Deposited 2024-03-12 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 158 PDB declaration: 171-meric
Chain Sf 85–151（67 aa）
Chain sf 85–151（67 aa）
Not recorded ZN ZINC ION × 12 MG MAGNESIUM ION × 510 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9BKD The structure of human Pdcd4 bound to the 40S small ribosomal subunit Deposited 2024-04-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain k 1–156（156 aa）
Not recorded ZN ZINC ION × 3 K POTASSIUM ION × 19 MG MAGNESIUM ION × 88 SPD SPERMIDINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
9BLN The structure of human Pdcd4 bound to the 40S-eIF4A-eIF3-eIF1 complex Deposited 2024-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 50-meric
Chain k 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 88 K POTASSIUM ION × 19 SPD SPERMIDINE × 1 ZN ZINC ION × 3 ACY ACETIC ACID × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
9C3H Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site. Deposited 2024-06-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 77 PDB declaration: 83-meric
Chain Sz 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 326 K POTASSIUM ION × 94 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.00 Å
9ED0 Human LARP1 bound to the 40S small ribosomal subunit Deposited 2024-11-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain f 1–156（156 aa）
Not recorded K POTASSIUM ION × 71 MG MAGNESIUM ION × 92 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9FQZ CRYO-EM STRUCTURE OF HCT15 POLYSOMES BOUND TO EEF2, EBP1, AND SERBP1 Deposited 2024-06-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain Sf 1–156（156 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 271 K POTASSIUM ION × 104 ZN ZINC ION × 8 PUT 1,4-DIAMINOBUTANE × 7 HYG HYGROMYCIN B × 1 SPD SPERMIDINE × 8 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ANM ANISOMYCIN × 1 NA SODIUM ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
9G8M human 80S ribosome bound by a SKI2-exosome complex Deposited 2024-07-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 87 PDB declaration: 92-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 232 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.30 Å
9G8O human 40S ribosome bound by a SKI238-exosome complex Deposited 2024-07-23 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain Sf 1–156（156 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.40 Å
9I14 CRYO-EM STRUCTURE OF HCT15 POLYSOMES IN HYBRID-PRE STATE Deposited 2025-01-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Sf 1–156（156 aa）
Not recorded K POTASSIUM ION × 40 MG MAGNESIUM ION × 267 NA SODIUM ION × 23 SPD SPERMIDINE × 1 PUT 1,4-DIAMINOBUTANE × 1 ZN ZINC ION × 7 HYG HYGROMYCIN B × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
9I2D NMT1-NAC bound human RNC with 10 amino acid ARF1-linker Deposited 2025-01-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 88-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 191 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.19 Å
9I2E NMT1-NAC bound human ribosome (combined translational states) Deposited 2025-01-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 256 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9IJU Sertraline enhances the deubiquitinase activity of USP7 by binding to its switching loop region Deposited 2024-06-25 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-tris pH 6.5, 0.2 M MgCl2, 25% PEG3350
Resolution 2.46 Å R-free 0.270
9IJU Sertraline enhances the deubiquitinase activity of USP7 by binding to its switching loop region Deposited 2024-06-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded SRE (1S,4S)-4-(3,4-dichlorophenyl)-N-methyl-1,2,3,4-tetrahydronaphthalen-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-tris pH 6.5, 0.2 M MgCl2, 25% PEG3350
Resolution 2.46 Å R-free 0.270
9IJU Sertraline enhances the deubiquitinase activity of USP7 by binding to its switching loop region Deposited 2024-06-25 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–75（75 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-tris pH 6.5, 0.2 M MgCl2, 25% PEG3350
Resolution 2.46 Å R-free 0.270
9IJU Sertraline enhances the deubiquitinase activity of USP7 by binding to its switching loop region Deposited 2024-06-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–75（75 aa）
Not recorded SRE (1S,4S)-4-(3,4-dichlorophenyl)-N-methyl-1,2,3,4-tetrahydronaphthalen-1-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-tris pH 6.5, 0.2 M MgCl2, 25% PEG3350
Resolution 2.46 Å R-free 0.270
9IML Sertraline enhances the deubiquitinase activity of USP7 by binding to its switching loop region Deposited 2024-07-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–75（75 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-tris pH 6.5, 0.2 M MgCl2, 25% PEG3350
Resolution 2.78 Å R-free 0.280
9IML Sertraline enhances the deubiquitinase activity of USP7 by binding to its switching loop region Deposited 2024-07-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–75（75 aa）
