Protein cereblon
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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain A； UniProt 318–426 | Mutation：C366S | Sal-like protein 4 × 1 （Q9UJQ4） F4U 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-5-oxidanyl-isoindole-1,3-dione × 1 ZN ZINC ION × 2 SO4 SULFATE ION × 2 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；22% PEG 4000, 0.1 M MES (pH 6.0), 0.2 M lithium sulfate | Resolution 1.80 Å R-free 0.223 |
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 7BQV | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 10AY Cryo-EM structure of CRBN-DDB1 in complex with HBS1L and TNG961 Deposited 2026-01-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric |
Chain B
40–442（403 aa）
Chain E
40–442（403 aa）
|
Not recorded | A1C4S N-{6-[(3R)-2,6-dioxopiperidin-3-yl]naphthalen-1-yl}-N'-{2-[6-(trifluoromethyl)-1-benzothiophen-2-yl]propan-2-yl}urea × 2 ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；0.1 M HEPES (pH 7.5), 0.24 M sodium chloride, 3 mM TCEP, 0.2 % n-octylglucoside
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 11MR Cryo-EM structure of CRBN in complex with HBS1L and TNG-4857 (focused refinement) Deposited 2026-03-05 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
40–442（403 aa）
Chain D
40–442（403 aa）
|
Not recorded | ZN ZINC ION × 2 A1C9W N-[(3S)-2,6-dioxopiperidin-3-yl]-2-fluoro-3-[(2-{4-[1-(trifluoromethyl)cyclopropyl]phenyl}propan-2-yl)carbamamido]benzamide × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；10 mM HEPES (pH 7.5), 240 mM NaCl, 3 mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.60 Å |
| 4M91 crystal structure of hN33/Tusc3-peptide 1 Deposited 2013-08-14 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
229–240（12 aa）
Fragment：unp residues 229-240
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；0.2 M KSCN,
10.5% PEG 8K, 10% PEG 1K in 100 mM cacodylic acid-NaOH, pH 6.5, VAPOR DIFFUSION, SITTING DROP
|
Resolution 1.10 Å R-free 0.160 |
| 4TZ4 Crystal Structure of Human Cereblon in Complex with DDB1 and Lenalidomide Deposited 2014-07-09 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
47–427（381 aa）
|
Not recorded | ZN ZINC ION × 1 LVY S-Lenalidomide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；100mM HEPES pH 7.5, 18% PEG 10K
|
Resolution 3.01 Å R-free 0.271 |
| 5FQD Structural basis of Lenalidomide induced CK1a degradation by the crl4crbn ubiquitin ligase Deposited 2015-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
41–442（402 aa）
|
Not recorded | ZN ZINC ION × 1 LVY S-Lenalidomide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
70 MM TRIS PH 7.0 140 MM MGCL2 7% W/V PEG 8000
|
Resolution 2.45 Å R-free 0.210 |
| 5FQD Structural basis of Lenalidomide induced CK1a degradation by the crl4crbn ubiquitin ligase Deposited 2015-12-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
41–442（402 aa）
|
Not recorded | ZN ZINC ION × 1 LVY S-Lenalidomide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
70 MM TRIS PH 7.0 140 MM MGCL2 7% W/V PEG 8000
|
Resolution 2.45 Å R-free 0.210 |
| 5HXB Cereblon in complex with DDB1, CC-885, and GSPT1 Deposited 2016-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain Z
39–441（403 aa）
|
Not recorded | ZN ZINC ION × 1 85C 1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；280 K；200mM Sodium Citrate, Tris pH 8.5, 18% PEG 3350
|
Resolution 3.60 Å R-free 0.273 |
| 5HXB Cereblon in complex with DDB1, CC-885, and GSPT1 Deposited 2016-01-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
39–441（403 aa）
|
Not recorded | ZN ZINC ION × 1 85C 1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；280 K；200mM Sodium Citrate, Tris pH 8.5, 18% PEG 3350
|
Resolution 3.60 Å R-free 0.273 |
| 5V3O Cereblon in complex with DDB1 and CC-220 Deposited 2017-03-07 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
40–442（403 aa）
Fragment：residues 40-442
|
Not recorded | 8W7 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；200mM NaCl, 20% PEG 3350
|
Resolution 3.20 Å R-free 0.267 |
| 6BN7 Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET23 PROTAC. Deposited 2017-11-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–441（441 aa）
|
Not recorded | ZN ZINC ION × 1 RN3 methyl {(6S)-4-(4-chlorophenyl)-2-[(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl)carbamoyl]-3,9-dimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl}acetate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9% (w/v) PEG20K, 18% (v/v) PEG MME 550, 0.09M BICINE pH8.5, 9% Silver bullet B5 (0.33% w/v 2,7-Naphthalenedisulfonic acid disodium salt, 0.33% w/v Azelaic acid, 0.33% w/v trans-Cinnamic acid, 0.02 M HEPES sodium pH 6.8)
|
Resolution 3.50 Å R-free 0.256 |
| 6BN8 Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET55 PROTAC. Deposited 2017-11-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–441（441 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9% PEG20K, 18% PEG MME 550, 0.09M BICINE pH8.5, 9% Silver bullet G4 (0.16% w/v 3-Indolebutyric acid, 0.16% w/v Hexadecanedioic acid, 0.16% w/v Oxamic acid, 0.16% w/v Pyromellitic acid, 0.16% w/v Sebacic acid, 0.16% w/v Suberic acid, 0.02 M HEPES sodium pH 6.8)
|
Resolution 3.99 Å R-free 0.333 |
| 6BN9 Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET70 PROTAC Deposited 2017-11-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–441（441 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；10% (w/v) PEG20K, 20% (v/v) PEG MME 550, 0.1M BICINE pH8.5, Silver Bullet F2 (0.2% w/v D-Fructose 1,6-bisphosphate trisodium salt hydrate, 0.2% w/v Glycerol phosphate disodium salt hydrate, 0.2% w/v L-O-Phosphoserine, 0.2% w/v O-Phospho-L-tyrosine, 0.2% w/v Phytic acid sodium salt hydrate, 0.02 M HEPES sodium pH 6.8)
|
Resolution 4.38 Å R-free 0.301 |
| 6BNB Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET57 PROTAC Deposited 2017-11-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–441（441 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.34M NaH2PO4, 0.33M K2HPO4
|
Resolution 6.34 Å R-free 0.381 |
| 6BOY Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET6 PROTAC. Deposited 2017-11-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–441（441 aa）
|
Not recorded | ZN ZINC ION × 1 RN6 2-[(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]-N-(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl)acetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；9% (w/v) PEG20K, 18% (v/v) PEG MME 550, 0.09M BICINE pH8.5, 9% (v/v) Silver bullet D11 (0.25% w/v 2,6-Naphthalenedisulfonic acid disodium salt, 0.25% w/v 4-Aminobenzoic acid, 0.25% w/v 5-Sulfosalicylic acid dihydrate, 0.25% w/v Naphthalene-1,3,6-trisulfonic acid trisodium salt hydrate, 0.02 M HEPES sodium pH 6.8)
|
Resolution 3.33 Å R-free 0.234 |
| 6H0F Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2) Deposited 2018-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
36–442（407 aa）
|
Mutation：N-terminally truncated (1-40 aa deleted) | ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；Protein solution:
350 uM IKZF1-ZF2, 70 uM DDB1/CRBN, 80 uM pomalidomide in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP
Crystallisation solution:
(Morpheus HT condition) 100 mM Morpheus buffer system 1 pH 6.5, 10% (v/v) Morpheus NPS solution, 15% (v/v) ethylene glycol and 9.5% (w/v) poly(ethylene glycol) 5000 monomethyl ether.
