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Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to compound furan 24

Method: ELECTRON MICROSCOPY D_max: 103.6 Å Quality: EXCELLENT

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1. Protein Identity and Related Structures Protein Identity & Related Structures

DDB1- and CUL4-associated factor 15

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 1–600	Not recorded	DNA damage-binding protein 1 × 1 （Q16531） DET1- and DDB1-associated protein 1 × 1 （Q9BW61） 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

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 8ROY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 2–275（274 aa） Chain C 384–600（217 aa）	Mutation：UNP residues 2-275,384-600 Mutation：UNP residues 2-275,384-600	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 O6M 3-cyano-N-(3-cyano-4-methyl-1H-indol-7-yl)benzene-1-sulfonamide × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M sodium HEPES, pH 7.0, 15% w/v PEG4000	Resolution 2.90 Å R-free 0.252
6Q0R Structure of DDB1-DDA1-DCAF15 complex bound to E7820 and RBM39 Deposited 2019-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 34–260（227 aa） Fragment：N-terminal domain Chain C 383–600（218 aa） Fragment：C-terminal domain	Not recorded	OXM OXAMIC ACID × 1 O6M 3-cyano-N-(3-cyano-4-methyl-1H-indol-7-yl)benzene-1-sulfonamide × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；300 K；20% PEG 4000	Resolution 2.90 Å R-free 0.251
6Q0V Structure of DDB1-DDA1-DCAF15 complex bound to tasisulam and RBM39 Deposited 2019-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 34–260（227 aa） Fragment：N-terminal domain Chain C 383–600（218 aa） Fragment：C-terminal domain	Not recorded	P7M N-[(5-bromothiophen-2-yl)sulfonyl]-2,4-dichlorobenzamide × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；300 K；20% PEG 4000	Resolution 2.90 Å R-free 0.242
6Q0W Structure of DDB1-DDA1-DCAF15 complex bound to Indisulam and RBM39 Deposited 2019-08-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 34–260（227 aa） Fragment：N-terminal domain Chain C 383–600（218 aa） Fragment：C-terminal 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
6SJ7 Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and Indisulam Deposited 2019-08-12	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–600（600 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
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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–600（599 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–600（599 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
8ROX Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to compound furan 12 Deposited 2024-01-12	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–600（600 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

8 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DCA15_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–603； UniProt 1–600