Not recorded XB7 1-[(4-fluorophenyl)methyl]-N-{1-[2-(4-methoxyphenyl)ethyl]piperidin-4-yl}-1H-benzimidazol-2-amine × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-tris pH 6.5, 0.2 M MgCl2, 25% PEG3350
Resolution 2.78 Å R-free 0.280
9IML Sertraline enhances the deubiquitinase activity of USP7 by binding to its switching loop region Deposited 2024-07-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–75（75 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-tris pH 6.5, 0.2 M MgCl2, 25% PEG3350
Resolution 2.78 Å R-free 0.280
9IML Sertraline enhances the deubiquitinase activity of USP7 by binding to its switching loop region Deposited 2024-07-03 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–75（75 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；0.1 M Bis-tris pH 6.5, 0.2 M MgCl2, 25% PEG3350
Resolution 2.78 Å R-free 0.280
9IPU cryo-EM structure of the RNF168(1-193)/UbcH5c-Ub ubiquitylation module bound to H1.0-K63-Ub3 modified chromatosome Deposited 2024-07-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain M 1–75（75 aa）
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9K4J Structure of substrate-engaged human 26S proteasome RP-CP subcomplex in state EA1.0 Deposited 2024-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 50 PDB declaration: 50-meric
Chain u 1–76（76 aa）
Chain w 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9K4K Structure of substrate-engaged human 26S proteasome RP-CP subcomplex in state EA1.1 Deposited 2024-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 51 PDB declaration: 51-meric
Chain u 1–76（76 aa）
Chain v 1–76（76 aa）
Chain w 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9K4L Structure of substrate-engaged 26S proteasome RP-CP subcomplex in state EA1.2 Deposited 2024-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain x 1–76（76 aa）
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.50 Å
9K4M Structure of substrate-engaged human 26S proteasome RP-CP subcomplex in state EA2.1 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain u 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9K4O Structure of substrate-engaged human 26S proteasome RP-CP subcomplex in state EA2.2 Deposited 2024-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 50 PDB declaration: 50-meric
Chain u 1–76（76 aa）
Chain x 1–76（76 aa）
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.00 Å
9K4P Structure of substrate-engaged human 26S proteasome RP-CP subcomplex in state EA2.3 Deposited 2024-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain u 1–76（76 aa）
Chain z 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.80 Å
9K4R Structure of substrate-engaged human 26S proteasome RP-CP subcomplex in state EB.1 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain u 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9K4S Structure of substrate-engaged 26S proteasome RP-CP subcomplex in state EB.2 Deposited 2024-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 50 PDB declaration: 50-meric
Chain u 1–76（76 aa）
Chain x 1–76（76 aa）
Chain y 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.70 Å
9K4T Structure of substrate-engaged human 26S proteasome RP-CP subcomplex in state EB.3 Deposited 2024-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 49 PDB declaration: 49-meric
Chain u 1–76（76 aa）
Chain z 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.10 Å
9K4U Structure of substrate-engaged human 26S proteasome RP-CP subcomplex in state EC1 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain u 1–76（76 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9K54 Structure of substrate-engaged human 26S proteasome RP-CP subcomplex in state ED2.2 Deposited 2024-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 51 PDB declaration: 51-meric
Chain w 1–76（76 aa）
Chain x 1–76（76 aa）
Chain y 1–76（76 aa）
Chain z 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9K55 Structure of substrate-engaged human 26S proteasome RP-CP subcomplex in state ED2.3 Deposited 2024-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 50 PDB declaration: 50-meric
Chain w 1–76（76 aa）
Chain x 1–76（76 aa）
Chain z 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.00 Å
9K56 Structure of substrate-engaged single-cap human proteasome in state EA1 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 47 PDB declaration: 47-meric
Chain w 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9K57 Structure of substrate-engaged single-cap human proteasome in state EA2 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain u 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 4 MG MAGNESIUM ION × 5 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
9K58 Structure of substrate-engaged single-cap human proteasome in state EB Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain u 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
9K59 Structure of substrate-engaged single-cap human proteasome in state EC1 Deposited 2024-10-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 48 PDB declaration: 48-meric
Chain u 1–76（76 aa）
