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9qo0

Pre-activated 9-subunit COP9 signalosome and neddylated SCF (Skp1-Skp2-Cks1) complex structure

Method: ELECTRON MICROSCOPY Dmax: 194.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

COP9 signalosome complex subunit 4

Homo sapiens

UniProt Q9BT78

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 × 15 PDB declaration: 15-meric（15） Consistent with protein copy count Chain D； UniProt 1–406 Not recorded COP9 signalosome complex subunit 7b × 1 （Q9H9Q2） NEDD8 × 1 （Q15843） Cyclin-dependent kinases regulatory subunit 1 × 1 （P61024） COP9 signalosome complex subunit 9 × 1 （Q8WXC6） COP9 signalosome complex subunit 1 × 1 （Q13098） COP9 signalosome complex subunit 2 × 1 （P61201） COP9 signalosome complex subunit 3 × 1 （Q9UNS2） COP9 signalosome complex subunit 5 × 1 （Q92905） COP9 signalosome complex subunit 6 × 1 （Q7L5N1） COP9 signalosome complex subunit 8 × 1 （Q99627） Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） S-phase kinase-associated protein 1 × 1 （P63208） S-phase kinase-associated protein 2 × 1 （Q13309） IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.26 Å

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 9QO0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4D0P Crystal structure of human CSN4 Deposited 2014-04-29 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–363（363 aa） Fragment：RESIDUES 1-363
Not recorded NA SODIUM ION × 2 CL CHLORIDE ION × 8 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；16 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM DTT WAS MIXED EQUALLY WITH 100 MM HEPES PH 7.5, 4.3 M NACL. CRYSTALS WERE GROWN BY VAPOR DIFFUSION
Resolution 1.60 Å R-free 0.193
4D10 Crystal structure of the COP9 signalosome Deposited 2014-04-30 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 L 1–406（406 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4, 10 MM UREA.
Resolution 3.80 Å R-free 0.228
4D10 Crystal structure of the COP9 signalosome Deposited 2014-04-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 1–406（406 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4, 10 MM UREA.
Resolution 3.80 Å R-free 0.228
4D18 Crystal structure of the COP9 signalosome Deposited 2014-05-01 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 1–406（406 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTAL GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4. CRYSTAL DEHYDRATED OVERNIGHT WITH 20% PEG 6000 IN WELL
Resolution 4.08 Å R-free 0.253
4D18 Crystal structure of the COP9 signalosome Deposited 2014-05-01 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain L 1–406（406 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTAL GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4. CRYSTAL DEHYDRATED OVERNIGHT WITH 20% PEG 6000 IN WELL
Resolution 4.08 Å R-free 0.253
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 1–406（406 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain L 1–406（406 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain T 1–406（406 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain b 1–406（406 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain j 1–406（406 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain r 1–406（406 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
6R6H Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain D 1–406（406 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5 100 mM NaCl 0.5 mM DTT 1% glycerol
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 8.40 Å
6R7F Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain D 1–406（406 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCL 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.20 Å
6R7H Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain D 1–406（406 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCl 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.80 Å
6R7I Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain D 1–406（406 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
6R7N Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain D 1–406（406 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCl 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.50 Å
8H38 Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(mutate) complex Deposited 2022-10-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain D 1–406（406 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
Resolution 4.25 Å
8H3A Cryo-EM Structure of the KBTBD2-CRL3~N8(removed)-CSN complex Deposited 2022-10-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain D 1–406（406 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.51 Å
8H3F Cryo-EM Structure of the KBTBD2-CRL3-CSN complex Deposited 2022-10-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain D 1–406（406 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.73 Å
9E5Z Cryo-EM structure of COP9 signalosome Deposited 2024-10-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 1–406（406 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9E77 Cryo-EM structure of CSN-N8 in complex with CSN5i-3 Deposited 2024-11-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain D 1–406（406 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9E81 Cryo-EM structure of COP9 signalosome in complex with CSN5i-3 Deposited 2024-11-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 1–406（406 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9EFM Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-1 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain D 1–406（406 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9EFQ Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-2 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain D 1–406（406 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.96 Å
9EFV Cryo-EM structure of CSN-N8CUL1 in complex with CSN5i-3 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain D 1–406（406 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
9EG1 COP9 signalosome deneddylation complex with cullin-5 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain D 1–406（406 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.52 Å
9EG8 Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-4A Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain D 1–406（406 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9EGL Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-3 Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain D 1–406（406 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
9PH4 Cryo-EM structure of COP9 signalosome in complex with CSN5i-1a Deposited 2025-07-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 1–406（406 aa）
Not recorded ZN ZINC ION × 1 A1CH3 6-[(4R,5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-carbonitrile × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9QO1 Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure Deposited 2025-03-25 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain D 1–406（406 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
9QO2 Dissociation-state-1 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain D 1–406（406 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9QO3 Dissociation-state-2 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: 13-meric
Chain D 1–406（406 aa）
Not recorded ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
9QO4 Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain D 1–406（406 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9QO5 Dissociation-state-4 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain D 1–406（406 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9QO6 9-subunit COP9 signalosome complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain D 1–406（406 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