|
Resolution 3.25 Å R-free 0.234 |
| 6H0F Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2) Deposited 2018-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
36–442（407 aa）
|
Mutation：N-terminally truncated (1-40 aa deleted) | ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；Protein solution:
350 uM IKZF1-ZF2, 70 uM DDB1/CRBN, 80 uM pomalidomide in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP
Crystallisation solution:
(Morpheus HT condition) 100 mM Morpheus buffer system 1 pH 6.5, 10% (v/v) Morpheus NPS solution, 15% (v/v) ethylene glycol and 9.5% (w/v) poly(ethylene glycol) 5000 monomethyl ether.
|
Resolution 3.25 Å R-free 0.234 |
| 6H0F Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2) Deposited 2018-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
36–442（407 aa）
|
Mutation：N-terminally truncated (1-40 aa deleted) | ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；Protein solution:
350 uM IKZF1-ZF2, 70 uM DDB1/CRBN, 80 uM pomalidomide in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP
Crystallisation solution:
(Morpheus HT condition) 100 mM Morpheus buffer system 1 pH 6.5, 10% (v/v) Morpheus NPS solution, 15% (v/v) ethylene glycol and 9.5% (w/v) poly(ethylene glycol) 5000 monomethyl ether.
|
Resolution 3.25 Å R-free 0.234 |
| 6H0F Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2) Deposited 2018-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain K
36–442（407 aa）
|
Mutation：N-terminally truncated (1-40 aa deleted) | ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；Protein solution:
350 uM IKZF1-ZF2, 70 uM DDB1/CRBN, 80 uM pomalidomide in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP
Crystallisation solution:
(Morpheus HT condition) 100 mM Morpheus buffer system 1 pH 6.5, 10% (v/v) Morpheus NPS solution, 15% (v/v) ethylene glycol and 9.5% (w/v) poly(ethylene glycol) 5000 monomethyl ether.
|
Resolution 3.25 Å R-free 0.234 |
| 6H0G Structure of the DDB1-CRBN-pomalidomide complex bound to ZNF692(ZF4) Deposited 2018-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
41–442（402 aa）
|
Mutation：N-terminally truncated (1-40 aa deleted) | ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；Protein-drug solution:
350 uM ZNF692-ZF4, 70 uM DDB1/CRBN, 80 uM pomalidomide and in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP
Crystallisation solution:
14.1% (w/v) PEG 5K MME and 70 mM Tris-HCl pH 7.5
|
Resolution 4.25 Å R-free 0.256 |
| 6H0G Structure of the DDB1-CRBN-pomalidomide complex bound to ZNF692(ZF4) Deposited 2018-07-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
41–442（402 aa）
|
Mutation：N-terminally truncated (1-40 aa deleted) | ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；Protein-drug solution:
350 uM ZNF692-ZF4, 70 uM DDB1/CRBN, 80 uM pomalidomide and in 50 mM HEPES pH 7.4, 200 mM NaCl, 0.25 mM TCEP
Crystallisation solution:
14.1% (w/v) PEG 5K MME and 70 mM Tris-HCl pH 7.5
|
Resolution 4.25 Å R-free 0.256 |
| 6UML Structural Basis for Thalidomide Teratogenicity Revealed by the Cereblon-DDB1-SALL4-Pomalidomide Complex Deposited 2019-10-09 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
40–442（403 aa）
|
Not recorded | ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；10% PEG MME 500, 8% PEG 20K, 210mM calcium acetate, 100mM tris pH 7.5
|
Resolution 3.58 Å R-free 0.267 |
| 6XK9 Cereblon in complex with DDB1, CC-90009, and GSPT1 Deposited 2020-06-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain Z
40–442（403 aa）
|
Not recorded | V4M 2-(4-chlorophenyl)-N-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)-2,2-difluoroacetamide × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 100mM Tris-HCl (pH 7.5), 300mM sodium citrate
|
Resolution 3.64 Å R-free 0.245 |
| 6XK9 Cereblon in complex with DDB1, CC-90009, and GSPT1 Deposited 2020-06-25 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
40–442（403 aa）
|
Not recorded | V4M 2-(4-chlorophenyl)-N-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)-2,2-difluoroacetamide × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% PEG 3350, 100mM Tris-HCl (pH 7.5), 300mM sodium citrate
|
Resolution 3.64 Å R-free 0.245 |
| 7BQU Cereblon in complex with SALL4 and (S)-thalidomide Deposited 2020-03-25 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
318–426（109 aa）
|
Not recorded | EF2 S-Thalidomide × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；27% PEG 4000, 0.1 M sodium acetate (pH 5.5), 0.1 M magnesium chloride
|
Resolution 1.90 Å R-free 0.236 |
| 7LPS Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) Deposited 2021-02-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
47–436（390 aa）
|
Not recorded | ZN ZINC ION × 2 RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.57；293 K；30% (w/v) PEG3350, 0.1 M Tris pH 8.57
|
Resolution 3.78 Å R-free 0.303 |
| 7LPS Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) Deposited 2021-02-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
47–436（390 aa）
|
Not recorded | ZN ZINC ION × 2 RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.57；293 K；30% (w/v) PEG3350, 0.1 M Tris pH 8.57
|
Resolution 3.78 Å R-free 0.303 |
| 7LPS Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) Deposited 2021-02-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
47–436（390 aa）
|
Not recorded | ZN ZINC ION × 2 RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.57；293 K；30% (w/v) PEG3350, 0.1 M Tris pH 8.57
|
Resolution 3.78 Å R-free 0.303 |
| 7LPS Crystal structure of DDB1-CRBN-ALV1 complex bound to Helios (IKZF2 ZF2) Deposited 2021-02-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain K
47–436（390 aa）
|
Not recorded | ZN ZINC ION × 2 RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.57；293 K；30% (w/v) PEG3350, 0.1 M Tris pH 8.57
|
Resolution 3.78 Å R-free 0.303 |
| 7U8F Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2) and the molecular glue DKY709 Deposited 2022-03-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
40–442（403 aa）
|
Not recorded | ZN ZINC ION × 2 LWK (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 SO4 SULFATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5
|
Resolution 3.15 Å R-free 0.243 |
| 7U8F Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2) and the molecular glue DKY709 Deposited 2022-03-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
40–442（403 aa）
|
Not recorded | ZN ZINC ION × 2 LWK (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 SO4 SULFATE ION × 4 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5
|
Resolution 3.15 Å R-free 0.243 |
| 8CVP Cereblon-DDB1 in the Apo form Deposited 2022-05-18 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE；Manual plunge in 4? coldroom
|
Resolution 3.40 Å |
| 8D7U Cereblon~DDB1 bound to CC-92480 with DDB1 in the linear conformation Deposited 2022-06-07 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 1 QFC Mezigdomide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE；Manual plunge in 4 degree C cold room
|
Resolution 3.10 Å |
| 8D7V Cereblon~DDB1 bound to CC-92480 with DDB1 in the twisted conformation Deposited 2022-06-07 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 1 QFC Mezigdomide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE；Manual plunge in 4 degree C cold room
|
Resolution 3.20 Å |
| 8D7W Cereblon~DDB1 bound to CC-92480 with DDB1 in the hinged conformation Deposited 2022-06-07 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 1 QFC Mezigdomide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE；Manual plunge in 4 degree C cold room
|
Resolution 3.10 Å |
| 8D7X Cereblon~DDB1 in the Apo form with DDB1 in the hinged conformation Deposited 2022-06-07 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；20mM HEPES pH 7, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE；Manual plunge in 4 degree C cold room
|
Resolution 3.40 Å |