DNA damage-binding protein 1

Homo sapiens

UniProt Q16531

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 1–395 Chain B； UniProt 706–1140	Not recorded	DDB1- and CUL4-associated factor 15 × 1 （Q66K64） DET1- and DDB1-associated protein 1 × 1 （Q9BW61） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8ROY	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 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–1140（1140 aa）	Not recorded	ZN ZINC ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；100mM NaHEPES, 7-9% PEG4000, 10% iso-propanol, 5mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.10 Å R-free 0.316
3E0C Crystal Structure of DNA Damage-Binding protein 1(DDB1) Deposited 2008-07-31	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1140（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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–1140（1140 aa）	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；298 K；100mM Ca-Acetate, 100mM MES pH 5.7, 12-14 % PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.80 Å R-free 0.278
3EI2 Structure of hsDDB1-drDDB2 bound to a 16 bp abasic site containing DNA-duplex Deposited 2008-09-15	Different 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 × 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1140（1140 aa）	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.7；298 K；100mM Ca-Acetate, 100mM MES pH 5.7, 12-14% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.251
3EI4 Structure of the hsDDB1-hsDDB2 complex Deposited 2008-09-15	Different 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	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 method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–1140（1140 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；200 mM (NH4)2SO4; 800 mM LiSO2; 100 mM Na-Citrate pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.30 Å R-free 0.288
3EI4 Structure of the hsDDB1-hsDDB2 complex Deposited 2008-09-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1140（1140 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.279
3I7K Crystal Structure of DDB1 in Complex with the H-Box Motif of WHX Deposited 2009-07-08	Different 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	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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1140（1140 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005 M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.289
3I7N Crystal Structure of DDB1 in Complex with the H-Box Motif of WDTC1 Deposited 2009-07-08	Different 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	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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1140（1140 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.320
3I7P Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR40A Deposited 2009-07-08	Different 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	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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1140（1140 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.00 Å R-free 0.304
3I8C Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR21A Deposited 2009-07-09	Different 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	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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1140（1140 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；16% PEG 4000, 0.2M SODIUM CHLORIDE, 0.1M MES, 0.005M DTT , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 3.40 Å R-free 0.338
3I8E Crystal Structure of DDB1 in Complex with the H-Box Motif of WDR42A Deposited 2009-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–1140（1140 aa）	Mutation：YES	MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 CA CALCIUM ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；100 MM MES, 25 MM NAOH, 18% PEG 350MME., pH 5.6	Resolution 3.00 Å R-free 0.294
4A09 Structure of hsDDB1-drDDB2 bound to a 15 bp CPD-duplex (purine at D-1 position) at 3.1 A resolution (CPD 2) Deposited 2011-09-08	Different 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 × 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 1–1140（1140 aa）	Mutation：YES	CA CALCIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.6；100 MM MES, 28 MM NAOH, 16% PEG 350MME., pH 5.6	Resolution 3.60 Å R-free 0.347
4A0B Structure of hsDDB1-drDDB2 bound to a 16 bp CPD-duplex (pyrimidine at D-1 position) at 3.8 A resolution (CPD 4) Deposited 2011-09-08	Different 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 × 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 method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain C 1–1140（1140 aa）	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.3；100 MM MES, 15 MM NAOH, 18% PEG 350MME., pH 5.3	Resolution 3.80 Å R-free 0.319
4A0K STRUCTURE OF DDB1-DDB2-CUL4A-RBX1 BOUND TO A 12 BP ABASIC SITE CONTAINING DNA-DUPLEX Deposited 2011-09-09	Different 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 × 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 1–1140（1140 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；100MM MES PH 6.2, 3.1% PEG 6000, 4% ETHYLENEGLYCOL	Resolution 7.40 Å R-free 0.320
4A0L Structure of DDB1-DDB2-CUL4B-RBX1 bound to a 12 bp abasic site containing DNA-duplex Deposited 2011-09-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain C 1–1140（1140 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.2；100MM MES PH 6.2, 3.1% PEG 6000, 4% ETHYLENEGLYCOL	Resolution 7.40 Å R-free 0.320
4A11 Structure of the hsDDB1-hsCSA complex Deposited 2011-09-13	Different 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	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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1140（1140 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 EF2 S-Thalidomide × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；PROTEIN WAS CRYSTALLIZED FROM 100 MM NA-CACODYLATE; 80 MM NAH2PO4; 120 MM K2HPO4; 800 MM TRI-NA CITRATE., pH 6	Resolution 2.98 Å R-free 0.233
4CI2 Structure of the DDB1-CRBN E3 ubiquitin ligase bound to lenalidomide Deposited 2013-12-05	Different 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 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1140（1140 aa）	Not recorded	ZN ZINC ION × 1 Y70 S-Pomalidomide × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；PROTEIN WAS CRYSTALLIZED FROM 100 MM NA-CACOCYLATE, 80 MM NAH2PO4, 120 MM K2HPO4, 700 MM TRI-NA CITRATE., pH 6.5	Resolution 3.50 Å R-free 0.235
4E54 Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair Deposited 2012-03-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 2–1140（1139 aa） Fragment：DNA DAMAGE-BINDING PROTEIN 1 (DDB1; p127)	Mutation：NT-His10-DDB1	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；277 K；20mM Tris pH 7.5, 2mM MgCl2, 1mM EDTA, 2mM TECP, 5% Glycerol, 0.02% azide. UV-DDB-AP24 complex (molar ratio of 1:3 UV-DDB:DNA) at 2.5 mg/mL. 'AP24' refers to synthetic DNA substrate of 24-bpr with a central abasic site mimic., VAPOR DIFFUSION, temperature 277K	Resolution 2.85 Å R-free 0.281
4E5Z Damaged DNA induced UV-damaged DNA-binding protein (UV-DDB) dimerization and its roles in chromatinized DNA repair Deposited 2012-03-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain A 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–1140（1139 aa）	Not recorded	ZN ZINC ION × 1 LVY S-Lenalidomide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；100mM HEPES pH 7.5, 18% PEG 10K	Resolution 3.01 Å R-free 0.271
5FQD Structural basis of Lenalidomide induced CK1a degradation by the crl4crbn ubiquitin ligase Deposited 2015-12-09	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 709–1140（432 aa）	Not recorded	ZN ZINC ION × 1 LVY S-Lenalidomide × 1	X-RAY DIFFRACTION X-ray crystallization conditions 70 MM TRIS PH 7.0 140 MM MGCL2 7% W/V PEG 8000	Resolution 2.45 Å R-free 0.210
5FQD Structural basis of Lenalidomide induced CK1a degradation by the crl4crbn ubiquitin ligase Deposited 2015-12-09	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 709–1140（432 aa）	Not recorded	ZN ZINC ION × 1 LVY S-Lenalidomide × 1	X-RAY DIFFRACTION X-ray crystallization conditions 70 MM TRIS PH 7.0 140 MM MGCL2 7% W/V PEG 8000	Resolution 2.45 Å R-free 0.210
5HXB Cereblon in complex with DDB1, CC-885, and GSPT1 Deposited 2016-01-30	Different 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 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 method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–1140（1140 aa）	Not recorded	ZN ZINC ION × 1 85C 1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；280 K；200mM Sodium Citrate, Tris pH 8.5, 18% PEG 3350	Resolution 3.60 Å R-free 0.273
5JK7 The X-ray structure of the DDB1-DCAF1-Vpr-UNG2 complex Deposited 2016-04-26	Different 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	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 method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–1140（1140 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions BATCH MODE；289.15 K；100 mM Na Ctrate, pH 5.6, 11% PEG 20000	Resolution 3.49 Å R-free 0.206
5V3O Cereblon in complex with DDB1 and CC-220 Deposited 2017-03-07	Different 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	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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 706–1140（435 aa）	Not recorded	ZN ZINC ION × 1 RN3 methyl {(6S)-4-(4-chlorophenyl)-2-[(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl)carbamoyl]-3,9-dimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl}acetate × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9% (w/v) PEG20K, 18% (v/v) PEG MME 550, 0.09M BICINE pH8.5, 9% Silver bullet B5 (0.33% w/v 2,7-Naphthalenedisulfonic acid disodium salt, 0.33% w/v Azelaic acid, 0.33% w/v trans-Cinnamic acid, 0.02 M HEPES sodium pH 6.8)	Resolution 3.50 Å R-free 0.256
6BN8 Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET55 PROTAC. Deposited 2017-11-16	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 706–1140（435 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9% PEG20K, 18% PEG MME 550, 0.09M BICINE pH8.5, 9% Silver bullet G4 (0.16% w/v 3-Indolebutyric acid, 0.16% w/v Hexadecanedioic acid, 0.16% w/v Oxamic acid, 0.16% w/v Pyromellitic acid, 0.16% w/v Sebacic acid, 0.16% w/v Suberic acid, 0.02 M HEPES sodium pH 6.8)	Resolution 3.99 Å R-free 0.333
6BN9 Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET70 PROTAC Deposited 2017-11-16	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 706–1140（435 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；10% (w/v) PEG20K, 20% (v/v) PEG MME 550, 0.1M BICINE pH8.5, Silver Bullet F2 (0.2% w/v D-Fructose 1,6-bisphosphate trisodium salt hydrate, 0.2% w/v Glycerol phosphate disodium salt hydrate, 0.2% w/v L-O-Phosphoserine, 0.2% w/v O-Phospho-L-tyrosine, 0.2% w/v Phytic acid sodium salt hydrate, 0.02 M HEPES sodium pH 6.8)	Resolution 4.38 Å R-free 0.301
6BNB Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET57 PROTAC Deposited 2017-11-16	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 706–1140（435 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.34M NaH2PO4, 0.33M K2HPO4	Resolution 6.34 Å R-free 0.381
6BOY Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET6 PROTAC. Deposited 2017-11-21	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 706–1140（435 aa）	Not recorded	ZN ZINC ION × 1 RN6 2-[(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]-N-(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl)acetamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9% (w/v) PEG20K, 18% (v/v) PEG MME 550, 0.09M BICINE pH8.5, 9% (v/v) Silver bullet D11 (0.25% w/v 2,6-Naphthalenedisulfonic acid disodium salt, 0.25% w/v 4-Aminobenzoic acid, 0.25% w/v 5-Sulfosalicylic acid dihydrate, 0.25% w/v Naphthalene-1,3,6-trisulfonic acid trisodium salt hydrate, 0.02 M HEPES sodium pH 6.8)	Resolution 3.33 Å R-free 0.234