Not recorded ADP ADENOSINE-5'-DIPHOSPHATE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 3 MG MAGNESIUM ION × 3 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.30 Å
9K5E Structure of substrate-engaged double-cap human proteasome in state EA1-EA1 Deposited 2024-10-21 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 68 PDB declaration: 68-meric
Chain Au 1–76（76 aa）
Chain Aw 1–76（76 aa）
Chain Bu 1–76（76 aa）
Chain Bw 1–76（76 aa）
Not recorded ATP ADENOSINE-5'-TRIPHOSPHATE × 8 MG MAGNESIUM ION × 10 ADP ADENOSINE-5'-DIPHOSPHATE × 4 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9KEN cryo-EM structure of TRIP12 in complex with K29/48 branched-triUb Deposited 2024-11-05 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–76（76 aa）
Chain D 1–76（76 aa）
Mutation：K29C No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.63 Å
9KHS Cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked diUb (monomeric conformation) Deposited 2024-11-11 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.31 Å
9KHT cryo-EM structure of Ufd2/Ubc4-Ub in complex with K29-linked triUb (dimeric conformation) Deposited 2024-11-11 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain C 1–76（76 aa）
Chain E 1–76（76 aa）
Chain F 1–76（76 aa）
Chain c 1–76（76 aa）
Chain e 1–76（76 aa）
Chain f 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.85 Å
9KKF Structure of the human 40S ribosome complexed with HCV IRES and eIF3 Deposited 2024-11-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 43 PDB declaration: 45-meric
Chain sh 1–156（156 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9KMT Bat SARSr-CoV RaTG15 Nsp1 bound to the Human 40S Ribosomal subunit-State1 Deposited 2024-11-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain f 78–151（74 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.81 Å
9KMU Bat SARSr-CoV RaTG15 Nsp1 bound to the Human 40S Ribosomal subunit-State2 Deposited 2024-11-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain f 78–151（74 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.87 Å
9KMV SARSr-MpCoV-GX Nsp1 bound to the Human 40S Ribosomal subunit-State1 Deposited 2024-11-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain f 78–151（74 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
9KMW SARSr-MpCoV-GX Nsp1 bound to the Human 40S Ribosomal subunit-State2 Deposited 2024-11-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain f 78–151（74 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.73 Å
9KMX Bat MERSr-CoV NeoCoV Nsp1 bound to the Human 40S Ribosomal subunit-State1 Deposited 2024-11-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain f 78–151（74 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
9KMY Bat MERSr-CoV NeoCoV Nsp1 bound to the Human 40S Ribosomal subunit-State2 Deposited 2024-11-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain f 78–151（74 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
9KMZ Bat MERSr-CoV NL140422 Nsp1 bound to the Human 40S Ribosomal subunit-State1 Deposited 2024-11-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain f 78–151（74 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
9KN0 Bat MERSr-CoV NL140422 Nsp1 bound to the Human 40S Ribosomal subunit-State2 Deposited 2024-11-18 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 35 PDB declaration: 36-meric
Chain f 78–151（74 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
9KN5 Structure of the human 40S ribosome complexed with HCV IRES, eIF1A and eIF3 Deposited 2024-11-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 46-meric
Chain sh 1–156（156 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9KN6 Structure of the HCV IRES-dependent pre-48S translation initiation complex with eIF1A, eIF5B, and eIF3 Deposited 2024-11-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 48-meric
Chain sh 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 8 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9KRP Structure of the HCV IRES-dependent 48S translation initiation complex with eIF5B and eIF3 Deposited 2024-11-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 47-meric
Chain sh 1–156（156 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 9 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
9KZU Cryo-EM structure of the HCV IRES-dependently initiated CMV-stalled 80S ribosome (non-rotated state) in complexed with eIF3 Deposited 2024-12-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 85 PDB declaration: 92-meric
Chain sh 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 81 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9KZX Cryo-EM structure of the HCV IRES-dependently initiated CMV-stalled 80S ribosome (rotated state) in complexed with eIF3 Deposited 2024-12-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 85 PDB declaration: 93-meric
Chain sh 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 66 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9L3L Crystal structure of the C lobe of E6AP in complex with K48-linked diUb Deposited 2024-12-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–76（76 aa）