| 8D7Y Cereblon-DDB1 in the Apo form with DDB1 in the twisted conformation Deposited 2022-06-07 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE；Manual plunge in 4 degree C cold room
|
Resolution 3.40 Å |
| 8D7Z Cereblon-DDB1 bound to CC-92480 and Ikaros ZF1-2-3 Deposited 2022-06-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 2 QFC Mezigdomide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE；Manual plunge in 4 degree C cold room
|
Resolution 3.10 Å |
| 8D80 Cereblon~DDB1 bound to Iberdomide and Ikaros ZF1-2-3 Deposited 2022-06-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 2 8W7 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；20mM HEPES pH 7.0, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE；Manual plunge in 4 degree C cold room
|
Resolution 3.60 Å |
| 8D81 Cereblon~DDB1 bound to Pomalidomide Deposited 2022-06-07 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 1 Y70 S-Pomalidomide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；20mM HEPES pH 7, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE；Manual plunge in 4 degree C cold room
|
Resolution 3.90 Å |
| 8DEY Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2,3) and the molecular glue DKY709 Deposited 2022-06-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
70–442（373 aa）
|
Not recorded | ZN ZINC ION × 3 LWK (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5
|
Resolution 3.70 Å R-free 0.348 |
| 8DEY Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2,3) and the molecular glue DKY709 Deposited 2022-06-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
70–442（373 aa）
|
Not recorded | ZN ZINC ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；1.6 M potassium/sodium phosphate, pH 6.5
|
Resolution 3.70 Å R-free 0.348 |
| 8G66 Structure with SJ3149 Deposited 2023-02-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
41–442（402 aa）
|
Not recorded | ZN ZINC ION × 1 YOT (3S)-3-{5-[(1,2-benzoxazol-3-yl)amino]-1-oxo-1,3-dihydro-2H-isoindol-2-yl}piperidine-2,6-dione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；70 MM TRIS PH 7.0, 140 MM MGCL2, 7% W/V
PEG 8000
|
Resolution 3.45 Å R-free 0.272 |
| 8G66 Structure with SJ3149 Deposited 2023-02-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain E
41–442（402 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293.15 K；70 MM TRIS PH 7.0, 140 MM MGCL2, 7% W/V
PEG 8000
|
Resolution 3.45 Å R-free 0.272 |
| 8OIZ Crystal structure of human CRBN-DDB1 in complex with Pomalidomide Deposited 2023-03-23 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
40–442（403 aa）
|
Not recorded | 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 ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
40–442（403 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 9 ZN ZINC ION × 1 VP9 4-azanyl-2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-7-methoxy-isoindole-1,3-dione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.2；291 K；0.8 microliter of CRBN-DDB1 complex at 25 mg/mL (including 1 mM compound and 2 % DMSO final) plus 0.8 microliter of a crystallisation solution consisting of 0.1 M Hepes pH 8.2, 0.2 M NaCl and 10-16 % PEG Smear Medium, plus 0.2 microliter of seeds (established from the same conditions), against 500 microliter of crystallisation solution.
|
Resolution 2.72 Å R-free 0.254 |
| 8RQ1 Crystal structure of CRBN-midi Deposited 2024-01-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
41–187（147 aa）
Chain A
249–426（178 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M sodium citrate, 20% (w/v) PEG 3350, and 0.1 M BIS-TRIS propane pH 6.5
|
Resolution 3.11 Å R-free 0.300 |
| 8RQ8 Crystal structure of CRBN-midi in complex with mezigdomide Deposited 2024-01-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
41–187（147 aa）
Chain A
249–426（178 aa）
|
Not recorded | ZN ZINC ION × 1 QFC Mezigdomide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；277 K；214 uM mezigdomide
0.2 M sodium acetate, 25% (w/v) PEG 3350, and 0.1 M BIS-TRIS pH 6.5
|
Resolution 2.19 Å R-free 0.285 |
| 8RQ9 Crystal structure of PROTAC CFT-1297 in complex with CRBN-midi and BRD4(BD2) Deposited 2024-01-17 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
41–187（147 aa）
Chain A
249–426（178 aa）
|
Not recorded | A1H2F (3~{S})-3-[7-[1-[7-[4-[6-(4-chlorophenyl)-1-methyl-spiro[[1,2,4]triazolo[4,3-a][1,4]benzodiazepine-4,1'-cyclopropane]-8-yl]pyrazol-1-yl]heptyl]piperidin-4-yl]-3-oxidanylidene-1~{H}-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG 3350, 0.2 M sodium citrate and 0.1 M Bis-Tris Propane pH 7.5
|
Resolution 2.91 Å R-free 0.293 |
| 8RQ9 Crystal structure of PROTAC CFT-1297 in complex with CRBN-midi and BRD4(BD2) Deposited 2024-01-17 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
41–187（147 aa）
Chain C
249–426（178 aa）
|
Not recorded | A1H2F (3~{S})-3-[7-[1-[7-[4-[6-(4-chlorophenyl)-1-methyl-spiro[[1,2,4]triazolo[4,3-a][1,4]benzodiazepine-4,1'-cyclopropane]-8-yl]pyrazol-1-yl]heptyl]piperidin-4-yl]-3-oxidanylidene-1~{H}-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；20% (w/v) PEG 3350, 0.2 M sodium citrate and 0.1 M Bis-Tris Propane pH 7.5
|
Resolution 2.91 Å R-free 0.293 |
| 8RQA Crystal structure of CRBN-midi in complex with Lenalidomide Deposited 2024-01-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
41–187（147 aa）
Chain A
249–426（178 aa）
|
Not recorded | LVY S-Lenalidomide × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；0.1 M Tris pH 8, 20 % w/v PEG 4000, 1.2 % myo-inositol
|
Resolution 2.50 Å R-free 0.342 |
| 8RQC Crystal structure of CRBN-midi in complex with mezigdomide and IKZF1 ZF2 Deposited 2024-01-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
41–187（147 aa）
Chain A
249–426（178 aa）
Chain D
41–187（147 aa）
Chain D
249–426（178 aa）
|
Not recorded | ZN ZINC ION × 4 QFC Mezigdomide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M ammonium sulphate, 25% (w/v) PEG 3350, and 0.1 M HEPES pH 7.5
|
Resolution 2.15 Å R-free 0.286 |
| 8TNP Cryo-EM structure of DDB1dB:CRBN:Pomalidomide:SD40 Deposited 2023-08-02 | Different construct Different 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 B
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 2 Y70 S-Pomalidomide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；20 mM HEPES/NaOH pH 7.0, 150 mM NaCl, and 3 mM TCEP. DMSO concentrations were kept below 2% (v/v)
cryo-EM vitrification conditions
Cryogen ETHANE；Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.
|
Resolution 3.30 Å |
| 8TNQ Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 1 Deposited 2023-08-02 | Different construct Different 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 B
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 2 MIQ 2-[(3S)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1H-isoindole-1,3(2H)-dione × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；20 mM HEPES/NaOH pH 7.0, 150 mM NaCl, and 3 mM TCEP. DMSO concentrations were kept below 2% (v/v)
cryo-EM vitrification conditions
Cryogen ETHANE；Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.
|
Resolution 2.41 Å |
| 8TNR Cryo-EM structure of DDB1dB:CRBN:PT-179:SD40, conformation 2 Deposited 2023-08-02 | Different construct Different 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 B
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 2 MIQ 2-[(3S)-2,6-dioxopiperidin-3-yl]-5-(morpholin-4-yl)-1H-isoindole-1,3(2H)-dione × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；20 mM HEPES/NaOH pH 7.0, 150 mM NaCl, and 3 mM TCEP. DMSO concentrations were kept below 2% (v/v)
cryo-EM vitrification conditions
Cryogen ETHANE；Leica EM-GP plunge freezer with chamber conditions of 10 C and 90% relative humidity. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixture 1 diluted 10-fold--with the dilution buffer during the 1-minute incubation time--was applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C.
