DNA damage-binding protein 1
Homo sapiens
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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count | Chain A； UniProt 1–393 Chain A； UniProt 709–1140 | Not recorded | Protein cereblon × 1 （Q96SW2） GLUL-cN × 1 （P15104） 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 |
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 9NR3 | 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 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 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 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
1–1140（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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 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
1–1140（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 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
1–1140（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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 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
1–1140（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 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
1–1140（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 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
1–1140（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 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
1–1140（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 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
1–1140（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 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
1–1140（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 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
1–1140（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 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
1–1140（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 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
1–1140（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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 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
1–1140（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 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
1–1140（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 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
1–1140（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 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
1–1140（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 ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 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
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 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
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 ligand/ion 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 construct Different mutation/modification Different ligand/ion 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 construct Different mutation/modification Different ligand/ion 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 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
1–1140（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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 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
1–1140（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 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 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 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 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 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 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 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 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
1–1140（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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 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
1–1140（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 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）
|
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 ligand/ion 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 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
1–1140（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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 construct 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 × 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 construct 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 × 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 construct 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 × 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 construct 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 × 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 oligomeric state Different ligand/ion Different experimental method 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 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
1–1140（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 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
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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–395（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 oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–395（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 construct Different mutation/modification 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 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 mutation/modification Different ligand/ion 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 construct Different mutation/modification Different ligand/ion 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 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
1–1140（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 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
1–1140（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 construct Different mutation/modification 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 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 mutation/modification Different ligand/ion 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 construct Different mutation/modification Different ligand/ion 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 construct Different mutation/modification Different ligand/ion 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 ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 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 | 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 ligand/ion 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 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
1–1140（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 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
1–1140（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 oligomeric state Different ligand/ion Different experimental method 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 experimental method 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 experimental method 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 construct Different mutation/modification 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 | 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 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
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 construct Different mutation/modification 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 | 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 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 × 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 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 × 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 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
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 ligand/ion 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 ligand/ion 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 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
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 ligand/ion 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 ligand/ion 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 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 | 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 ligand/ion 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 ligand/ion 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 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
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 ligand/ion 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 ligand/ion 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 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 | 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 | 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 ligand/ion 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 ligand/ion 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 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
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 ligand/ion 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 ligand/ion 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 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 | 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 ligand/ion 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 ligand/ion 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 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
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 ligand/ion 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 ligand/ion 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 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
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 ligand/ion 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 ligand/ion 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 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
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 ligand/ion 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 ligand/ion 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 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
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 ligand/ion 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 ligand/ion 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 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
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 ligand/ion 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 ligand/ion 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 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
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 ligand/ion 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 ligand/ion 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 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
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 ligand/ion 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 ligand/ion 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 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 | 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 ligand/ion 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 ligand/ion 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 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 | 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 ligand/ion 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 ligand/ion 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 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
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 ligand/ion 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 ligand/ion 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 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 | 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 ligand/ion 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 ligand/ion 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 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 | 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 ligand/ion 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 ligand/ion 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 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
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 ligand/ion 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 ligand/ion 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 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
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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 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
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 ligand/ion 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 ligand/ion 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 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
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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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
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 ligand/ion 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 ligand/ion 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 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
1–1140（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 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
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 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
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 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
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 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
1–1140（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 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
1–1140（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 construct Different mutation/modification 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 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 mutation/modification 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 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 method 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 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）
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 ligand/ion 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 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
1–395（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 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 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 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 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
1–1140（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 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
1–1140（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 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
1–1140（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 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 | 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 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 | 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 construct Different mutation/modification 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 | 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 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 | 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 method 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 method 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 method 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 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）
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 ligand/ion 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 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 | 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 ligand/ion 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 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 | 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 ligand/ion 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 construct Different mutation/modification 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 | 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 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
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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
1–395（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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 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 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 construct Different mutation/modification 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 | 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 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
1–1140（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 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
1–1140（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 mutation/modification 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
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 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 | 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 ligand/ion 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 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 | 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 ligand/ion 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 method 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 construct Different mutation/modification 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 |
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 mutation/modification 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
1–1140（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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 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
1–1140（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 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 construct Different mutation/modification 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 | 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 mutation/modification 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 | 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 mutation/modification Different ligand/ion 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 construct Different mutation/modification 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）
|
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 construct Different mutation/modification 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）
|
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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification 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 | 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 construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method 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 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
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 construct Different mutation/modification 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 | 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 construct Different mutation/modification 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 | 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 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 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 oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification 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 | 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 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 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 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 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 oligomeric state Different ligand/ion Different experimental method 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 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 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 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 × 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 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 × 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 oligomeric state Different ligand/ion Different experimental method 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 construct Different mutation/modification 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 | 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 mutation/modification 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 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 mutation/modification 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 |
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 |
| 9NWS Cryo-EM structure of DDB1dB:CRBN:mezigdomide:SALL4(392-449) Deposited 2025-03-24 | Different construct 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 × 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 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 × 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 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
1–1140（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 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
1–1140（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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–391（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 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 × 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 method 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 ligand/ion 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 ligand/ion Different experimental method 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 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
1–1140（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 construct Different mutation/modification 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 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 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 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 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
1–1140（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 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
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 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 × 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 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
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 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 × 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 |
| 9V0B Cryo-EM structure of avadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 | 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 × 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 3.54 Å |
| 9V0F Cryo-EM structure of cemsidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 | 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 × 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 construct Different mutation/modification 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 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–393； UniProt 1–393 Author chain A； PDBConstruct 395–826； UniProt 709–1140 |