6DSZ Crystal structure of DDB1 in complex with DET1- and DDB1-associated protein 1 (DDA1) Deposited 2018-06-14	Different 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	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 method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–1140（1140 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1 M MES monohydrate, pH 6.5, 20% (w/v) PEG4000, 180 mM NaCl, 5 mM DTT	Resolution 3.09 Å R-free 0.307
6FCV Structure of the human DDB1-CSA complex Deposited 2017-12-21	Different 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	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 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 1–395（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 mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 706–1140（435 aa）	Mutation：;Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG) ; Mutation：;Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG),Central WD40 propeller domain (516-725 aa) replaced with a linker (sequence GNGNSG) ;	ZN ZINC ION × 2 Y70 S-Pomalidomide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；293 K；Protein-drug solution: 350 uM ZNF692-ZF4, 70 uM DDB1/CRBN, 80 uM pomalidomide and in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP Crystallisation solution: 14.1% (w/v) PEG 5K MME and 70 mM Tris-HCl pH 7.5	Resolution 4.25 Å R-free 0.256
6PAI Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and sulfonamide E7820 Deposited 2019-06-11	Different 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	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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–395（395 aa） Fragment：internal deletion of the BPB domain Chain A 706–1140（435 aa） Fragment：internal deletion of the BPB domain	Not recorded	OXM OXAMIC ACID × 1 O6M 3-cyano-N-(3-cyano-4-methyl-1H-indol-7-yl)benzene-1-sulfonamide × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；300 K；20% PEG 4000	Resolution 2.90 Å R-free 0.251
6Q0V Structure of DDB1-DDA1-DCAF15 complex bound to tasisulam and RBM39 Deposited 2019-08-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–395（395 aa） Fragment：internal deletion of the BPB domain Chain A 706–1140（435 aa） Fragment：internal deletion of the BPB domain	Not recorded	P7M N-[(5-bromothiophen-2-yl)sulfonyl]-2,4-dichlorobenzamide × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；300 K；20% PEG 4000	Resolution 2.90 Å R-free 0.242
6Q0W Structure of DDB1-DDA1-DCAF15 complex bound to Indisulam and RBM39 Deposited 2019-08-02	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–395（395 aa） Fragment：internal deletion of the BPB domain Chain A 706–1140（435 aa） Fragment：internal deletion of the BPB domain	Not recorded	EF6 N~1~-(3-chloro-1H-indol-7-yl)benzene-1,4-disulfonamide × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；300 K；20% PEG 4000	Resolution 2.90 Å R-free 0.264
6R8Y Cryo-EM structure of NCP-6-4PP(-1)-UV-DDB Deposited 2019-04-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain 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 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 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 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 oligomeric state Different ligand/ion 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 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 708–1140（433 aa）	Not recorded	RC8 (2R)-2-({9-(1-methylethyl)-6-[(4-pyridin-2-ylbenzyl)amino]-9H-purin-2-yl}amino)butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；0.9 M ammonium citrate tribasic	Resolution 3.46 Å R-free 0.220
6TD3 Structure of DDB1 bound to CR8-engaged CDK12-cyclinK Deposited 2019-11-07	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 708–1140（433 aa）	Not recorded	RC8 (2R)-2-({9-(1-methylethyl)-6-[(4-pyridin-2-ylbenzyl)amino]-9H-purin-2-yl}amino)butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；0.9 M ammonium citrate tribasic	Resolution 3.46 Å R-free 0.220
6TD3 Structure of DDB1 bound to CR8-engaged CDK12-cyclinK Deposited 2019-11-07	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 708–1140（433 aa）	Not recorded	RC8 (2R)-2-({9-(1-methylethyl)-6-[(4-pyridin-2-ylbenzyl)amino]-9H-purin-2-yl}amino)butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；292 K；0.9 M ammonium citrate tribasic	Resolution 3.46 Å R-free 0.220
6UD7 Crystal structure of full-length human DCAF15-DDB1(deltaBPB)-DDA1-RBM39 in complex with indisulam Deposited 2019-09-18	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–395（395 aa） Chain B 706–1140（435 aa）	Not recorded	GOL GLYCEROL × 2 EF6 N~1~-(3-chloro-1H-indol-7-yl)benzene-1,4-disulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；2% (v:v) TacsimateTM, pH 5.0, 0.1 M sodium citrate tribasic dihydrate, pH 5.6, and 10-20% (w:v) polyethylene glycol 3350	Resolution 2.30 Å R-free 0.248
6UE5 Crystal structure of full-length human DCAF15-DDB1-deltaPBP-DDA1-RBM39 in complex with 4-(aminomethyl)-N-(3-cyano-4-methyl-1H-indol-7-yl)benzenesulfonamide Deposited 2019-09-20	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–395（395 aa） Chain B 706–1140（435 aa）	Not recorded	Q5J 4-(aminomethyl)-N-(3-cyano-4-methyl-1H-indol-7-yl)benzene-1-sulfonamide × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；291.5 K；2% (v:v) TacsimateTM, pH 5.0, 0.1 M sodium citrate tribasic 676 dihydrate, pH 5.6, and 10-20% (w:v) polyethylene glycol 3350	Resolution 2.61 Å R-free 0.266
6UML Structural Basis for Thalidomide Teratogenicity Revealed by the Cereblon-DDB1-SALL4-Pomalidomide Complex Deposited 2019-10-09	Different 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 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain Y 1–1140（1140 aa）	Not recorded	V4M 2-(4-chlorophenyl)-N-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)-2,2-difluoroacetamide × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 100mM Tris-HCl (pH 7.5), 300mM sodium citrate	Resolution 3.64 Å R-free 0.245
6XK9 Cereblon in complex with DDB1, CC-90009, and GSPT1 Deposited 2020-06-25	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–1140（1140 aa）	Not recorded	V4M 2-(4-chlorophenyl)-N-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)-2,2-difluoroacetamide × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 100mM Tris-HCl (pH 7.5), 300mM sodium citrate	Resolution 3.64 Å R-free 0.245
6ZUE Crystal structure of human DDB1 bound to human DCAF1 (amino acid residues 1046-1396) Deposited 2020-07-22	Different 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	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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1140（1140 aa）	Not recorded	GOL GLYCEROL × 8 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277.15 K；8-10% PEG 4000 (w/v), 200 mM MgCl2, 100 mM HEPES-NaOH, pH 7.0-8.2.	Resolution 2.52 Å R-free 0.260
7LPS Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) Deposited 2021-02-12	Different 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 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 method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–1140（1140 aa）	Not recorded	ZN ZINC ION × 2 RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.57；293 K；30% (w/v) PEG3350, 0.1 M Tris pH 8.57	Resolution 3.78 Å R-free 0.303
7LPS Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) Deposited 2021-02-12	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–1140（1140 aa）	Not recorded	ZN ZINC ION × 2 RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.57；293 K；30% (w/v) PEG3350, 0.1 M Tris pH 8.57	Resolution 3.78 Å R-free 0.303
7LPS Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) Deposited 2021-02-12	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain J 1–1140（1140 aa）	Not recorded	ZN ZINC ION × 2 RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.57；293 K；30% (w/v) PEG3350, 0.1 M Tris pH 8.57	Resolution 3.78 Å R-free 0.303
7OKQ Cryo-EM Structure of the DDB1-DCAF1-CUL4A-RBX1 Complex Deposited 2021-05-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 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 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 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 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 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–395（395 aa） Chain B 706–1140（435 aa）	Not recorded	ZN ZINC ION × 2 LWK (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5	Resolution 3.15 Å R-free 0.243
7U8F Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2) and the molecular glue DKY709 Deposited 2022-03-08	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–395（395 aa） Chain E 706–1140（435 aa）	Not recorded	ZN ZINC ION × 2 LWK (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 SO4 SULFATE ION × 4 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5	Resolution 3.15 Å R-free 0.243
7UKN Crystal Structure of DDB1 in Complex with the H-Box Motif of pUL145 Deposited 2022-04-01	Different 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	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 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 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–396（396 aa） Chain A 706–1140（435 aa）	Mutation：delta396-705 GNGNSG Mutation：delta396-705 GNGNSG	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE；45 seconds adsorption 2 seconds blot	Resolution 3.78 Å
7ZNN Cryo-EM structure of RCMV-E E27 bound to human DDB1 (deltaBPB) and full-length rat STAT2 Deposited 2022-04-21	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–396（396 aa） Chain A 706–1140（435 aa）	Mutation：Residues 396-705 have been replaced by a GNGNSG-linker Mutation：Residues 396-705 have been replaced by a GNGNSG-linker	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE；45 seconds adsorption 2 seconds blot	Resolution 4.80 Å
8AJM Structure of human DDB1-DCAF12 in complex with the C-terminus of CCT5 Deposited 2022-07-28	Different 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	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 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 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 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	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 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 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 709–1140（432 aa）	Not recorded	GOL GLYCEROL × 5 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, NDSB-256 additive	Resolution 2.98 Å R-free 0.218
8BU1 Structure of DDB1 bound to DS17-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 709–1140（432 aa）	Not recorded	GOL GLYCEROL × 5 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, NDSB-256 additive	Resolution 2.98 Å R-free 0.218
8BU1 Structure of DDB1 bound to DS17-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 709–1140（432 aa）	Not recorded	GOL GLYCEROL × 5 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, NDSB-256 additive	Resolution 2.98 Å R-free 0.218
8BU2 Structure of DDB1 bound to DS18-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 12 RVQ ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-2-morpholin-4-yl-9-propan-2-yl-purin-6-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M ammonium sulphate, 0.07 M HEPES, pH 6.8	Resolution 3.13 Å R-free 0.217
8BU2 Structure of DDB1 bound to DS18-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 16 RVQ ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-2-morpholin-4-yl-9-propan-2-yl-purin-6-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M ammonium sulphate, 0.07 M HEPES, pH 6.8	Resolution 3.13 Å R-free 0.217
8BU2 Structure of DDB1 bound to DS18-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 13 RVQ ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-2-morpholin-4-yl-9-propan-2-yl-purin-6-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M ammonium sulphate, 0.07 M HEPES, pH 6.8	Resolution 3.13 Å R-free 0.217