|
Resolution 2.50 Å |
| 8TZX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue dWIZ-1 Deposited 2023-08-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
70–442（373 aa）
|
Not recorded | ZN ZINC ION × 2 U3I (3S)-3-(5-{(1R)-1-[(2R)-1-ethylpiperidin-2-yl]ethoxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 SO4 SULFATE ION × 2 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350
|
Resolution 3.15 Å R-free 0.252 |
| 8TZX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue dWIZ-1 Deposited 2023-08-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
70–442（373 aa）
|
Not recorded | ZN ZINC ION × 2 U3I (3S)-3-(5-{(1R)-1-[(2R)-1-ethylpiperidin-2-yl]ethoxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350
|
Resolution 3.15 Å R-free 0.252 |
| 8U15 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to CC-220 Deposited 2023-08-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
70–442（373 aa）
|
Not recorded | ZN ZINC ION × 3 8W7 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 SO4 SULFATE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
|
Resolution 2.95 Å R-free 0.272 |
| 8U15 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to CC-220 Deposited 2023-08-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
70–442（373 aa）
|
Not recorded | ZN ZINC ION × 3 8W7 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 SO4 SULFATE ION × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
|
Resolution 2.95 Å R-free 0.272 |
| 8U16 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to Pomalidomide Deposited 2023-08-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
70–442（373 aa）
|
Not recorded | ZN ZINC ION × 3 Y70 S-Pomalidomide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
|
Resolution 2.90 Å R-free 0.273 |
| 8U16 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-short bound to Pomalidomide Deposited 2023-08-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
70–442（373 aa）
|
Not recorded | ZN ZINC ION × 3 Y70 S-Pomalidomide × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
|
Resolution 2.90 Å R-free 0.273 |
| 8U17 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-long bound to Pomalidomide Deposited 2023-08-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
70–442（373 aa）
|
Not recorded | ZN ZINC ION × 3 Y70 S-Pomalidomide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
|
Resolution 3.10 Å R-free 0.346 |
| 8U17 The ternary complex structure of DDB1-CRBN-SALL4(ZF1,2)-long bound to Pomalidomide Deposited 2023-08-30 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
70–442（373 aa）
|
Not recorded | ZN ZINC ION × 3 Y70 S-Pomalidomide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Sodium malonate, 20% PEG 3350
|
Resolution 3.10 Å R-free 0.346 |
| 8UH6 Degrader-induced complex between PTPN2 and CRBN-DDB1 Deposited 2023-10-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–442（442 aa）
|
Not recorded | WO8 (5P)-3-(carboxymethoxy)-4-chloro-5-(3-{[(4S)-1-({3-[(4-{1-[(3R)-2,6-dioxopiperidin-3-yl]-3-methyl-2-oxo-2,3-dihydro-1H-benzimidazol-5-yl}piperidine-1-carbonyl)amino]phenyl}methanesulfonyl)-2,2-dimethylpiperidin-4-yl]amino}phenyl)thiophene-2-carboxylic acid × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9CUO Crystal structure of CRBN with compound 3 Deposited 2024-07-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
319–427（109 aa）
Chain B
319–427（109 aa）
Chain C
319–427（109 aa）
|
Not recorded | ZN ZINC ION × 3 A1A0J (3S)-3-(3-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-1-yl)piperidine-2,6-dione × 3 SO4 SULFATE ION × 8 EDO 1,2-ETHANEDIOL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.7；291 K；0.1M Acetate, pH4.7, 0.2M sodium chloride, 1.1M ammonium sulfate
|
Resolution 1.60 Å R-free 0.205 |
| 9CUO Crystal structure of CRBN with compound 3 Deposited 2024-07-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain D
319–427（109 aa）
Chain E
319–427（109 aa）
Chain F
319–427（109 aa）
|
Not recorded | ZN ZINC ION × 3 A1A0J (3S)-3-(3-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-1-yl)piperidine-2,6-dione × 3 SO4 SULFATE ION × 5 EDO 1,2-ETHANEDIOL × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.7；291 K；0.1M Acetate, pH4.7, 0.2M sodium chloride, 1.1M ammonium sulfate
|
Resolution 1.60 Å R-free 0.205 |
| 9D0W Cryo-EM structure of CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 4 Deposited 2024-08-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
40–442（403 aa）
|
Not recorded | ZN ZINC ION × 1 A1A1I (3R)-3-(5-{4-[(2-{4-[(8-cyclopentyl-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl)amino]-3-methylbenzene-1-sulfonyl}-7-azaspiro[3.5]nonan-7-yl)methyl]piperidin-1-yl}-4-fluoro-3-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-1-yl)piperidine-2,6-dione × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.95 Å |
| 9D0X Cryo-EM structure of CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 4 (local mask) Deposited 2024-08-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
40–442（403 aa）
|
Not recorded | ZN ZINC ION × 1 A1A1I (3R)-3-(5-{4-[(2-{4-[(8-cyclopentyl-7-oxo-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl)amino]-3-methylbenzene-1-sulfonyl}-7-azaspiro[3.5]nonan-7-yl)methyl]piperidin-1-yl}-4-fluoro-3-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-1-yl)piperidine-2,6-dione × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.84 Å |
| 9DJT Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-5 Deposited 2024-09-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
70–442（373 aa）
|
Not recorded | ZN ZINC ION × 2 SO4 SULFATE ION × 1 A1A5H (3S)-3-(5-{[(4R)-6-ethyl-6-azaspiro[2.5]octan-4-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350
|
Resolution 2.95 Å R-free 0.260 |
| 9DJT Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-5 Deposited 2024-09-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
70–442（373 aa）
|
Not recorded | ZN ZINC ION × 2 SO4 SULFATE ION × 1 A1A5H (3S)-3-(5-{[(4R)-6-ethyl-6-azaspiro[2.5]octan-4-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1 M Bis-Tris Propane pH 7.5, 20% w/v PEG 3350
|
Resolution 2.95 Å R-free 0.260 |
| 9DJX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-6 Deposited 2024-09-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
70–442（373 aa）
|
Not recorded | ZN ZINC ION × 2 SO4 SULFATE ION × 1 A1A5I (3S)-3-(5-{[(3R,6S)-1-ethyl-6-methylpiperidin-3-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1M BIS-TRIS Propane pH 7.5, 20% PEG3350 (Qiagen PACT G8)
|