28 other PDB entries and 35 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CSN4_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain D； PDBConstruct 1–406； UniProt 1–406

COP9 signalosome complex subunit 7b

Homo sapiens

UniProt Q9H9Q2

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 × 15 PDB declaration: 15-meric（15） Consistent with protein copy count Chain G； UniProt 1–264 Not recorded COP9 signalosome complex subunit 4 × 1 （Q9BT78） NEDD8 × 1 （Q15843） Cyclin-dependent kinases regulatory subunit 1 × 1 （P61024） COP9 signalosome complex subunit 9 × 1 （Q8WXC6） COP9 signalosome complex subunit 1 × 1 （Q13098） COP9 signalosome complex subunit 2 × 1 （P61201） COP9 signalosome complex subunit 3 × 1 （Q9UNS2） COP9 signalosome complex subunit 5 × 1 （Q92905） COP9 signalosome complex subunit 6 × 1 （Q7L5N1） COP9 signalosome complex subunit 8 × 1 （Q99627） Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） S-phase kinase-associated protein 1 × 1 （P63208） S-phase kinase-associated protein 2 × 1 （Q13309） IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.26 Å

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 9QO0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6R6H Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain G 9–214（206 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5 100 mM NaCl 0.5 mM DTT 1% glycerol
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 8.40 Å
6R7F Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain G 8–215（208 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCL 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.20 Å
6R7H Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 8–215（208 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCl 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.80 Å
6R7I Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain G 1–215（215 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
8H38 Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(mutate) complex Deposited 2022-10-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain G 1–264（264 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
Resolution 4.25 Å
8H3A Cryo-EM Structure of the KBTBD2-CRL3~N8(removed)-CSN complex Deposited 2022-10-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 1–264（264 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.51 Å
8H3F Cryo-EM Structure of the KBTBD2-CRL3-CSN complex Deposited 2022-10-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 1–220（220 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.73 Å
9E5Z Cryo-EM structure of COP9 signalosome Deposited 2024-10-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain G 1–264（264 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9E77 Cryo-EM structure of CSN-N8 in complex with CSN5i-3 Deposited 2024-11-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain G 1–264（264 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9E81 Cryo-EM structure of COP9 signalosome in complex with CSN5i-3 Deposited 2024-11-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain G 1–264（264 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9EFM Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-1 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain G 1–264（264 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9EFQ Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-2 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain G 1–264（264 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.96 Å
9EFV Cryo-EM structure of CSN-N8CUL1 in complex with CSN5i-3 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain G 1–264（264 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
9EG1 COP9 signalosome deneddylation complex with cullin-5 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain G 1–264（264 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.52 Å
9EG8 Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-4A Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain G 1–264（264 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9EGL Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-3 Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain G 1–264（264 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
9PH4 Cryo-EM structure of COP9 signalosome in complex with CSN5i-1a Deposited 2025-07-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain G 1–264（264 aa）
Not recorded ZN ZINC ION × 1 A1CH3 6-[(4R,5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-carbonitrile × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9QO1 Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure Deposited 2025-03-25 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain G 1–264（264 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
9QO2 Dissociation-state-1 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain G 1–264（264 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9QO3 Dissociation-state-2 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: 13-meric
Chain G 1–264（264 aa）
Not recorded ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
9QO4 Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain G 1–264（264 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9QO5 Dissociation-state-4 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain G 1–264（264 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9QO6 9-subunit COP9 signalosome complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain G 1–264（264 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

23 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CSN7B_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain G； PDBConstruct 1–264； UniProt 1–264