8BU3 Structure of DDB1 bound to DS19-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 706–1140（435 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 6 RSI 2-morpholin-4-yl-9-propan-2-yl-~{N}-[(4-pyridin-2-ylphenyl)methyl]purin-6-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.49 M ammonium sulfate, ammonium citrate, 0.07 M HEPES pH 6.8	Resolution 3.42 Å R-free 0.213
8BU3 Structure of DDB1 bound to DS19-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 706–1140（435 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 5 RSI 2-morpholin-4-yl-9-propan-2-yl-~{N}-[(4-pyridin-2-ylphenyl)methyl]purin-6-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.49 M ammonium sulfate, ammonium citrate, 0.07 M HEPES pH 6.8	Resolution 3.42 Å R-free 0.213
8BU3 Structure of DDB1 bound to DS19-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 706–1140（435 aa）	Not recorded	SO4 SULFATE ION × 9 RSI 2-morpholin-4-yl-9-propan-2-yl-~{N}-[(4-pyridin-2-ylphenyl)methyl]purin-6-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.49 M ammonium sulfate, ammonium citrate, 0.07 M HEPES pH 6.8	Resolution 3.42 Å R-free 0.213
8BU4 Structure of DDB1 bound to DS22-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 5 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 M ammonium citrate, 0.07 M HEPES pH 7	Resolution 3.09 Å R-free 0.223
8BU4 Structure of DDB1 bound to DS22-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 6 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 M ammonium citrate, 0.07 M HEPES pH 7	Resolution 3.09 Å R-free 0.223
8BU4 Structure of DDB1 bound to DS22-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 3 RQL (2~{R})-2-[[6-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methylamino]-9-(1-methylpyrazol-4-yl)purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 M ammonium citrate, 0.07 M HEPES pH 7	Resolution 3.09 Å R-free 0.223
8BU5 Structure of DDB1 bound to SR-4835-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 706–1140（435 aa）	Not recorded	SO4 SULFATE ION × 1 RMF ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.28 M ammonium sulphate, 0.72 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0	Resolution 3.13 Å R-free 0.220
8BU5 Structure of DDB1 bound to SR-4835-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 706–1140（435 aa）	Not recorded	RMF ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.28 M ammonium sulphate, 0.72 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0	Resolution 3.13 Å R-free 0.220
8BU5 Structure of DDB1 bound to SR-4835-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 706–1140（435 aa）	Not recorded	SO4 SULFATE ION × 2 RMF ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.28 M ammonium sulphate, 0.72 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0	Resolution 3.13 Å R-free 0.220
8BU6 Structure of DDB1 bound to DS55-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 2 RQE ~{N}-(1~{H}-benzimidazol-2-ylmethyl)-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.3	Resolution 3.45 Å R-free 0.249
8BU6 Structure of DDB1 bound to DS55-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 2 RQE ~{N}-(1~{H}-benzimidazol-2-ylmethyl)-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.3	Resolution 3.45 Å R-free 0.249
8BU6 Structure of DDB1 bound to DS55-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 2 RQE ~{N}-(1~{H}-benzimidazol-2-ylmethyl)-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.3	Resolution 3.45 Å R-free 0.249
8BU7 Structure of DDB1 bound to 21195-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 706–1140（435 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 RS5 1-[2,6-bis(chloranyl)phenyl]-6-[[4-(2-hydroxyethyloxy)phenyl]methyl]-3-propan-2-yl-5H-pyrazolo[3,4-d]pyrimidin-4-one × 1 SO4 SULFATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.33 M ammonium sulfate, 0.045 M ammonium citrate, 0.07M HEPES pH 7	Resolution 3.25 Å R-free 0.219
8BU7 Structure of DDB1 bound to 21195-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 706–1140（435 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 2 RS5 1-[2,6-bis(chloranyl)phenyl]-6-[[4-(2-hydroxyethyloxy)phenyl]methyl]-3-propan-2-yl-5H-pyrazolo[3,4-d]pyrimidin-4-one × 1 SO4 SULFATE ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.33 M ammonium sulfate, 0.045 M ammonium citrate, 0.07M HEPES pH 7	Resolution 3.25 Å R-free 0.219
8BU7 Structure of DDB1 bound to 21195-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 706–1140（435 aa）	Not recorded	RS5 1-[2,6-bis(chloranyl)phenyl]-6-[[4-(2-hydroxyethyloxy)phenyl]methyl]-3-propan-2-yl-5H-pyrazolo[3,4-d]pyrimidin-4-one × 1 SO4 SULFATE ION × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.33 M ammonium sulfate, 0.045 M ammonium citrate, 0.07M HEPES pH 7	Resolution 3.25 Å R-free 0.219
8BU9 Structure of DDB1 bound to roscovitine-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 5 RRC R-ROSCOVITINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.42 M ammonium sulphate, 0.63 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0	Resolution 3.51 Å R-free 0.223
8BU9 Structure of DDB1 bound to roscovitine-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 5 RRC R-ROSCOVITINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.42 M ammonium sulphate, 0.63 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0	Resolution 3.51 Å R-free 0.223
8BU9 Structure of DDB1 bound to roscovitine-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 5 RRC R-ROSCOVITINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.42 M ammonium sulphate, 0.63 M ammonium citrate tribasic pH 7.0, 0.07 M HEPES pH 7.0	Resolution 3.51 Å R-free 0.223
8BUA Structure of DDB1 bound to 919278-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 706–1140（435 aa）	Not recorded	CIT CITRIC ACID × 2 RVH (2~{R})-~{N}-(1~{H}-benzimidazol-2-yl)-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate, 100 %w/v SB38D2, 0.07 M HEPES pH 7	Resolution 3.19 Å R-free 0.225
8BUA Structure of DDB1 bound to 919278-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 706–1140（435 aa）	Not recorded	CIT CITRIC ACID × 3 RVH (2~{R})-~{N}-(1~{H}-benzimidazol-2-yl)-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate, 100 %w/v SB38D2, 0.07 M HEPES pH 7	Resolution 3.19 Å R-free 0.225
8BUA Structure of DDB1 bound to 919278-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 706–1140（435 aa）	Not recorded	CIT CITRIC ACID × 4 RVH (2~{R})-~{N}-(1~{H}-benzimidazol-2-yl)-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate, 100 %w/v SB38D2, 0.07 M HEPES pH 7	Resolution 3.19 Å R-free 0.225
8BUB Structure of DDB1 bound to dCeMM4-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 709–1140（432 aa）	Not recorded	CIT CITRIC ACID × 2 RNU ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 1 M sodium malonate additive	Resolution 3.42 Å R-free 0.237
8BUB Structure of DDB1 bound to dCeMM4-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 709–1140（432 aa）	Not recorded	CIT CITRIC ACID × 3 RNU ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 1 M sodium malonate additive	Resolution 3.42 Å R-free 0.237
8BUB Structure of DDB1 bound to dCeMM4-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 709–1140（432 aa）	Not recorded	CIT CITRIC ACID × 2 RNU ~{N}-(5-methyl-2,3-dihydro-1,3-thiazol-2-yl)-3-(5-methylfuran-2-yl)carbonyl-1,3-thiazolidine-4-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 1 M sodium malonate additive	Resolution 3.42 Å R-free 0.237
8BUC Structure of DDB1 bound to dCeMM3-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 4 RKO 2-(1~{H}-benzimidazol-2-ylsulfanyl)-~{N}-(5-chloranylpyridin-2-yl)ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 ammonium citrate, 0.07 M HEPES pH 7	Resolution 3.85 Å R-free 0.224
8BUC Structure of DDB1 bound to dCeMM3-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 1 RKO 2-(1~{H}-benzimidazol-2-ylsulfanyl)-~{N}-(5-chloranylpyridin-2-yl)ethanamide × 1 CIT CITRIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 ammonium citrate, 0.07 M HEPES pH 7	Resolution 3.85 Å R-free 0.224
8BUC Structure of DDB1 bound to dCeMM3-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 4 RKO 2-(1~{H}-benzimidazol-2-ylsulfanyl)-~{N}-(5-chloranylpyridin-2-yl)ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.07 M ammonium sulfate, 0.855 ammonium citrate, 0.07 M HEPES pH 7	Resolution 3.85 Å R-free 0.224
8BUD Structure of DDB1 bound to Z7-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 10 RP9 ~{N}-(5-bromanylpyridin-2-yl)-3-(4-oxidanylidenequinazolin-3-yl)propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M ammonium sulphate, 0.07 M HEPES, pH 7.0	Resolution 3.20 Å R-free 0.220
8BUD Structure of DDB1 bound to Z7-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 15 RP9 ~{N}-(5-bromanylpyridin-2-yl)-3-(4-oxidanylidenequinazolin-3-yl)propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M ammonium sulphate, 0.07 M HEPES, pH 7.0	Resolution 3.20 Å R-free 0.220
8BUD Structure of DDB1 bound to Z7-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 14 RP9 ~{N}-(5-bromanylpyridin-2-yl)-3-(4-oxidanylidenequinazolin-3-yl)propanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M ammonium sulphate, 0.07 M HEPES, pH 7.0	Resolution 3.20 Å R-free 0.220
8BUE Structure of DDB1 bound to Z11-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 12 RVU ~{N}-(1~{H}-benzimidazol-2-yl)-1-(2-methoxy-5-methyl-phenyl)-5-oxidanylidene-pyrrolidine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.45 M ammonium sulphate, 0.07 M HEPES, pH 7.1	Resolution 3.25 Å R-free 0.213
8BUE Structure of DDB1 bound to Z11-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 16 RVU ~{N}-(1~{H}-benzimidazol-2-yl)-1-(2-methoxy-5-methyl-phenyl)-5-oxidanylidene-pyrrolidine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.45 M ammonium sulphate, 0.07 M HEPES, pH 7.1	Resolution 3.25 Å R-free 0.213
8BUE Structure of DDB1 bound to Z11-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 15 RVU ~{N}-(1~{H}-benzimidazol-2-yl)-1-(2-methoxy-5-methyl-phenyl)-5-oxidanylidene-pyrrolidine-3-carboxamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.45 M ammonium sulphate, 0.07 M HEPES, pH 7.1	Resolution 3.25 Å R-free 0.213
8BUF Structure of DDB1 bound to Z12-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 12 RW6 2-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-ylmethyl)-6,7-dimethoxy-3~{H}-quinazolin-4-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.47 M amonium sulphate, 0.07 M HEPES, pH 7.0	Resolution 3.30 Å R-free 0.220
8BUF Structure of DDB1 bound to Z12-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 17 RW6 2-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-ylmethyl)-6,7-dimethoxy-3~{H}-quinazolin-4-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.47 M amonium sulphate, 0.07 M HEPES, pH 7.0	Resolution 3.30 Å R-free 0.220
8BUF Structure of DDB1 bound to Z12-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 17 RW6 2-(6,7-dihydro-4~{H}-thieno[3,2-c]pyridin-5-ylmethyl)-6,7-dimethoxy-3~{H}-quinazolin-4-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.47 M amonium sulphate, 0.07 M HEPES, pH 7.0	Resolution 3.30 Å R-free 0.220
8BUG Structure of DDB1 bound to HQ461-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 709–1140（432 aa）	Not recorded	CIT CITRIC ACID × 2 RPW 2-[2-[(6-methylpyridin-2-yl)amino]-1,3-thiazol-4-yl]-~{N}-(5-methyl-1,3-thiazol-2-yl)ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 0.1 M TMA additive	Resolution 3.53 Å R-free 0.231
8BUG Structure of DDB1 bound to HQ461-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 709–1140（432 aa）	Not recorded	CIT CITRIC ACID × 2 RPW 2-[2-[(6-methylpyridin-2-yl)amino]-1,3-thiazol-4-yl]-~{N}-(5-methyl-1,3-thiazol-2-yl)ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 0.1 M TMA additive	Resolution 3.53 Å R-free 0.231