Resolution 3.35 Å R-free 0.271 |
| 9DJX Ternary complex structure of Cereblon-DDB1 bound to WIZ(ZF7) and the molecular glue WIZ-6 Deposited 2024-09-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
70–442（373 aa）
|
Not recorded | ZN ZINC ION × 2 SO4 SULFATE ION × 2 A1A5I (3S)-3-(5-{[(3R,6S)-1-ethyl-6-methylpiperidin-3-yl]oxy}-1-oxo-1,3-dihydro-2H-isoindol-2-yl)piperidine-2,6-dione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2 M Sodium Sulfate, 0.1M BIS-TRIS Propane pH 7.5, 20% PEG3350 (Qiagen PACT G8)
|
Resolution 3.35 Å R-free 0.271 |
| 9DOM PVTX-405: A Potent, Highly Selective, and Orally Efficacious Molecular Glue Degrader of IKZF2 for Cancer Immunotherapy Deposited 2024-09-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
319–426（108 aa）
|
Not recorded | A1A8N (3S)-3-(1'-benzyl-6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.4 M Magnesium chloride
0.1 M TRIS pH 7.5
27% w/v PEG 4000
|
Resolution 1.69 Å R-free 0.234 |
| 9DOM PVTX-405: A Potent, Highly Selective, and Orally Efficacious Molecular Glue Degrader of IKZF2 for Cancer Immunotherapy Deposited 2024-09-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
319–426（108 aa）
|
Not recorded | A1A8N (3S)-3-(1'-benzyl-6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.4 M Magnesium chloride
0.1 M TRIS pH 7.5
27% w/v PEG 4000
|
Resolution 1.69 Å R-free 0.234 |
| 9DOM PVTX-405: A Potent, Highly Selective, and Orally Efficacious Molecular Glue Degrader of IKZF2 for Cancer Immunotherapy Deposited 2024-09-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
319–426（108 aa）
|
Not recorded | A1A8N (3S)-3-(1'-benzyl-6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.4 M Magnesium chloride
0.1 M TRIS pH 7.5
27% w/v PEG 4000
|
Resolution 1.69 Å R-free 0.234 |
| 9DOM PVTX-405: A Potent, Highly Selective, and Orally Efficacious Molecular Glue Degrader of IKZF2 for Cancer Immunotherapy Deposited 2024-09-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
319–426（108 aa）
|
Not recorded | A1A8N (3S)-3-(1'-benzyl-6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.4 M Magnesium chloride
0.1 M TRIS pH 7.5
27% w/v PEG 4000
|
Resolution 1.69 Å R-free 0.234 |
| 9DQD cryo-EM structure of human Cereblon/DDB1 in complex with a non-traditional CRBN binder Deposited 2024-09-23 | Different construct Different mutation/modification 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
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 1 A1BEP (3R)-3-{1-methyl-6-[(piperidin-4-yl)amino]-1H-indazol-3-yl}piperidine-2,6-dione × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9DUR Cryo-EM Structure of CRBN:dHTC1:ENL YEATS Deposited 2024-10-04 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 1 A1IQT 2-[3-[2-[4-[[(5~{S})-1,3-bis(oxidanylidene)-2,7-diazaspiro[4.4]nonan-7-yl]sulfonylamino]piperidin-1-yl]ethylcarbamoyl]phenyl]-~{N}-cyclobutyl-imidazo[1,2-a]pyridine-6-carboxamide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；30 mM HEPES/NaOH pH7.4, 150 mM NaCl. DMSO concentrations were kept below 2% (v/v)
cryo-EM vitrification conditions
Cryogen ETHANE；Grids were vitrified using a Leica EM GP plunge freezer operated at 90% humidity and 10 C. Grids were first pre-incubated with 4 uL of 10 uM CRBN-agnostic IKZF1_140-196_Q146A,G151N for 1 minute and then blotted from behind for 4 s. Immediately, 4 uL of mixturewas applied to the grids before blotting for 4 s and plunging into liquid ethane at -181 C
|
Resolution 2.90 Å |
| 9DWV Ternary complex of CRBN-DDB1-PPIL4 RRM domain with FPFT-2216 Deposited 2024-10-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 1 A1BC8 (3S)-3-[(4M)-4-(4-methoxythiophen-3-yl)-1H-1,2,3-triazol-1-yl]piperidine-2,6-dione × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 9DWW Ternary complex of CRBN-DDB1-PDE6D with FPFT-2216 Deposited 2024-10-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 1 A1BC8 (3S)-3-[(4M)-4-(4-methoxythiophen-3-yl)-1H-1,2,3-triazol-1-yl]piperidine-2,6-dione × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain J
1–441（441 aa）
|
Not recorded | RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
|
Resolution 4.11 Å R-free 0.289 |
| 9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–441（441 aa）
|
Not recorded | RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
|
Resolution 4.11 Å R-free 0.289 |
| 9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
1–441（441 aa）
|
Not recorded | RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
|
Resolution 4.11 Å R-free 0.289 |
| 9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
1–441（441 aa）
|
Not recorded | RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
|
Resolution 4.11 Å R-free 0.289 |
| 9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain H
1–441（441 aa）
|
Not recorded | RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
|
Resolution 4.11 Å R-free 0.289 |
| 9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain L
1–441（441 aa）
|
Not recorded | RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
|
Resolution 4.11 Å R-free 0.289 |
| 9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 7 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain N
1–441（441 aa）
|
Not recorded | RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
|
Resolution 4.11 Å R-free 0.289 |
| 9E2U Crystal structure of DDB1-CRBN-ALV1 complex bound to triple ZnF of Helios (IKZF2 ZF1-3) Deposited 2024-10-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 8 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain P
1–441（441 aa）
|
Not recorded | RN9 3-[3-[[1-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-2,5-bis(oxidanylidene)pyrrol-3-yl]amino]phenyl]-~{N}-(3-chloranyl-4-methyl-phenyl)propanamide × 1 ZN ZINC ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20.455% PEG 3350, 0.214 M Li3 Cit
|
Resolution 4.11 Å R-free 0.289 |
| 9FJX Crystal structure of human CRBN-DDB1 in complex with Lenalidomide Deposited 2024-05-31 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
40–442（403 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 5 DMS DIMETHYL SULFOXIDE × 3 ZN ZINC ION × 1 LVY S-Lenalidomide × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.2；291 K；0.8 microliter of CRBN-DDB1 complex at 25 mg/mL (including 1 mM compound and 2 % DMSO final) plus 0.8 microliter of a crystallisation solution consisting of 0.1 M Hepes pH 8.2, 0.2 M NaCl and 10-16 % PEG Smear Medium, plus 0.2 microliter of seeds (established from the same conditions), against 500 microliter of crystallisation solution.