NEDD8

Homo sapiens

UniProt Q15843

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 15 PDB declaration: 15-meric（15） Consistent with protein copy count Chain K； UniProt 1–76 Not recorded COP9 signalosome complex subunit 4 × 1 （Q9BT78） COP9 signalosome complex subunit 7b × 1 （Q9H9Q2） Cyclin-dependent kinases regulatory subunit 1 × 1 （P61024） COP9 signalosome complex subunit 9 × 1 （Q8WXC6） COP9 signalosome complex subunit 1 × 1 （Q13098） COP9 signalosome complex subunit 2 × 1 （P61201） COP9 signalosome complex subunit 3 × 1 （Q9UNS2） COP9 signalosome complex subunit 5 × 1 （Q92905） COP9 signalosome complex subunit 6 × 1 （Q7L5N1） COP9 signalosome complex subunit 8 × 1 （Q99627） Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） S-phase kinase-associated protein 1 × 1 （P63208） S-phase kinase-associated protein 2 × 1 （Q13309） IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.26 Å

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

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

View Construct and Data Evidence
UniProt name NEDD8_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain K； PDBConstruct 1–76； UniProt 1–76

Cyclin-dependent kinases regulatory subunit 1

Homo sapiens

UniProt P61024

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 × 15 PDB declaration: 15-meric（15） Consistent with protein copy count Chain N； UniProt 1–79 Not recorded COP9 signalosome complex subunit 4 × 1 （Q9BT78） COP9 signalosome complex subunit 7b × 1 （Q9H9Q2） NEDD8 × 1 （Q15843） COP9 signalosome complex subunit 9 × 1 （Q8WXC6） COP9 signalosome complex subunit 1 × 1 （Q13098） COP9 signalosome complex subunit 2 × 1 （P61201） COP9 signalosome complex subunit 3 × 1 （Q9UNS2） COP9 signalosome complex subunit 5 × 1 （Q92905） COP9 signalosome complex subunit 6 × 1 （Q7L5N1） COP9 signalosome complex subunit 8 × 1 （Q99627） Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） S-phase kinase-associated protein 1 × 1 （P63208） S-phase kinase-associated protein 2 × 1 （Q13309） IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.26 Å

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 9QO0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1BUH CRYSTAL STRUCTURE OF THE HUMAN CDK2 KINASE COMPLEX WITH CELL CYCLE-REGULATORY PROTEIN CKSHS1 Deposited 1998-09-03 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–79（79 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；17-19% MEPEG 5K, 100 MM TRIS-HCL PH 7.5, 100 MM KCL
Resolution 2.60 Å R-free 0.250
1DKS CKSHS1: HUMAN CYCLIN DEPENDENT KINASE SUBUNIT, TYPE 1 IN COMPLEX WITH PHOSPHATE Deposited 1995-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–79（79 aa）
Chain B 1–79（79 aa）
Not recorded PO4 PHOSPHATE ION × 2 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 3.20 Å R-free 0.290
1DKT CKSHS1: HUMAN CYCLIN DEPENDENT KINASE SUBUNIT, TYPE 1 COMPLEX WITH METAVANADATE Deposited 1995-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–79（79 aa）
Chain B 1–79（79 aa）
Not recorded V7O META VANADATE × 1 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.90 Å R-free 0.258
2ASS Crystal structure of the Skp1-Skp2-Cks1 complex Deposited 2005-08-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 5–73（69 aa）
Not recorded PO4 PHOSPHATE ION × 3 BEN BENZAMIDINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；BTP, sodium/potassium phosphate, benzamidine, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.242
2ASS Crystal structure of the Skp1-Skp2-Cks1 complex Deposited 2005-08-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 5–73（69 aa）
Not recorded PO4 PHOSPHATE ION × 6 BEN BENZAMIDINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；BTP, sodium/potassium phosphate, benzamidine, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.242
2ASS Crystal structure of the Skp1-Skp2-Cks1 complex Deposited 2005-08-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 5–73（69 aa）
Not recorded PO4 PHOSPHATE ION × 6 BEN BENZAMIDINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；BTP, sodium/potassium phosphate, benzamidine, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.242
2AST Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide Deposited 2005-08-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 5–73（69 aa）
Not recorded BEN BENZAMIDINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG8K, 5% benzamidine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.30 Å R-free 0.221
2AST Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide Deposited 2005-08-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 5–73（69 aa）
Not recorded BEN BENZAMIDINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG8K, 5% benzamidine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.30 Å R-free 0.221
2AST Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide Deposited 2005-08-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 5–73（69 aa）
Not recorded BEN BENZAMIDINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG8K, 5% benzamidine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.30 Å R-free 0.221
4YC6 CDK1/CKS1 Deposited 2015-02-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–79（79 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.3；277 K；16-18% PEG 10 000, 0.1M imidazole pH 8.2 -8.4
Resolution 2.60 Å R-free 0.267
4YC6 CDK1/CKS1 Deposited 2015-02-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–79（79 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.3；277 K；16-18% PEG 10 000, 0.1M imidazole pH 8.2 -8.4
Resolution 2.60 Å R-free 0.267
4YC6 CDK1/CKS1 Deposited 2015-02-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–79（79 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.3；277 K；16-18% PEG 10 000, 0.1M imidazole pH 8.2 -8.4
Resolution 2.60 Å R-free 0.267
4YC6 CDK1/CKS1 Deposited 2015-02-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–79（79 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 8.3；277 K；16-18% PEG 10 000, 0.1M imidazole pH 8.2 -8.4
Resolution 2.60 Å R-free 0.267
7B5L Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27-UBE2L3~Ub~ARIH1. Transition State 1 Deposited 2020-12-04 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain K 1–73（73 aa）
Not recorded ZN ZINC ION × 9 SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7B5M Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1. Transition State 2 Deposited 2020-12-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain K 1–79（79 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.91 Å
7B5R Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27 Deposited 2020-12-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain K 1–79（79 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7NJ0 CryoEM structure of the human Separase-Cdk1-cyclin B1-Cks1 complex Deposited 2021-02-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–79（79 aa）
Not recorded PO4 PHOSPHATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8BYA Cryo-EM structure of SKP1-SKP2-CKS1-CDK2-CyclinA-p27KIP1 Complex Deposited 2022-12-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain F 1–79（79 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å
8BYL Cryo-EM structure of SKP1-SKP2-CKS1 from the SCFSKP2 E3 ligase complex Deposited 2022-12-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–79（79 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8OR0 CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2 Deposited 2023-04-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain G 1–73（73 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8OR4 Partially dissociated CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2 Deposited 2023-04-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain G 5–73（69 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9QO2 Dissociation-state-1 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain N 1–79（79 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9QO3 Dissociation-state-2 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: 13-meric
Chain N 1–79（79 aa）
Not recorded ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
9QO4 Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain N 1–79（79 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9QO5 Dissociation-state-4 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain N 1–79（79 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å