8BUG Structure of DDB1 bound to HQ461-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 709–1140（432 aa）	Not recorded	CIT CITRIC ACID × 3 RPW 2-[2-[(6-methylpyridin-2-yl)amino]-1,3-thiazol-4-yl]-~{N}-(5-methyl-1,3-thiazol-2-yl)ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, 0.1 M TMA additive	Resolution 3.53 Å R-free 0.231
8BUH Structure of DDB1 bound to WX3-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 5 RR9 6-[[[2-[[(2~{R})-1-oxidanylbutan-2-yl]amino]-9-propan-2-yl-purin-6-yl]amino]methyl]-3-pyridin-2-yl-1~{H}-pyridin-2-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.7 M ammonium sulfate, 0.45 M ammonium citrate, 0.07 M HEPES pH 7	Resolution 3.79 Å R-free 0.232
8BUH Structure of DDB1 bound to WX3-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 3 RR9 6-[[[2-[[(2~{R})-1-oxidanylbutan-2-yl]amino]-9-propan-2-yl-purin-6-yl]amino]methyl]-3-pyridin-2-yl-1~{H}-pyridin-2-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.7 M ammonium sulfate, 0.45 M ammonium citrate, 0.07 M HEPES pH 7	Resolution 3.79 Å R-free 0.232
8BUH Structure of DDB1 bound to WX3-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 4 RR9 6-[[[2-[[(2~{R})-1-oxidanylbutan-2-yl]amino]-9-propan-2-yl-purin-6-yl]amino]methyl]-3-pyridin-2-yl-1~{H}-pyridin-2-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.7 M ammonium sulfate, 0.45 M ammonium citrate, 0.07 M HEPES pH 7	Resolution 3.79 Å R-free 0.232
8BUI Structure of DDB1 bound to DRF-053-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 706–1140（435 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 7 RV6 (2~{R})-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)amino]purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 6.8	Resolution 3.50 Å R-free 0.221
8BUI Structure of DDB1 bound to DRF-053-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 706–1140（435 aa）	Not recorded	SO4 SULFATE ION × 7 RV6 (2~{R})-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)amino]purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 6.8	Resolution 3.50 Å R-free 0.221
8BUI Structure of DDB1 bound to DRF-053-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 706–1140（435 aa）	Not recorded	SO4 SULFATE ION × 7 RV6 (2~{R})-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)amino]purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 6.8	Resolution 3.50 Å R-free 0.221
8BUJ Structure of DDB1 bound to DS06-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 706–1140（435 aa）	Not recorded	SO4 SULFATE ION × 5 RUW (2~{R})-2-[[6-(octylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.38 M ammonium sulphate, 0.07 M HEPES, pH 7.0	Resolution 3.62 Å R-free 0.206
8BUJ Structure of DDB1 bound to DS06-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 706–1140（435 aa）	Not recorded	SO4 SULFATE ION × 4 RUW (2~{R})-2-[[6-(octylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.38 M ammonium sulphate, 0.07 M HEPES, pH 7.0	Resolution 3.62 Å R-free 0.206
8BUJ Structure of DDB1 bound to DS06-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 706–1140（435 aa）	Not recorded	SO4 SULFATE ION × 5 RUW (2~{R})-2-[[6-(octylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.38 M ammonium sulphate, 0.07 M HEPES, pH 7.0	Resolution 3.62 Å R-free 0.206
8BUK Structure of DDB1 bound to DS08-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 7 RWE (2~{R})-2-[[6-(naphthalen-2-ylmethylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.84 M ammonium sulfate, 0.36 M ammonium citrate, 0.07 M HEPES pH 7	Resolution 3.41 Å R-free 0.210
8BUK Structure of DDB1 bound to DS08-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 6 RWE (2~{R})-2-[[6-(naphthalen-2-ylmethylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1 CIT CITRIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.84 M ammonium sulfate, 0.36 M ammonium citrate, 0.07 M HEPES pH 7	Resolution 3.41 Å R-free 0.210
8BUK Structure of DDB1 bound to DS08-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 7 RWE (2~{R})-2-[[6-(naphthalen-2-ylmethylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.84 M ammonium sulfate, 0.36 M ammonium citrate, 0.07 M HEPES pH 7	Resolution 3.41 Å R-free 0.210
8BUL Structure of DDB1 bound to DS11-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 706–1140（435 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 8 RSU (2~{R})-2-[[6-(3-phenylpropylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M amonium sulphate, 0.07 M HEPES, pH 6.8	Resolution 3.40 Å R-free 0.215
8BUL Structure of DDB1 bound to DS11-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 706–1140（435 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 8 RSU (2~{R})-2-[[6-(3-phenylpropylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M amonium sulphate, 0.07 M HEPES, pH 6.8	Resolution 3.40 Å R-free 0.215
8BUL Structure of DDB1 bound to DS11-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 706–1140（435 aa）	Not recorded	SO4 SULFATE ION × 9 RSU (2~{R})-2-[[6-(3-phenylpropylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.30 M amonium sulphate, 0.07 M HEPES, pH 6.8	Resolution 3.40 Å R-free 0.215
8BUM Structure of DDB1 bound to DS15-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 706–1140（435 aa）	Not recorded	SO4 SULFATE ION × 11 T6X (2R)-2-[[6-(5-naphthalen-1-ylpentylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M amonium sulphate, 0.07 M HEPES, pH 6.8	Resolution 3.36 Å R-free 0.212
8BUM Structure of DDB1 bound to DS15-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 706–1140（435 aa）	Not recorded	SO4 SULFATE ION × 15 T6X (2R)-2-[[6-(5-naphthalen-1-ylpentylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M amonium sulphate, 0.07 M HEPES, pH 6.8	Resolution 3.36 Å R-free 0.212
8BUM Structure of DDB1 bound to DS15-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 706–1140（435 aa）	Not recorded	SO4 SULFATE ION × 13 T6X (2R)-2-[[6-(5-naphthalen-1-ylpentylamino)-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.50 M amonium sulphate, 0.07 M HEPES, pH 6.8	Resolution 3.36 Å R-free 0.212
8BUN Structure of DDB1 bound to DS16-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 10 RNF (2~{R})-2-[[6-[(4-phenylphenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 6.8	Resolution 3.08 Å R-free 0.211
8BUN Structure of DDB1 bound to DS16-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 12 RNF (2~{R})-2-[[6-[(4-phenylphenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 6.8	Resolution 3.08 Å R-free 0.211
8BUN Structure of DDB1 bound to DS16-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 12 RNF (2~{R})-2-[[6-[(4-phenylphenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 6.8	Resolution 3.08 Å R-free 0.211
8BUO Structure of DDB1 bound to DS24-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different 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 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 method Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 706–1140（435 aa）	Not recorded	SO4 SULFATE ION × 7 RLC (2~{R})-2-[[6-[(3-fluoranyl-4-pyridin-2-yl-phenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.47 M ammonium sulphate, 0.07 M HEPES, pH 6.8	Resolution 3.58 Å R-free 0.219
8BUO Structure of DDB1 bound to DS24-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 706–1140（435 aa）	Not recorded	SO4 SULFATE ION × 10 RLC (2~{R})-2-[[6-[(3-fluoranyl-4-pyridin-2-yl-phenyl)methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.47 M ammonium sulphate, 0.07 M HEPES, pH 6.8	Resolution 3.58 Å R-free 0.219
8BUP Structure of DDB1 bound to DS30-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 11 RWN (2~{R})-2-[[6-[3-(3-methylphenyl)propylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.44 M ammonium sulphate, 2.143 %v/v PEG 200, 0.07 M HEPES pH 7.5	Resolution 3.41 Å R-free 0.223
8BUP Structure of DDB1 bound to DS30-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 22 RWN (2~{R})-2-[[6-[3-(3-methylphenyl)propylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.44 M ammonium sulphate, 2.143 %v/v PEG 200, 0.07 M HEPES pH 7.5	Resolution 3.41 Å R-free 0.223
8BUP Structure of DDB1 bound to DS30-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 24 RWN (2~{R})-2-[[6-[3-(3-methylphenyl)propylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.44 M ammonium sulphate, 2.143 %v/v PEG 200, 0.07 M HEPES pH 7.5	Resolution 3.41 Å R-free 0.223
8BUQ Structure of DDB1 bound to DS43-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 709–1140（432 aa）	Not recorded	CIT CITRIC ACID × 2 RQ9 (2~{R})-2-[[6-[[1-(3-chlorophenyl)pyrazol-3-yl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, Jeff600 additive	Resolution 3.20 Å R-free 0.216
8BUQ Structure of DDB1 bound to DS43-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 709–1140（432 aa）	Not recorded	CIT CITRIC ACID × 2 RQ9 (2~{R})-2-[[6-[[1-(3-chlorophenyl)pyrazol-3-yl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, Jeff600 additive	Resolution 3.20 Å R-free 0.216
8BUQ Structure of DDB1 bound to DS43-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 709–1140（432 aa）	Not recorded	CIT CITRIC ACID × 2 RQ9 (2~{R})-2-[[6-[[1-(3-chlorophenyl)pyrazol-3-yl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.9 M ammonium citrate tribasic pH 7.0, Jeff600 additive	Resolution 3.20 Å R-free 0.216
8BUR Structure of DDB1 bound to DS50-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 7 RQU ~{N}-[2-(2-methoxyphenyl)ethyl]-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.0	Resolution 3.64 Å R-free 0.234
8BUR Structure of DDB1 bound to DS50-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 10 RQU ~{N}-[2-(2-methoxyphenyl)ethyl]-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.0	Resolution 3.64 Å R-free 0.234
8BUR Structure of DDB1 bound to DS50-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 7 RQU ~{N}-[2-(2-methoxyphenyl)ethyl]-2-[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]ethanamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.42 M ammonium sulphate, 0.07 M HEPES, pH 7.0	Resolution 3.64 Å R-free 0.234
8BUS Structure of DDB1 bound to DS59-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 706–1140（435 aa）	Not recorded	SO4 SULFATE ION × 5 RMX 1,3-dimethyl-5-[[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]methyl]pyrazole-4-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 7.0	Resolution 3.26 Å R-free 0.228
8BUS Structure of DDB1 bound to DS59-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 706–1140（435 aa）	Not recorded	SO4 SULFATE ION × 3 RMX 1,3-dimethyl-5-[[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]methyl]pyrazole-4-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 7.0	Resolution 3.26 Å R-free 0.228
8BUS Structure of DDB1 bound to DS59-engaged CDK12-cyclin K Deposited 2022-11-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 706–1140（435 aa）	Not recorded	SO4 SULFATE ION × 6 RMX 1,3-dimethyl-5-[[[9-propan-2-yl-6-[(4-pyridin-2-ylphenyl)methylamino]purin-2-yl]amino]methyl]pyrazole-4-sulfonamide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.40 M ammonium sulphate, 0.07 M HEPES, pH 7.0	Resolution 3.26 Å R-free 0.228
8BUT Structure of DDB1 bound to DS61-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 7 RQ5 2-[[6-[[4-(2-hydroxyethyloxy)phenyl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.374 M ammonium sulfate, 0.07 M HEPES pH 7.3	Resolution 3.25 Å R-free 0.217
8BUT Structure of DDB1 bound to DS61-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 6 RQ5 2-[[6-[[4-(2-hydroxyethyloxy)phenyl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.374 M ammonium sulfate, 0.07 M HEPES pH 7.3	Resolution 3.25 Å R-free 0.217
8BUT Structure of DDB1 bound to DS61-engaged CDK12-cyclin K Deposited 2022-11-30	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Chain G 709–1140（432 aa）	Not recorded	SO4 SULFATE ION × 8 RQ5 2-[[6-[[4-(2-hydroxyethyloxy)phenyl]methylamino]-9-propan-2-yl-purin-2-yl]amino]butan-1-ol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；1.374 M ammonium sulfate, 0.07 M HEPES pH 7.3	Resolution 3.25 Å R-free 0.217