|
Resolution 2.00 Å R-free 0.232 |
| 9GAO Crystal structure of CRBNmidi in complex with 2-(4-(2,6-dioxopiperidin-3-yl)phenoxy)-N-methylacetamide Deposited 2024-07-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
41–187（147 aa）
Chain A
249–426（178 aa）
Chain C
41–187（147 aa）
Chain C
249–426（178 aa）
|
Not recorded | A1IJM 2-[4-[(3~{R})-2,6-bis(oxidanylidene)piperidin-3-yl]phenoxy]-~{N}-methyl-ethanamide × 2 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；100 mM Buffer system I (Molecular Dimensions), 15.45% v/v Precipitant mix 2 (MD), 180 mM Monosaccharides (MD)
|
Resolution 1.95 Å R-free 0.286 |
| 9GY3 Crystal structure of CRBNmidi in complex with (S)-dHTC1 Deposited 2024-10-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
41–187（147 aa）
Chain A
249–426（178 aa）
|
Not recorded | A1IQT 2-[3-[2-[4-[[(5~{S})-1,3-bis(oxidanylidene)-2,7-diazaspiro[4.4]nonan-7-yl]sulfonylamino]piperidin-1-yl]ethylcarbamoyl]phenyl]-~{N}-cyclobutyl-imidazo[1,2-a]pyridine-6-carboxamide × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus H10 (0.1 M Buffer System 3 pH 8.5, 0.12 M Alcohols, 30 % Precipitant Mix 2) (Molecular Dimensions)
|
Resolution 2.50 Å R-free 0.303 |
| 9GY3 Crystal structure of CRBNmidi in complex with (S)-dHTC1 Deposited 2024-10-01 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
41–187（147 aa）
Chain C
249–426（178 aa）
|
Not recorded | A1IQT 2-[3-[2-[4-[[(5~{S})-1,3-bis(oxidanylidene)-2,7-diazaspiro[4.4]nonan-7-yl]sulfonylamino]piperidin-1-yl]ethylcarbamoyl]phenyl]-~{N}-cyclobutyl-imidazo[1,2-a]pyridine-6-carboxamide × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Morpheus H10 (0.1 M Buffer System 3 pH 8.5, 0.12 M Alcohols, 30 % Precipitant Mix 2) (Molecular Dimensions)
|
Resolution 2.50 Å R-free 0.303 |
| 9H59 Cryo-EM structure of DDB1-CRBN in complex with NK7-902 and NEK7 Deposited 2024-10-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
2–442（441 aa）
|
Not recorded | A1ISP 2-[(3S)-2,6-bis(oxidanylidene)piperidin-3-yl]-5-[(1S,2R,5S)-2-(ethylamino)-8-azabicyclo[3.2.1]octan-8-yl]isoindole-1,3-dione × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9HNE Cereblon in complex with DDB1, GSPT1 and Compound-1 Deposited 2024-12-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
40–442（403 aa）
|
Not recorded | ZN ZINC ION × 1 A1IWG 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1-oxidanylidene-3~{H}-isoindole-5-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Sodium citrate, 0.1 M Bis-Tris propane pH 7.5, 20% w/v PEG 3350
|
Resolution 3.90 Å R-free 0.336 |
| 9HNE Cereblon in complex with DDB1, GSPT1 and Compound-1 Deposited 2024-12-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain F
40–442（403 aa）
|
Not recorded | ZN ZINC ION × 1 A1IWG 2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1-oxidanylidene-3~{H}-isoindole-5-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M Sodium citrate, 0.1 M Bis-Tris propane pH 7.5, 20% w/v PEG 3350
|
Resolution 3.90 Å R-free 0.336 |
| 9HPI Cryo-EM structure of DDB1dB-CRBN-MRT-0031619, conformation 1 Deposited 2024-12-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
41–442（402 aa）
Chain C
41–442（402 aa）
|
Not recorded | ZN ZINC ION × 2 A1IW1 (3~{S})-3-[3-oxidanylidene-5-[8-(phenylcarbonyl)-2,8-diazaspiro[4.5]decan-2-yl]-1~{H}-isoindol-2-yl]piperidine-2,6-dione × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；Sample supplemented with DDM directly before vitrification
cryo-EM vitrification conditions
Cryogen ETHANE；LEICA EMGP2
|
Resolution 2.93 Å |
| 9HPJ Cryo-EM structure of DDB1dB-CRBN-MRT-0031619, conformation 2 Deposited 2024-12-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
41–442（402 aa）
Chain C
41–442（402 aa）
|
Not recorded | ZN ZINC ION × 2 A1IW1 (3~{S})-3-[3-oxidanylidene-5-[8-(phenylcarbonyl)-2,8-diazaspiro[4.5]decan-2-yl]-1~{H}-isoindol-2-yl]piperidine-2,6-dione × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；Sample supplemented with DDM directly before vitrification
cryo-EM vitrification conditions
Cryogen ETHANE；LEICA EMGP2
|
Resolution 3.10 Å |
| 9NFQ Crystal structure of CRBN-DDB1 and MRT-3486 in complex with NEK7 Deposited 2025-02-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–442（442 aa）
|
Not recorded | A1BX6 (3S)-N-{[(4R)-3-(2,4-dioxo-1,3-diazinan-1-yl)imidazo[1,2-a]pyridin-7-yl]methyl}-2-(phenylmethanesulfonyl)-1,2,3,4-tetrahydroisoquinoline-3-carboxamide × 1 ZN ZINC ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.029 M HEPES salt, 0.071 M MOPS acid, 0.06 M NaNO3, 0.06 M Na2HPO4, 0.06 M (NH4)2SO4, 11 % (w/v) PEG 8,000 and 25 % (v/v) ethylene glycol.
|
Resolution 3.25 Å R-free 0.261 |
| 9NFR Crystal structure of CRBN-DDB1 and MRT-23227 in complex with VAV1 Deposited 2025-02-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 1 A1BYX (3R)-3-{2-chloro-4'-[(1-methyl-1H-pyrazol-3-yl)methoxy][1,1'-biphenyl]-3-yl}piperidine-2,6-dione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2.6 % PEG Smear Low, 6.1 % PEG Smear Medium, 4.3 % PEG Smear High, 5 % glycerol, 0.1 M CaCl2, and 0.1 M MES pH 5.8
|
Resolution 3.40 Å R-free 0.271 |
| 9NGT Crystal structure of CRBN-DDB1 and FPFT-2216 in complex with mTOR Deposited 2025-02-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 1 A1BC8 (3S)-3-[(4M)-4-(4-methoxythiophen-3-yl)-1H-1,2,3-triazol-1-yl]piperidine-2,6-dione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；70 mM MES pH 6.0, 1.8-3.2 % (w/v) PEG 3,000, and 13-24 % (w/v) PEG 200
|
Resolution 2.95 Å R-free 0.260 |
| 9NR3 CRBN-DDB1 in complex with GLUL-cN Deposited 2025-03-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
41–442（402 aa）
|
Not recorded | ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；8% v/v TacsimateTM pH 6.0, 20% w/v Polyethylene glycol 3,350
|
Resolution 2.93 Å R-free 0.278 |
| 9NWS Cryo-EM structure of DDB1dB:CRBN:mezigdomide:SALL4(392-449) Deposited 2025-03-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 2 QFC Mezigdomide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；50 mM HEPES/NaOH pH 7.4, 150 mM NaCl, 3 mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE；UltrAuFoil R 0.6/1 300 mesh grids were glow-discharged for 2 min at 20 mA and 39 Pa, pre-incubated with 4 uL of 10 uM FLAG-IKZF1(140-196;Q146A/G151N) for 1 min, and blotted from behind for 4 s. 4 uL of the sample was then applied to the grid. Grids were vitrified using an EM GP plunge freezer operated at 90% humidity and 10 C with 0 s pre-blot, 4 s blot, and 0 s post-blot.
|
Resolution 2.70 Å |
| 9NWT Cryo-EM structure of DDB1dB:CRBN:mezigdomide:SALL4(392-449;G416A) Deposited 2025-03-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 2 QFC Mezigdomide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4；50 mM HEPES/NaOH pH 7.4, 150 mM NaCl, 3 mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE；UltrAuFoil R 0.6/1 300 mesh grids were glow-discharged for 2 min at 20 mA and 39 Pa, pre-incubated with 4 uL of 10 uM FLAG-IKZF1(140-196;Q146A/G151N) for 1 min, and blotted from behind for 4 s. 4 uL of the sample was then applied to the grid. Grids were vitrified using an EM GP plunge freezer operated at 90% humidity and 10 C with 0 s pre-blot, 4 s blot, and 0 s post-blot.