Chain C 1–73（73 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2 M Sodium citrate tribasic dihydrate, 0.1 M TRIS hydrochloride pH 8.5, 30% v/v Polyethylene glycol 400
Resolution 2.59 Å R-free 0.269
9M7O Cryo-EM structure of Ufd2/Ubc4-ub complex with K29triUb(monomeric conformation) Deposited 2025-03-10 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.14 Å
9O3V Human 80S ribosome stalled on MYC nascent chain Deposited 2025-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 352 K POTASSIUM ION × 165 SPD SPERMIDINE × 14 PUT 1,4-DIAMINOBUTANE × 7 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM Tris, 100mM KOAc, 7.5mM MgOAc, 0.25mM Spermidine, 2mM DTT, 0.05% w/v b-OG
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
9O3W Human 80S ribosome bound to IDB-001 stalled on MYC nascent chain Deposited 2025-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain Sf 1–156（156 aa）
Not recorded K POTASSIUM ION × 170 PUT 1,4-DIAMINOBUTANE × 7 SPD SPERMIDINE × 14 A1B75 (2R,3S,4S)-4-hydroxy-2-[(4-methoxyphenyl)methyl]pyrrolidin-3-yl {2-[(2S)-pyrrolidin-2-yl]ethyl}carbamate × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 MG MAGNESIUM ION × 371 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM Tris, 100mM KOAc, 7.5mM MgOAc, 0.25mM Spermidine, 2mM DTT, 0.05% w/v b-OG, 50uM IDB-001
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 1.90 Å
9O3Y Human 80S ribosome bound to IDB-002 stalled on FPAK-containing nascent chain Deposited 2025-04-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 82-meric
Chain Sf 1–156（156 aa）
Not recorded K POTASSIUM ION × 168 SPD SPERMIDINE × 14 PUT 1,4-DIAMINOBUTANE × 7 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 MG MAGNESIUM ION × 332 A1B76 (2R,3S,4S)-4-hydroxy-2-[(4-methoxyphenyl)methyl]pyrrolidin-3-yl [(3-fluorophenyl)methyl]carbamate × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；20mM Tris, 100mM KOAc, 7.5mM MgOAc, 0.25mM Spermidine, 2mM DTT, 0.05% w/v b-OG, 50uM IDB-001
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
9P6Z In situ human P-Z state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.97 Å
9P72 In situ human P-E state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9P73 In situ human eEF2-A/P-P/E state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 218 ZN ZINC ION × 6 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.66 Å
9P76 In situ human eEF1A-A/T-P state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.83 Å
9P78 In situ human Hibernating rotate 3 with E-site tRNA state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 218 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9P79 In situ human Hibernating rotate3 with Z site tRNA state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 218 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9P7A In situ human hibernating class2 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 218 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.81 Å
9P7C In situ human Hibernating class3 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 218 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.78 Å
9P7D In situ human Hibernating class4 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 218 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
9P7E In situ human Hibernating class5 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 218 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.59 Å
9P7F In situ HHT and CHX treated A-P state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain Sf 85–151（67 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.56 Å
9P7G In situ HHT and CHX treated A-P-Z state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 85-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 219 ZN ZINC ION × 6 SPM SPERMINE × 7 SPD SPERMIDINE × 10 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
9P7H In situ HHT and CHX treated human eEF1A-A/T-P state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.68 Å
9P7I In situ HHT and CHX treated human eEF1A-A/T-P-Z state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.69 Å
9P7J In situ HHT and CHX treated human P state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.91 Å
9P7K In situ human post eEF1A-A/T-P-E state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
9P7L In situ human Post-eEF1A-AT-P state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 85-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.92 Å
9P7N In situ human Post-eEF1A-A/T-P-Z state 80S ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.83 Å
9P7O In situ human AT-P-Z state ribosome Deposited 2025-06-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.65 Å
9P7W In situ human A-P state 80S ribosome Deposited 2025-06-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 219 ZN ZINC ION × 6 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
9P7X In situ human A-P-Z state 80S ribosome Deposited 2025-06-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 85-meric
Chain Sf 85–151（67 aa）
Not recorded ZN ZINC ION × 6 MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.83 Å