8CVP Cereblon-DDB1 in the Apo form Deposited 2022-05-18	Different 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	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 conditions	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 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 conditions	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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1140（1140 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7；20mM HEPES pH 7, 240mM NaCl, 3mM TCEP cryo-EM vitrification conditions Cryogen ETHANE；Manual plunge in 4 degree C cold room	Resolution 3.40 Å
8D7Y Cereblon-DDB1 in the Apo form with DDB1 in the twisted conformation Deposited 2022-06-07	Different 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	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 conditions	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 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 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–395（395 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140 Chain B 706–1140（435 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140	Not recorded	ZN ZINC ION × 3 LWK (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5	Resolution 3.70 Å R-free 0.348
8DEY Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2,3) and the molecular glue DKY709 Deposited 2022-06-21	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–395（395 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140 Chain E 706–1140（435 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140	Not recorded	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5	Resolution 3.70 Å R-free 0.348
8G46 Cryo-EM structure of DDB1deltaB-DDA1-DCAF16-BRD4(BD2)-MMH2 Deposited 2023-02-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–395（395 aa） Fragment：UNP residues 1-395 + GNGNSG linker + UNP residues 706-1140 Chain A 706–1140（435 aa） Fragment：UNP residues 1-395 + GNGNSG linker + UNP residues 706-1140	Not recorded	ZN ZINC ION × 1 YK3 tert-butyl [(6S,10P)-4-{4-[(ethanesulfonyl)amino]phenyl}-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]acetate × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；50 mM HEPES pH 7.4, 200 mM NaCl, 2 mM TCEP, 0.011% LMNG cryo-EM vitrification conditions Cryogen ETHANE；detergent added directly before grid application	Resolution 2.20 Å
8G66 Structure with SJ3149 Deposited 2023-02-14	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 706–1140（435 aa）	Not recorded	ZN ZINC ION × 1 YOT (3S)-3-{5-[(1,2-benzoxazol-3-yl)amino]-1-oxo-1,3-dihydro-2H-isoindol-2-yl}piperidine-2,6-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；70 MM TRIS PH 7.0, 140 MM MGCL2, 7% W/V PEG 8000	Resolution 3.45 Å R-free 0.272
8G66 Structure with SJ3149 Deposited 2023-02-14	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–395（395 aa） Chain D 706–1140（435 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；70 MM TRIS PH 7.0, 140 MM MGCL2, 7% W/V PEG 8000	Resolution 3.45 Å R-free 0.272
8OIZ Crystal structure of human CRBN-DDB1 in complex with Pomalidomide Deposited 2023-03-23	Different 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	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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1140（1140 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 9 ZN ZINC ION × 1 VP9 4-azanyl-2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-7-methoxy-isoindole-1,3-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；291 K；0.8 microliter of CRBN-DDB1 complex at 25 mg/mL (including 1 mM compound and 2 % DMSO final) plus 0.8 microliter of a crystallisation solution consisting of 0.1 M Hepes pH 8.2, 0.2 M NaCl and 10-16 % PEG Smear Medium, plus 0.2 microliter of seeds (established from the same conditions), against 500 microliter of crystallisation solution.	Resolution 2.72 Å R-free 0.254
8QH5 CryoEM structure of UVSSA(VHS)-CSA-DDB1-DDA1 Deposited 2023-09-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 ligand/ion 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
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 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 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	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 mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 706–1140（435 aa）	Mutation：residues 396-705 deleted Mutation：residues 396-705 deleted	ZN ZINC ION × 2 Y70 S-Pomalidomide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7；20 mM HEPES/NaOH pH 7.0, 150 mM NaCl, and 3 mM TCEP. DMSO concentrations were kept below 2% (v/v) cryo-EM vitrification conditions Cryogen ETHANE；Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.	Resolution 3.30 Å
8TNQ Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 1 Deposited 2023-08-02	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 706–1140（435 aa）	Mutation：residues 396-705 deleted Mutation：residues 396-705 deleted	ZN ZINC ION × 2 MIQ 2-[(3S)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1H-isoindole-1,3(2H)-dione × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7；20 mM HEPES/NaOH pH 7.0, 150 mM NaCl, and 3 mM TCEP. DMSO concentrations were kept below 2% (v/v) cryo-EM vitrification conditions Cryogen ETHANE；Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.	Resolution 2.41 Å
8TNR Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 2 Deposited 2023-08-02	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 706–1140（435 aa）	Mutation：residues 396-705 deleted Mutation：residues 396-705 deleted	ZN ZINC ION × 2 MIQ 2-[(3S)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1H-isoindole-1,3(2H)-dione × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7；20 mM HEPES/NaOH pH 7.0, 150 mM NaCl, and 3 mM TCEP. DMSO concentrations were kept below 2% (v/v) cryo-EM vitrification conditions Cryogen ETHANE；Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.	Resolution 2.50 Å
8TZX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue dWIZ-1 Deposited 2023-08-28	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–395（395 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140 Chain B 706–1140（435 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140	Not recorded	ZN ZINC ION × 2 U3I (3S)-3-(5-{(1R)-1-[(2R)-1-ethylpiperidin-2-yl]ethoxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350	Resolution 3.15 Å R-free 0.252
8TZX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue dWIZ-1 Deposited 2023-08-28	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–395（395 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140 Chain E 706–1140（435 aa） Fragment：UNP residues 1-395,706-1140,UNP residues 1-395,706-1140	Not recorded	ZN ZINC ION × 2 U3I (3S)-3-(5-{(1R)-1-[(2R)-1-ethylpiperidin-2-yl]ethoxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350	Resolution 3.15 Å R-free 0.252
8U16 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to Pomalidomide Deposited 2023-08-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–395（395 aa） Chain B 706–1140（435 aa）	Not recorded	ZN ZINC ION × 3 Y70 S-Pomalidomide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350	Resolution 2.90 Å R-free 0.273
8U16 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to Pomalidomide Deposited 2023-08-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–395（395 aa） Chain E 706–1140（435 aa）	Not recorded	ZN ZINC ION × 3 Y70 S-Pomalidomide × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350	Resolution 2.90 Å R-free 0.273
8U17 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-long bound to Pomalidomide Deposited 2023-08-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–395（395 aa） Chain B 706–1140（435 aa）	Not recorded	ZN ZINC ION × 3 Y70 S-Pomalidomide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350	Resolution 3.10 Å R-free 0.346
8U17 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-long bound to Pomalidomide Deposited 2023-08-30	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–395（395 aa） Chain E 706–1140（435 aa）	Not recorded	ZN ZINC ION × 3 Y70 S-Pomalidomide × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350	Resolution 3.10 Å R-free 0.346
8UH6 Degrader-induced complex between PTPN2 and CRBN-DDB1 Deposited 2023-10-06	Different 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	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 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1140（1140 aa）	Not recorded	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；287 K；0.1M MES (pH 6.5), 0.1M sodium acetate, 27%(w/v) PEG 400	Resolution 2.25 Å R-free 0.229
9BBE Co-crystal structure of human DDB1 bound to fragment UB028668 Deposited 2024-04-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1140（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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1140（1140 aa）	Not recorded	TLA L(+)-TARTARIC ACID × 2 A1ALA 1H-indol-6-amine × 1 EDO 1,2-ETHANEDIOL × 6 UNX UNKNOWN LIGAND × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% (v/w) PEG 3350, 0.2 M di-NH4tart	Resolution 1.70 Å R-free 0.218
9BBH Co-crystal structure of human DDB1 bound to fragment UB028670 Deposited 2024-04-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1140（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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1140（1140 aa）	Not recorded	TLA L(+)-TARTARIC ACID × 2 A1ALB 3-([1,3]oxazolo[4,5-b]pyridin-2-yl)aniline × 1 UNX UNKNOWN LIGAND × 6	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；20% (v/w) PEG 3350, 0.2 M di-NH4tart	Resolution 1.90 Å R-free 0.221
9BJZ Structure of the human DDD-Ube2e2 complex Deposited 2024-04-26	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–395（395 aa） 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 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 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 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 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 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 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 ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–395（395 aa） Chain B 706–1140（435 aa）	Not recorded	ZN ZINC ION × 2 SO4 SULFATE ION × 1 A1A5H (3S)-3-(5-{[(4R)-6-ethyl-6-azaspiro[2.5]octan-4-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350	Resolution 2.95 Å R-free 0.260
9DJT Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-5 Deposited 2024-09-06	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–395（395 aa） Chain E 706–1140（435 aa）	Not recorded	ZN ZINC ION × 2 SO4 SULFATE ION × 1 A1A5H (3S)-3-(5-{[(4R)-6-ethyl-6-azaspiro[2.5]octan-4-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350	Resolution 2.95 Å R-free 0.260
9DJX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-6 Deposited 2024-09-07	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–395（395 aa） Chain B 706–1140（435 aa）	Not recorded	ZN ZINC ION × 2 SO4 SULFATE ION × 1 A1A5I (3S)-3-(5-{[(3R,6S)-1-ethyl-6-methylpiperidin-3-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1M BIS-TRIS Propane pH 7.5, 20% PEG3350 (Qiagen PACT G8)	Resolution 3.35 Å R-free 0.271
9DJX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-6 Deposited 2024-09-07	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–395（395 aa） Chain E 706–1140（435 aa）	Not recorded	ZN ZINC ION × 2 SO4 SULFATE ION × 2 A1A5I (3S)-3-(5-{[(3R,6S)-1-ethyl-6-methylpiperidin-3-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1M BIS-TRIS Propane pH 7.5, 20% PEG3350 (Qiagen PACT G8)	Resolution 3.35 Å R-free 0.271