|
Resolution 2.70 Å |
| 9NYR Cryo-EM structure of CDK2/CyclinE1 in complex with CRBN/DDB1 and Cpd 24 Deposited 2025-03-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
40–442（403 aa）
|
Not recorded | A1B7G N-{(1R,4S)-4-[(4-{3-chloro-4-[(3R)-2,6-dioxo-1,2,3,6-tetrahydropyridin-3-yl]phenyl}piperazin-1-yl)methyl]cyclohexyl}-4-({4-[(3S)-3-hydroxy-3-methylpiperidin-1-yl]-5-(trifluoromethyl)pyrimidin-2-yl}amino)-3-methylbenzene-1-sulfonamide × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；50mM HEPES, pH 7.5, 150mM NaCl, 2mM TCEP, 2 mM FFC8, protein = 13.4 mg/ml
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 9O91 Structure of IKZF2:CRBN:Compound 5 ternary structure Deposited 2025-04-17 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
318–426（109 aa）
Fragment：CULT domain
|
Not recorded | A1CAC (3S)-3-[(5M)-1-oxo-5-{4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2 M Magnesium chloride
0.1 M TRIS pH 8.5
33 % w/v PEG 4000
|
Resolution 1.86 Å R-free 0.218 |
| 9O91 Structure of IKZF2:CRBN:Compound 5 ternary structure Deposited 2025-04-17 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
318–426（109 aa）
Fragment：CULT domain
|
Not recorded | A1CAC (3S)-3-[(5M)-1-oxo-5-{4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2 M Magnesium chloride
0.1 M TRIS pH 8.5
33 % w/v PEG 4000
|
Resolution 1.86 Å R-free 0.218 |
| 9O91 Structure of IKZF2:CRBN:Compound 5 ternary structure Deposited 2025-04-17 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
318–426（109 aa）
Fragment：CULT domain
|
Not recorded | A1CAC (3S)-3-[(5M)-1-oxo-5-{4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2 M Magnesium chloride
0.1 M TRIS pH 8.5
33 % w/v PEG 4000
|
Resolution 1.86 Å R-free 0.218 |
| 9O91 Structure of IKZF2:CRBN:Compound 5 ternary structure Deposited 2025-04-17 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
318–426（109 aa）
Fragment：CULT domain
|
Not recorded | A1CAC (3S)-3-[(5M)-1-oxo-5-{4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291.15 K；0.2 M Magnesium chloride
0.1 M TRIS pH 8.5
33 % w/v PEG 4000
|
Resolution 1.86 Å R-free 0.218 |
| 9ODR Structure of CRBN TBD bound to compound C1 Deposited 2025-04-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
319–426（108 aa）
Fragment：TBD domain
|
Not recorded | A1CAV (3S)-3-(6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；277 K；0.2M tri-Sodium citrate
18 % w/v PEG 3,350
|
Resolution 2.42 Å R-free 0.228 |
| 9ODR Structure of CRBN TBD bound to compound C1 Deposited 2025-04-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
319–426（108 aa）
Fragment：TBD domain
|
Not recorded | A1CAV (3S)-3-(6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；277 K；0.2M tri-Sodium citrate
18 % w/v PEG 3,350
|
Resolution 2.42 Å R-free 0.228 |
| 9ODR Structure of CRBN TBD bound to compound C1 Deposited 2025-04-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
319–426（108 aa）
Fragment：TBD domain
|
Not recorded | A1CAV (3S)-3-(6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；277 K；0.2M tri-Sodium citrate
18 % w/v PEG 3,350
|
Resolution 2.42 Å R-free 0.228 |
| 9ODR Structure of CRBN TBD bound to compound C1 Deposited 2025-04-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
319–426（108 aa）
Fragment：TBD domain
|
Not recorded | A1CAV (3S)-3-(6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；277 K；0.2M tri-Sodium citrate
18 % w/v PEG 3,350
|
Resolution 2.42 Å R-free 0.228 |
| 9ODS Structure of CRBN TBD bound to compound C3 Deposited 2025-04-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
319–426（108 aa）
Fragment：TBD domain
|
Not recorded | A1CAW (1P)-1-[(4S)-8H-spiro[furo[2,3-c]imidazo[1,2-a]pyridine-7,4'-piperidin]-3-yl]pyrimidine-2,4(1H,3H)-dione × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；291 K；0.2M tri-Sodium citrate
18 % w/v PEG 3,350
|
Resolution 2.61 Å R-free 0.248 |
| 9ODS Structure of CRBN TBD bound to compound C3 Deposited 2025-04-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
319–426（108 aa）
Fragment：TBD domain
|
Not recorded | A1CAW (1P)-1-[(4S)-8H-spiro[furo[2,3-c]imidazo[1,2-a]pyridine-7,4'-piperidin]-3-yl]pyrimidine-2,4(1H,3H)-dione × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；291 K；0.2M tri-Sodium citrate
18 % w/v PEG 3,350
|
Resolution 2.61 Å R-free 0.248 |
| 9ODS Structure of CRBN TBD bound to compound C3 Deposited 2025-04-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
319–426（108 aa）
Fragment：TBD domain
|
Not recorded | A1CAW (1P)-1-[(4S)-8H-spiro[furo[2,3-c]imidazo[1,2-a]pyridine-7,4'-piperidin]-3-yl]pyrimidine-2,4(1H,3H)-dione × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；291 K；0.2M tri-Sodium citrate
18 % w/v PEG 3,350
|
Resolution 2.61 Å R-free 0.248 |
| 9ODS Structure of CRBN TBD bound to compound C3 Deposited 2025-04-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
319–426（108 aa）
Fragment：TBD domain
|
Not recorded | A1CAW (1P)-1-[(4S)-8H-spiro[furo[2,3-c]imidazo[1,2-a]pyridine-7,4'-piperidin]-3-yl]pyrimidine-2,4(1H,3H)-dione × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；291 K；0.2M tri-Sodium citrate
18 % w/v PEG 3,350
|
Resolution 2.61 Å R-free 0.248 |
| 9OHQ Structure of CRBN:IKZF2:Compound 15 Deposited 2025-05-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
319–426（108 aa）
|
Not recorded | A1CBH (3S)-3-[(5M)-5-{1-methyl-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；0.2M Magnesium Chloride, 0.5M Sodium Chloride, 0.1M Tris-HCl pH 8.5, 32.5% w/v PEG 3350
|
Resolution 1.60 Å R-free 0.201 |
| 9OHQ Structure of CRBN:IKZF2:Compound 15 Deposited 2025-05-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
319–426（108 aa）
|
Not recorded | A1CBH (3S)-3-[(5M)-5-{1-methyl-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；0.2M Magnesium Chloride, 0.5M Sodium Chloride, 0.1M Tris-HCl pH 8.5, 32.5% w/v PEG 3350
|
Resolution 1.60 Å R-free 0.201 |
| 9OHQ Structure of CRBN:IKZF2:Compound 15 Deposited 2025-05-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
319–426（108 aa）
|
Not recorded | A1CBH (3S)-3-[(5M)-5-{1-methyl-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；0.2M Magnesium Chloride, 0.5M Sodium Chloride, 0.1M Tris-HCl pH 8.5, 32.5% w/v PEG 3350
|
Resolution 1.60 Å R-free 0.201 |
| 9OHQ Structure of CRBN:IKZF2:Compound 15 Deposited 2025-05-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
319–426（108 aa）
|
Not recorded | A1CBH (3S)-3-[(5M)-5-{1-methyl-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；0.2M Magnesium Chloride, 0.5M Sodium Chloride, 0.1M Tris-HCl pH 8.5, 32.5% w/v PEG 3350
|
Resolution 1.60 Å R-free 0.201 |
| 9OHR Structure of CRBN:IKZF2:Compound 35 Deposited 2025-05-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
319–426（108 aa）
|
Not recorded | A1CBG (3S)-3-[(5M)-5-{1-(oxetan-3-yl)-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；0.2 M Magnesium Chloride, 0.5 M Sodium Chloride, 0.1 M Tris-HCl pH 8.1, 32.5% w/v PEG 3350
|
Resolution 2.34 Å R-free 0.290 |
| 9OHR Structure of CRBN:IKZF2:Compound 35 Deposited 2025-05-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
319–426（108 aa）
|
Not recorded | A1CBG (3S)-3-[(5M)-5-{1-(oxetan-3-yl)-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；0.2 M Magnesium Chloride, 0.5 M Sodium Chloride, 0.1 M Tris-HCl pH 8.1, 32.5% w/v PEG 3350
|
Resolution 2.34 Å R-free 0.290 |
| 9OHR Structure of CRBN:IKZF2:Compound 35 Deposited 2025-05-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
319–426（108 aa）
|