18 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CKS1_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain N； PDBConstruct 1–79； UniProt 1–79

COP9 signalosome complex subunit 9

Homo sapiens

UniProt Q8WXC6

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 × 15 PDB declaration: 15-meric（15） Consistent with protein copy count Chain P； UniProt 1–57 Not recorded COP9 signalosome complex subunit 4 × 1 （Q9BT78） COP9 signalosome complex subunit 7b × 1 （Q9H9Q2） NEDD8 × 1 （Q15843） Cyclin-dependent kinases regulatory subunit 1 × 1 （P61024） COP9 signalosome complex subunit 1 × 1 （Q13098） COP9 signalosome complex subunit 2 × 1 （P61201） COP9 signalosome complex subunit 3 × 1 （Q9UNS2） COP9 signalosome complex subunit 5 × 1 （Q92905） COP9 signalosome complex subunit 6 × 1 （Q7L5N1） COP9 signalosome complex subunit 8 × 1 （Q99627） Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） S-phase kinase-associated protein 1 × 1 （P63208） S-phase kinase-associated protein 2 × 1 （Q13309） IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.26 Å

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 9QO0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
9QO1 Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure Deposited 2025-03-25 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain P 1–57（57 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
9QO2 Dissociation-state-1 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain P 1–57（57 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9QO3 Dissociation-state-2 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: 13-meric
Chain P 1–57（57 aa）
Not recorded ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
9QO4 Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain P 1–57（57 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9QO5 Dissociation-state-4 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain P 1–57（57 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9QO6 9-subunit COP9 signalosome complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain P 1–57（57 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CSN9_HUMAN
Isoform —
PDB entities 5
Chains and sequence ranges Author chain P； PDBConstruct 1–57； UniProt 1–57

COP9 signalosome complex subunit 1

Homo sapiens

UniProt Q13098

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 × 15 PDB declaration: 15-meric（15） Consistent with protein copy count Chain A； UniProt 1–491 Not recorded COP9 signalosome complex subunit 4 × 1 （Q9BT78） COP9 signalosome complex subunit 7b × 1 （Q9H9Q2） NEDD8 × 1 （Q15843） Cyclin-dependent kinases regulatory subunit 1 × 1 （P61024） COP9 signalosome complex subunit 9 × 1 （Q8WXC6） COP9 signalosome complex subunit 2 × 1 （P61201） COP9 signalosome complex subunit 3 × 1 （Q9UNS2） COP9 signalosome complex subunit 5 × 1 （Q92905） COP9 signalosome complex subunit 6 × 1 （Q7L5N1） COP9 signalosome complex subunit 8 × 1 （Q99627） Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） S-phase kinase-associated protein 1 × 1 （P63208） S-phase kinase-associated protein 2 × 1 （Q13309） IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.26 Å