9DQD cryo-EM structure of human Cereblon/DDB1 in complex with a non-traditional CRBN binder Deposited 2024-09-23	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–395（395 aa） Chain B 706–1140（435 aa）	Mutation：deletion of residues 396-705 Mutation：deletion of residues 396-705	ZN ZINC ION × 1 A1BEP (3R)-3-{1-methyl-6-[(piperidin-4-yl)amino]-1H-indazol-3-yl}piperidine-2,6-dione × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9DWV Ternary complex of CRBN-DDB1-PPIL4 RRM domain with FPFT-2216 Deposited 2024-10-10	Different construct Different mutation/modification Different ligand/ion 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 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain I 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain Chain I 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain	Not recorded	RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit	Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain Chain A 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain	Not recorded	RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit	Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain Chain C 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain	Not recorded	RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit	Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain Chain E 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain	Not recorded	RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit	Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain G 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain Chain G 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain	Not recorded	RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit	Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain K 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain Chain K 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain	Not recorded	RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit	Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 7 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain M 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain Chain M 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain	Not recorded	RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit	Resolution 4.11 Å R-free 0.289
9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 8 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain O 1–395（395 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain Chain O 706–1140（435 aa） Fragment：internal deletion of the BPB domain,internal deletion of the BPB domain	Not recorded	RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit	Resolution 4.11 Å R-free 0.289
9EJQ Crystal structure of DDB1 in complex with XS381952 Deposited 2024-11-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–1140（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 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 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–1140（1140 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 5 DMS DIMETHYL SULFOXIDE × 3 ZN ZINC ION × 1 LVY S-Lenalidomide × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.2；291 K；0.8 microliter of CRBN-DDB1 complex at 25 mg/mL (including 1 mM compound and 2 % DMSO final) plus 0.8 microliter of a crystallisation solution consisting of 0.1 M Hepes pH 8.2, 0.2 M NaCl and 10-16 % PEG Smear Medium, plus 0.2 microliter of seeds (established from the same conditions), against 500 microliter of crystallisation solution.	Resolution 2.00 Å R-free 0.232
9FMR Structure of DDB1/Cdk12/Cyclin K with molecular glue SR-4835 Deposited 2024-06-07	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric	Chain A 1–391（391 aa） Chain A 708–1140（433 aa） Chain D 1–391（391 aa） Chain D 708–1140（433 aa） Chain G 1–391（391 aa） Chain G 708–1140（433 aa）	Not recorded	RMF ~{N}-[[5,6-bis(chloranyl)-1~{H}-benzimidazol-2-yl]methyl]-9-(1-methylpyrazol-4-yl)-2-morpholin-4-yl-purin-6-amine × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；283 K；1 M potassium citrate and 15% glycerol	Resolution 3.90 Å R-free 0.250
9H59 Cryo-EM structure of DDB1-CRBN in complex with NK7-902 and NEK7 Deposited 2024-10-22	Different construct Different mutation/modification Different ligand/ion 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–1140（1140 aa）	Not recorded	ZN ZINC ION × 1 A1IWG 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1-oxidanylidene-3~{H}-isoindole-5-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Sodium citrate, 0.1 M Bis-Tris propane pH 7.5, 20% w/v PEG 3350	Resolution 3.90 Å R-free 0.336
9HNE Cereblon in complex with DDB1, GSPT1 and Compound-1 Deposited 2024-12-10	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–1140（1140 aa）	Not recorded	ZN ZINC ION × 1 A1IWG 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1-oxidanylidene-3~{H}-isoindole-5-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Sodium citrate, 0.1 M Bis-Tris propane pH 7.5, 20% w/v PEG 3350	Resolution 3.90 Å R-free 0.336
9HPI Cryo-EM structure of DDB1dB-CRBN-MRT-0031619, conformation 1 Deposited 2024-12-13	Different 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）	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 conditions	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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1140（1140 aa）	Not recorded	A1BX6 (3S)-N-{[(4R)-3-(2,4-dioxo-1,3-diazinan-1-yl)imidazo[1,2-a]pyridin-7-yl]methyl}-2-(phenylmethanesulfonyl)-1,2,3,4-tetrahydroisoquinoline-3-carboxamide × 1 ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.029 M HEPES salt, 0.071 M MOPS acid, 0.06 M NaNO3, 0.06 M Na2HPO4, 0.06 M (NH4)2SO4, 11 % (w/v) PEG 8,000 and 25 % (v/v) ethylene glycol.	Resolution 3.25 Å R-free 0.261
9NFR Crystal structure of CRBN-DDB1 and MRT-23227 in complex with VAV1 Deposited 2025-02-21	Different 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 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–1140（1140 aa）	Not recorded	ZN ZINC ION × 1 A1BC8 (3S)-3-[(4M)-4-(4-methoxythiophen-3-yl)-1H-1,2,3-triazol-1-yl]piperidine-2,6-dione × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；70 mM MES pH 6.0, 1.8-3.2 % (w/v) PEG 3,000, and 13-24 % (w/v) PEG 200	Resolution 2.95 Å R-free 0.260
9NR3 CRBN-DDB1 in complex with GLUL-cN Deposited 2025-03-13	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–393（393 aa） Chain A 709–1140（432 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；8% v/v TacsimateTM pH 6.0, 20% w/v Polyethylene glycol 3,350	Resolution 2.93 Å R-free 0.278
9NWS Cryo-EM structure of DDB1dB:CRBN:mezigdomide:SALL4(392-449) Deposited 2025-03-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 706–1140（435 aa）	Not recorded	ZN ZINC ION × 2 QFC Mezigdomide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；50 mM HEPES/NaOH pH 7.4, 150 mM NaCl, 3 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE；UltrAuFoil R 0.6/1 300 mesh grids were glow-discharged for 2 min at 20 mA and 39 Pa, pre-incubated with 4 uL of 10 uM FLAG-IKZF1(140-196;Q146A/G151N) for 1 min, and blotted from behind for 4 s. 4 uL of the sample was then applied to the grid. Grids were vitrified using an EM GP plunge freezer operated at 90% humidity and 10 C with 0 s pre-blot, 4 s blot, and 0 s post-blot.	Resolution 2.70 Å
9NWT Cryo-EM structure of DDB1dB:CRBN:mezigdomide:SALL4(392-449;G416A) Deposited 2025-03-24	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 706–1140（435 aa）	Not recorded	ZN ZINC ION × 2 QFC Mezigdomide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；50 mM HEPES/NaOH pH 7.4, 150 mM NaCl, 3 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE；UltrAuFoil R 0.6/1 300 mesh grids were glow-discharged for 2 min at 20 mA and 39 Pa, pre-incubated with 4 uL of 10 uM FLAG-IKZF1(140-196;Q146A/G151N) for 1 min, and blotted from behind for 4 s. 4 uL of the sample was then applied to the grid. Grids were vitrified using an EM GP plunge freezer operated at 90% humidity and 10 C with 0 s pre-blot, 4 s blot, and 0 s post-blot.	Resolution 2.70 Å
9NYR Cryo-EM structure of CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 24 Deposited 2025-03-28	Different 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	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 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 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 706–1140（435 aa）	Not recorded	ZN ZINC ION × 2 A1CEK N-{2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7；10mM HEPES, 240mM NaCl, 3mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.69 Å
9OUL DDB1-CRBN with Ikaros(ZF2), SB-405483, and DEG-47: composite map and model submission Deposited 2025-05-28	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–395（395 aa） Chain A 706–1140（435 aa）	Not recorded	ZN ZINC ION × 1 A1CEG N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea × 1 A1CEK N-{2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7；10mM HEPES, 240mM NaCl, 3mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.97 Å
9Q22 Crystal structure of ternary complex Helios-ZF2:I-19:CRBN:DDB1 Deposited 2025-08-14	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–381（381 aa） Fragment：UNP residues 1-381,706-1140 Chain A 706–1140（435 aa） Fragment：UNP residues 1-381,706-1140	Not recorded	A1CNP (3S)-3-[5-(1-benzyl-4-hydroxypiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.148 M lithium citrate, 0.1 M Tris, pH 7.5, 19.4% PEG3350	Resolution 3.41 Å R-free 0.252
9Q2D Cryo-EM structure of ternary complex Ikaros-ZF2:CC-885:CRBN:DDB1 (molecular glue degrader) Deposited 2025-08-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–395（395 aa） Fragment：UNP residues 1-395,706-1140 Chain C 706–1140（435 aa） Fragment：UNP residues 1-395,706-1140	Not recorded	ZN ZINC ION × 2 85C 1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE；blot time 4 sec blot force 4	Resolution 2.94 Å
9S3R Ternary complex structure of compound 1 bound to SMARCA2 bromodomain and DCAF16:DDB1deltaBPB Deposited 2025-07-25	Different 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 × 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 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–395（395 aa） Chain A 706–1140（435 aa）	Not recorded	ZN ZINC ION × 1 A1JM3 N-[(2S)-1-[[(3S)-2,5-bis(oxidanylidene)pyrrolidin-3-yl]amino]-1-oxidanylidene-propan-2-yl]-9-[2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]nonanamide × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES, 100 mM NaCl, 0.25 mM TCEP, pH: 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.66 Å
9SFM Crystal structure of Cereblon-DDB1 in complex with SB-405483 and Lenalidomide Deposited 2025-08-19	Different 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	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 conditions	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 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 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 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 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 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 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 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–393（393 aa） Chain A 706–1140（435 aa）	Not recorded	A1C4E (3S,5S)-1-{(4P)-4-(2,2-difluoro-2H-1,3-benzodioxol-4-yl)-3-[(propan-2-yl)oxy]benzene-1-carbonyl}-N-methyl-5-phenylpiperidine-3-carboxamide × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M ammonium acetate, 0.1M Bis Tris pH 5.5-6.5, and 25% PEG 3350	Resolution 2.19 Å R-free 0.246
9ZXN DDB1 delta with compound 26 Deposited 2026-01-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–393（393 aa） Chain A 706–1140（435 aa）	Not recorded	A1C4F (3S,5S)-1-{(4P)-4-(2,2-difluoro-2H-1,3-benzodioxol-4-yl)-1-methyl-5-[(propan-2-yl)oxy]-1H-1,3-benzimidazole-7-carbonyl}-N-methyl-5-phenylpiperidine-3-carboxamide × 1 GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M ammonium acetate, 0.1M Bis Tris pH 5.5-6.5, and 25% PEG 3350	Resolution 2.07 Å R-free 0.235