Not recorded | A1CBG (3S)-3-[(5M)-5-{1-(oxetan-3-yl)-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；0.2 M Magnesium Chloride, 0.5 M Sodium Chloride, 0.1 M Tris-HCl pH 8.1, 32.5% w/v PEG 3350
|
Resolution 2.34 Å R-free 0.290 |
| 9OHR Structure of CRBN:IKZF2:Compound 35 Deposited 2025-05-05 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain G
319–426（108 aa）
|
Not recorded | A1CBG (3S)-3-[(5M)-5-{1-(oxetan-3-yl)-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；0.2 M Magnesium Chloride, 0.5 M Sodium Chloride, 0.1 M Tris-HCl pH 8.1, 32.5% w/v PEG 3350
|
Resolution 2.34 Å R-free 0.290 |
| 9OS2 Cryo-EM structure of the DDB1/CRBN-MRT-5702-G3BP2 ternary complex Deposited 2025-05-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
47–424（378 aa）
|
Not recorded | ZN ZINC ION × 1 A1CED (1S,3S)-2-[(2-chlorophenyl)methanesulfonyl]-N-{[(4R)-3-(2,4-dioxo-1,3-diazinan-1-yl)imidazo[1,2-a]pyridin-7-yl]methyl}-1-methyl-1,2,3,4-tetrahydroisoquinoline-3-carboxamide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å |
| 9OTY DDB1-CRBN with CK1 alpha, SB-405483, and DEG-47: composite map and model submission Deposited 2025-05-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
46–427（382 aa）
|
Not recorded | ZN ZINC ION × 1 A1CEH N-{2-[(3R)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide × 1 A1CEG N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；10mM HEPES, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9OUK DDB1-CRBN with Ikaros(ZF2) and DEG-47: composite map and model submission Deposited 2025-05-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 2 A1CEK N-{2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；10mM HEPES, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.69 Å |
| 9OUL DDB1-CRBN with Ikaros(ZF2), SB-405483, and DEG-47: composite map and model submission Deposited 2025-05-28 | Different construct Different mutation/modification 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
1–427（427 aa）
|
Not recorded | ZN ZINC ION × 1 A1CEG N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea × 1 A1CEK N-{2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}benzamide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7；10mM HEPES, 240mM NaCl, 3mM TCEP
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.97 Å |
| 9Q03 Cryo-EM structure of ternary complex BCL6-CRBN-DDB1 with BCL6-760 (LDD, local refined) Deposited 2025-08-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 1 A1CM7 (3R)-3-(6-{4-[(5-chloro-4-{[3-(3-hydroxy-3-methylbutyl)-1-methyl-2-oxo-2,3-dihydro-1H-1,3-benzimidazol-5-yl]amino}pyrimidin-2-yl)(methyl)amino]piperidin-1-yl}-1-methyl-1H-indazol-3-yl)piperidine-2,6-dione × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.15 Å |
| 9Q22 Crystal structure of ternary complex Helios-ZF2:I-19:CRBN:DDB1 Deposited 2025-08-14 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
41–442（402 aa）
|
Not recorded | A1CNP (3S)-3-[5-(1-benzyl-4-hydroxypiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 ZN ZINC ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.148 M lithium citrate, 0.1 M Tris, pH 7.5, 19.4% PEG3350
|
Resolution 3.41 Å R-free 0.252 |
| 9Q2D Cryo-EM structure of ternary complex Ikaros-ZF2:CC-885:CRBN:DDB1 (molecular glue degrader) Deposited 2025-08-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 2 85C 1-(3-chloro-4-methylphenyl)-3-({2-[(3S)-2,6-dioxopiperidin-3-yl]-1-oxo-2,3-dihydro-1H-isoindol-5-yl}methyl)urea × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE；blot time 4 sec
blot force 4
|
Resolution 2.94 Å |
| 9Q33 Cereblon Ternary Complex with Blimp1 and compound 5 Deposited 2025-08-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–442（442 aa）
|
Not recorded | ZN ZINC ION × 1 A1CN1 N-({(4R)-7-[(1S)-2-amino-1-(4-bromo-2-methylphenyl)-2-oxoethyl]-5,6,7,8-tetrahydroimidazo[1,2-a]pyrazin-3-yl}methyl)-13-{4-[(3R)-2,6-dioxopiperidin-3-yl]anilino}tridecanamide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 3.20 Å |
| 9SAF Ternary PROTAC-mediated complex of BRD4-BD1/CRBN/DDB1 and JQ1-AcQ bifunctional degrader Deposited 2025-08-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
2–442（441 aa）
|
Not recorded | ZN ZINC ION × 1 A1JM8 ~{N}-[(2~{S})-1-[[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]amino]-1-oxidanylidene-propan-2-yl]-9-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,10,12-tetraen-9-yl]ethanoylamino]nonanamide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.55 Å |
| 9SAI Ternary PROTAC-mediated complex consisting of Cereblon, DDB1 and BRD4-BD1, non-covalently linked by JQ1-AcN Deposited 2025-08-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
2–442（441 aa）
|
Not recorded | ZN ZINC ION × 1 A1JM3 N-[(2S)-1-[[(3S)-2,5-bis(oxidanylidene)pyrrolidin-3-yl]amino]-1-oxidanylidene-propan-2-yl]-9-[2-[(9S)-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]nonanamide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5；20 mM HEPES, 100 mM NaCl, 0.25 mM TCEP, pH: 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.66 Å |
| 9SFM Crystal structure of Cereblon-DDB1 in complex with SB-405483 and Lenalidomide Deposited 2025-08-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
46–427（382 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 6 ZN ZINC ION × 1 LVY S-Lenalidomide × 1 A1CEG N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；291 K；20% w/v PEG 4000 0.1 M TRIS pH 8.2, 0.2 M
|
Resolution 2.39 Å R-free 0.244 |
| 9UUM Cryo-EM structure of mezigdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-07 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain C
41–442（402 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.41 Å |
| 9V0A Cryo-EM structure of pomalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain C
41–442（402 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.69 Å |
| 9V0B Cryo-EM structure of avadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain C
41–442（402 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.54 Å |
| 9V0F Cryo-EM structure of cemsidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain C
41–442（402 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions | Resolution 3.71 Å |
| 9W2F Cryo-EM structure of DDB1-CRBN in complex with dHuR-2 and HuR Deposited 2025-07-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain B
45–425（381 aa）
|
Not recorded | ZN ZINC ION × 1 A1EUN (3S)-3-[6-[1-[(4-methoxyphenyl)methyl]pyrazol-4-yl]-1-benzofuran-3-yl]piperidine-2,6-dione × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9Y7D Cereblon with Golcadomide and Ikaros ZF1-2-3 Deposited 2025-09-09 | Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
40–442（403 aa）
|
Not recorded | ZN ZINC ION × 2 A1AF4 Golcadomide × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen NITROGEN
|
Resolution 3.26 Å |
| 9YA9 Cryo-EM structure of ternary complex BCL6-CRBN-DDB1 with BMS-986458 (local refined), a potent and selective BCL6 ligand directed degrader (LDD) Deposited 2025-09-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
1–442（442 aa）
|
Not recorded | A1CTU (3R)-3-(6-{[(3R,4R)-1-{5-chloro-4-[(1-methyl-2-oxo-2,3-dihydro-1H-indol-5-yl)amino]pyrimidin-2-yl}-3-methylpiperidin-4-yl]amino}-1-methyl-1H-indazol-3-yl)piperidine-2,6-dione × 1 ZN ZINC ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.09 Å |
93 other PDB entries and 141 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | CRBN_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–109； UniProt 318–426 |