9P7Y In situ human A-P-E state 80S ribosome Deposited 2025-06-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 85-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 219 ZN ZINC ION × 6 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.75 Å
9P8B In situ human eEF1A-A/T-P-E state 80S ribosome Deposited 2025-06-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 86-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.48 Å
9P8C In situ human Hibernating class1 (rotate3) without E tRNA state 80S ribosome Deposited 2025-06-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 85-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 218 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.11 Å
9P8H In situ human A/P-P/E state 80S ribosome Deposited 2025-06-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 218 ZN ZINC ION × 6 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
9P8I In situ HHT and CHX treated human P-Z state 80S ribosome Deposited 2025-06-23 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 84-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 3HE 4-{(2R)-2-[(1S,3S,5S)-3,5-dimethyl-2-oxocyclohexyl]-2-hydroxyethyl}piperidine-2,6-dione × 1 HMT (3beta)-O~3~-[(2R)-2,6-dihydroxy-2-(2-methoxy-2-oxoethyl)-6-methylheptanoyl]cephalotaxine × 1 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.89 Å
9P9H In situ human unrotated hibernating with CCDC124 state 80S ribosome Deposited 2025-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 85-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.84 Å
9P9I In situ human unrotated hibernating without CCDC124 state 80S ribosome Deposited 2025-06-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.77 Å
9PA7 In situ human 80S consensus ribosome with EBP1 Deposited 2025-06-25 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 87-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 225 SPM SPERMINE × 8 SPD SPERMIDINE × 12 K POTASSIUM ION × 75 ZN ZINC ION × 7 PUT 1,4-DIAMINOBUTANE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.67 Å
9PBE In situ human 80S ribosome (composite map) Deposited 2025-06-26 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 84-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 225 SPM SPERMINE × 8 SPD SPERMIDINE × 12 K POTASSIUM ION × 75 ZN ZINC ION × 7 PUT 1,4-DIAMINOBUTANE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.19 Å
9PKG In situ human P state 80S ribosome Deposited 2025-07-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 78 PDB declaration: 83-meric
Chain Sf 85–151（67 aa）
Not recorded MG MAGNESIUM ION × 219 SPM SPERMINE × 7 SPD SPERMIDINE × 10 ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.26 Å
9QLO NMT1-NAC bound human RNC with full length ARF1 - State 1 Deposited 2025-03-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 88-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 191 G3D GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.47 Å
9QLP NMT1-NAC bound human RNC with full length ARF1 - State 2 Deposited 2025-03-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 88-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 191 G3D GUANOSINE-3'-MONOPHOSPHATE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.75 Å
9QLQ NMT1-NAC bound human RNC with full length ARF1 - alternative State Deposited 2025-03-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 88-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 191 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.57 Å
9RPV Structure of the ZAK-bound human disome Deposited 2025-06-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 154 PDB declaration: 168-meric
Chain Rf 1–156（156 aa）
Chain sh 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 830 ZN ZINC ION × 7 ANM ANISOMYCIN × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.35 Å
9RU7 WT-HEK 80S ribosome bound to Kozak mRNA (WT-Kozak) Deposited 2025-07-03 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Sf 1–156（156 aa）
Not recorded K POTASSIUM ION × 17 MG MAGNESIUM ION × 74 C CYTIDINE-5'-MONOPHOSPHATE × 2 NA SODIUM ION × 7 ZN ZINC ION × 5 HYG HYGROMYCIN B × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9RU9 RPS26dC HEK mutant 80S ribosome bound to Kozak mRNA (RPS26dC-Kozak) Deposited 2025-07-03 Different construct Different oligomeric state Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 82-meric
Chain Sf 1–156（156 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.97 Å
9S3B NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 1 Deposited 2025-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 88-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 191 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.38 Å
9S3C NMT1-NAC bound human RNC with 58 amino acid ARF1-linker - State 2 Deposited 2025-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 88-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 191 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.42 Å
9S3D NAC bound human RNC with 58 amino acid ARF1-linker Deposited 2025-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 87-meric
Chain Sf 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 191 ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.32 Å