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

View Construct and Data Evidence

UniProt name	DDB1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–395； UniProt 1–395 Author chain B； PDBConstruct 402–836； UniProt 706–1140

DET1- and DDB1-associated protein 1

Homo sapiens

UniProt Q9BW61

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 D； UniProt 1–102	Not recorded	DDB1- and CUL4-associated factor 15 × 1 （Q66K64） DNA damage-binding protein 1 × 1 （Q16531） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 8ROY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6DSZ Crystal structure of DDB1 in complex with DET1- and DDB1-associated protein 1 (DDA1) Deposited 2018-06-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–19（19 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–19（19 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
6PAI Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and sulfonamide E7820 Deposited 2019-06-11	Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–102（102 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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–102（102 aa）	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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–102（102 aa）	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 oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 1–102（102 aa）	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
6SJ7 Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to RBM39 and Indisulam Deposited 2019-08-12	Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 2–102（101 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
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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 2–102（101 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 method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 2–102（101 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
8G46 Cryo-EM structure of DDB1deltaB-DDA1-DCAF16-BRD4(BD2)-MMH2 Deposited 2023-02-08	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 1–102（102 aa）	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
8QH5 CryoEM structure of UVSSA(VHS)-CSA-DDB1-DDA1 Deposited 2023-09-06	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–102（102 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 ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain D 1–102（102 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
8TL6 Cryo-EM structure of DDB1deltaB-DDA1-DCAF5 Deposited 2023-07-26	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain E 1–102（102 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
9BJZ Structure of the human DDD-Ube2e2 complex Deposited 2024-04-26	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–102（102 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.83 Å
9BZ0 Structure of an STK19-containing TC-NER complex Deposited 2024-05-24	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: 22-meric	Chain e 1–102（102 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
9C5U Cryo EM structure of DCAF2:Compound 1 complex Deposited 2024-06-06	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–102（102 aa）	Not recorded	A1AUM 1'-acetyl-1',4'-dihydro-3'H-spiro[cyclopentane-1,2'-quinoxalin]-3'-one × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.05 Å
9C5V Cryo EM structure of a DCAF2:degrader:BRD4 ternary complex Deposited 2024-06-06	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 1–102（102 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
9DHD The ternary complex of DDB1, DDA1, DET1 Deposited 2024-09-03	Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain C 1–102（102 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
9FD2 Structure of Pol II-TC-NER-STK19 complex Deposited 2024-05-16	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 19 PDB declaration: 22-meric	Chain c 1–102（102 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
9LTJ Cryo-EM structure of DDB1-DDA1-DET1 complex Deposited 2025-02-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–102（102 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–102（102 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.93 Å
9LTO Cryo-EM structure of DDB1-DDA1-DET1-Ube2e2 complex Deposited 2025-02-06	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–102（102 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.92 Å
9LTR Cryo-EM structure of dimeric DDB1-DDA1-DET1-Ube2e2-COP1 complex Deposited 2025-02-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain I 1–102（102 aa） Chain P 1–102（102 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain F 1–102（102 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.25 Å
9LTZ protein structure of DDB1-DDA1-DET1-Ube2e2 complex Deposited 2025-02-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain F 1–102（102 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.26 Å
9LU1 protein structure of DDB1-DDA1-DET1-Ube2e2 bound to COP1 dimer Deposited 2025-02-07	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain B 1–102（102 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.62 Å
9LUL Local refinement of stacked like DDB1-DDA1-DET1-Ube2e2-COP1 complex (layer 1) Deposited 2025-02-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain L 2–67（66 aa） Chain h 2–67（66 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
9M0Y Local refinement of stacked like DDB1-DDA1-DET1-Ube2e2-COP1 complex (layer 2) Deposited 2025-02-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric	Chain j 1–102（102 aa） Chain n 1–102（102 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
9S3R Ternary complex structure of compound 1 bound to SMARCA2 bromodomain and DCAF16:DDB1deltaBPB Deposited 2025-07-25	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–102（102 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
9W90 DDB1-DDA1-DET1-Ube2e2-COP1-c-Jun-STK40 complex Deposited 2025-08-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain I 1–102（102 aa） Chain P 1–102（102 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

29 other PDB entries and 30 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DDA1_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain D； PDBConstruct 1–102； UniProt 1–102

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8roy
Deposition date deposition_date	2024-01-12
Structure title title	Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to compound furan 24
Keywords keywords	E3 ligase, Complex, LIGASE; LIGASE
Experimental Method method	ELECTRON MICROSCOPY

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	33.40 Å
Radius of gyration Rg (electron density) rg_electron	32.47 Å
Forward intensity I(0) i0	210713000.00
Molecular weight molecular_weight	117240.0 kDa
Excluded volume excluded_volume	147100 Å³
Envelope volume envelope_volume	199520 Å³
Hydration-shell volume shell_volume	49788 Å³
Envelope diameter envelope_diameter	112.9 Å
Shell Rg shell_rg	40.38 Å
Envelope Rg envelope_rg	32.28 Å
Shape Rg shape_rg	32.50 Å
Total Rg total_rg	33.04 Å
Total atoms total_atoms	8294
Residues n_residues	1174
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	103.6 Å
Rg (real space) rg_real	33.26 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	2.1070e+08
I(0) uncertainty (real space) i0_real_error	2.9540e+06
Rg (reciprocal space) rg_reciprocal	33.35 Å
I(0) (reciprocal space) i0_reciprocal	210700000.0000
Solution quality estimate total_estimate	0.9033
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	41.9 Å
Skewness Skewness skewness	0.167
Kurtosis Kurtosis kurtosis	-0.477
Angular range angular_range	— – 0.2350 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	49880000.0000
Real-space data points n_real_points	48
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.936

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	DDB1- and CUL4-associated factor 15
Molecular weight formula_weight	66822.6 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	8294

GSHMAPSSKSERNSGAGSGGGGPGGAGGKRAAGRRREHVLKQLERVKISGQLSPRLFRKLPPRVCVSLKNIVDEDFLYAGHIFLGFSKCGRYVLSYTSSSGDDDFSFYIYHLYWWEFNVHSKLKLVRQVRLFQDEEIYSDLYLTVCEWPSDASKVIVFGFNTRSANGMLMNMMMMSDENHRDIYVSTVAVPPPGRCAACQDASRAHPGDPNAQCLRHGFMLHTKYQVVYPFPTFQPAFQLKKDQVVLLNTSYSLVACAVSVHSAGDRSFCQILYDHSTCPLAPASPPEPQSPELPPALPSFCPEAAPARSSGSPEPSPAIAKAKEFVADIFRRAKEAKGGVPEEARPALCPGPSGSRCRAHSEPLALCGETAPRDSPPASEAPASEPGYVNYTKLYYVLESGEGTEPEDELEDDKISLPFVVTDLRGRNLRPMRERTAVQGQYLTVEQLTLDFEYVINEVIRHDATWGHQFCSFSDYDIVILEVCPETNQVLINIGLLLLAFPSPTEEGQLRPKTYHTSLKVAWDLNTGIFETVSVGDLTEVKGQTSGSVWSSYRKSCVDMVMKWLVPESSGRYVNRMTNEALHKGCSLKVLADSERYTWIVL

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	DNA damage-binding protein 1
Molecular weight formula_weight	93347.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGKIAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGIIGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICFVYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYHNGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDLRVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIVDMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGGNGNSGEIQKLHIRTVPLYESPRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHETSFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEEAEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELRTECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEILDDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGETSTPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTERKTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 3 Entity 3 polymer

Description description	DET1- and DDB1-associated protein 1
Molecular weight formula_weight	11855.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D

MADFLKGLPVYNKSNFSRFHADSVCKASNRRPSVYLPTREYPSEQIIVTEKTNILLRYLHQQWDKKNAAKKRDQEQVELEGESSAPPRKVARTDSPDMHEDT

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Spodoptera frugiperda

Entity 4 Entity 4 non-polymer

Description description	1-[5-[[3,4-bis(chloranyl)-1~{H}-indol-7-yl]sulfamoyl]-3-methyl-furan-2-yl]carbonyl-~{N}-methyl-piperidine-4-carboxamide
Molecular weight formula_weight	513.4 kDa
Source method src_method	syn
Copy count entity_count	1

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.10 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	405189

fit	/app/data/saxs_computation/ro/8roy/8roy.fit
pddf	/app/data/pr_computation/ro/8roy/8roy.pr.out
profile	/app/data/saxs_computation/ro/8roy/8roy.dat

Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to compound furan 24

1. Protein Identity and Related Structures Protein Identity & Related Structures

DDB1- and CUL4-associated factor 15

State in the Current Structure

Other States of the Same Protein in the Database

DNA damage-binding protein 1

State in the Current Structure

Other States of the Same Protein in the Database

DET1- and DDB1-associated protein 1

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)