9SPF CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING N1-METHYLPSEUDOURIDINE Deposited 2025-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 83-meric
Chain Sf 1–156（156 aa）
Not recorded K POTASSIUM ION × 151 MG MAGNESIUM ION × 225 NA SODIUM ION × 35 SPD SPERMIDINE × 19 PUT 1,4-DIAMINOBUTANE × 9 ZN ZINC ION × 7 HYG HYGROMYCIN B × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
9SPI CRYO-EM STRUCTURE OF HUMAN 80S RIBOSOME WITH A/P/E-SITE TRNA AND MRNA CONTAINING URIDINE Deposited 2025-09-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 75 PDB declaration: 83-meric
Chain Sf 1–156（156 aa）
Not recorded PUT 1,4-DIAMINOBUTANE × 8 SPD SPERMIDINE × 18 MG MAGNESIUM ION × 195 K POTASSIUM ION × 75 ZN ZINC ION × 7 HYG HYGROMYCIN B × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
9SYR Human quaternary complex of a translating 80S ribosome, NAC, MetAP1 and NatD Deposited 2025-10-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 80 PDB declaration: 86-meric
Chain Sr 1–156（156 aa）
Not recorded ZN ZINC ION × 10 COA COENZYME A × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.55 Å
9U5U The 1:1 cryo-EM structure of BAP1/ASXL1-K351Ub in complex with H2AK119Ub nucleosome Deposited 2025-03-21 Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric
Chain M 1–76（76 aa）
Chain O 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9UUM Cryo-EM structure of mezigdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-07 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain U 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.41 Å
9UV6 Encounter complex structure of E2N and Ubiquitin Deposited 2025-05-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–76（76 aa）
Not recorded A1EQF (5~{S},16~{S})-16-[2-[2,5-bis(oxidanylidene)pyrrolidin-1-yl]ethylamino]-2,11,12,17-tetraoxa-5,8-diaza-1$l^{4}-manganatricyclo[6.3.3.3^{1,5}]heptadecane-3,10,13-trione × 1 SOLUTION NMR
NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 0.02；Pressure 1
NMR sample composition 0.6 mM [U-15N] Ubi, 0.2 mM E2N, 20 mM HEPES, 90 % H2O, 10 % [U-2H] D2O, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
9V0A Cryo-EM structure of pomalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain U 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.69 Å
9V0F Cryo-EM structure of cemsidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain U 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.71 Å
9V9Q Cryo-EM structure of the cPRC1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome Deposited 2025-06-02 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain R 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 2.80 Å
9V9R Cryo-EM structure of the ncPRC1.1-UbcH5c E3-E2 complex bound to the H2BK120ub-modified nucleosome Deposited 2025-06-02 Different oligomeric state Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric
Chain R 1–76（76 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.20 Å

221 other PDB entries and 235 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RS27A_HUMAN
Isoform —
PDB entities 8
Chains and sequence ranges Author chain U； PDBConstruct 1–76； UniProt 1–76

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 9v0b

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9v0b
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9v0b
Deposition date deposition_date2025-05-17
Structure title titleCryo-EM structure of avadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly
Keywords keywordsMolecular glue degrader, avadomide, CRL4 ubiquitin ligase, DDB1, CRBN, Complex, LIGASE; LIGASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier55.03 Å
Radius of gyration Rg (electron density) rg_electron54.97 Å
Forward intensity I(0) i01233110000.00
Molecular weight molecular_weight295340.0 kDa
Excluded volume excluded_volume370600 ų
Envelope volume envelope_volume592290 ų
Hydration-shell volume shell_volume90802 ų
Envelope diameter envelope_diameter185.2 Å
Shell Rg shell_rg57.83 Å
Envelope Rg envelope_rg52.96 Å
Shape Rg shape_rg54.97 Å
Total Rg total_rg55.06 Å
Total atoms total_atoms20730
Residues n_residues2613
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax186.2 Å
Rg (real space) rg_real55.01 Å
Rg uncertainty (real space) rg_real_error1.88 Å
I(0) (real space) i0_real1.2330e+09
I(0) uncertainty (real space) i0_real_error2.5070e+07
Rg (reciprocal space) rg_reciprocal55.03 Å
I(0) (reciprocal space) i0_reciprocal1233000000.0000
Solution quality estimate total_estimate0.8851
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary64.2 Å
Skewness Skewness skewness0.250
Kurtosis Kurtosis kurtosis-0.529
Angular range angular_range— – 0.1450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha90040000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.901; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.800
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (10)

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8. Citations (1)

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9. Files and Curves (10)