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 9QO0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4D10 Crystal structure of the COP9 signalosome Deposited 2014-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain I 12–487（476 aa） Fragment：RESIDUES 52-527
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4, 10 MM UREA.
Resolution 3.80 Å R-free 0.228
4D10 Crystal structure of the COP9 signalosome Deposited 2014-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 12–487（476 aa） Fragment：RESIDUES 52-527
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4, 10 MM UREA.
Resolution 3.80 Å R-free 0.228
4D18 Crystal structure of the COP9 signalosome Deposited 2014-05-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 52–527（476 aa） Fragment：RESIDUES 52-527
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTAL GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4. CRYSTAL DEHYDRATED OVERNIGHT WITH 20% PEG 6000 IN WELL
Resolution 4.08 Å R-free 0.253
4D18 Crystal structure of the COP9 signalosome Deposited 2014-05-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain I 52–527（476 aa） Fragment：RESIDUES 52-527
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTAL GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4. CRYSTAL DEHYDRATED OVERNIGHT WITH 20% PEG 6000 IN WELL
Resolution 4.08 Å R-free 0.253
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 52–527（476 aa） Fragment：UNP residues 52-527
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain I 52–527（476 aa） Fragment：UNP residues 52-527
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain Q 52–527（476 aa） Fragment：UNP residues 52-527
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain Y 52–527（476 aa） Fragment：UNP residues 52-527
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain g 52–527（476 aa） Fragment：UNP residues 52-527
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain o 52–527（476 aa） Fragment：UNP residues 52-527
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
6R6H Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain A 1–491（491 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5 100 mM NaCl 0.5 mM DTT 1% glycerol
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 8.40 Å
6R7F Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain A 37–469（433 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCL 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.20 Å
6R7H Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 37–469（433 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCl 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.80 Å
6R7I Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain A 37–491（455 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
6R7N Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain A 1–491（491 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCl 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.50 Å
8H38 Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(mutate) complex Deposited 2022-10-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain A 12–491（480 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
Resolution 4.25 Å
8H3A Cryo-EM Structure of the KBTBD2-CRL3~N8(removed)-CSN complex Deposited 2022-10-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 12–491（480 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.51 Å
8H3F Cryo-EM Structure of the KBTBD2-CRL3-CSN complex Deposited 2022-10-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 12–491（480 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.73 Å
9E5Z Cryo-EM structure of COP9 signalosome Deposited 2024-10-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–491（491 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9E77 Cryo-EM structure of CSN-N8 in complex with CSN5i-3 Deposited 2024-11-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 1–491（491 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9E81 Cryo-EM structure of COP9 signalosome in complex with CSN5i-3 Deposited 2024-11-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–491（491 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9EFM Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-1 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain A 1–491（491 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9EFQ Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-2 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain A 1–491（491 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.96 Å
9EFV Cryo-EM structure of CSN-N8CUL1 in complex with CSN5i-3 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain A 1–491（491 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
9EG1 COP9 signalosome deneddylation complex with cullin-5 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain A 1–491（491 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.52 Å
9EG8 Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-4A Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain A 1–491（491 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9EGL Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-3 Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain A 1–491（491 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
9PH4 Cryo-EM structure of COP9 signalosome in complex with CSN5i-1a Deposited 2025-07-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–491（491 aa）
Not recorded ZN ZINC ION × 1 A1CH3 6-[(4R,5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-carbonitrile × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9QO1 Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure Deposited 2025-03-25 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain A 1–491（491 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
9QO2 Dissociation-state-1 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain A 1–491（491 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9QO3 Dissociation-state-2 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: 13-meric
Chain A 1–491（491 aa）
Not recorded ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
9QO4 Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain A 1–491（491 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9QO5 Dissociation-state-4 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain A 1–491（491 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9QO6 9-subunit COP9 signalosome complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 1–491（491 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

27 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CSN1_HUMAN
Isoform —
PDB entities 6
Chains and sequence ranges Author chain A； PDBConstruct 1–491； UniProt 1–491

COP9 signalosome complex subunit 2

Homo sapiens

UniProt P61201

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 × 15 PDB declaration: 15-meric（15） Consistent with protein copy count Chain B； UniProt 1–443 Not recorded COP9 signalosome complex subunit 4 × 1 （Q9BT78） COP9 signalosome complex subunit 7b × 1 （Q9H9Q2） NEDD8 × 1 （Q15843） Cyclin-dependent kinases regulatory subunit 1 × 1 （P61024） COP9 signalosome complex subunit 9 × 1 （Q8WXC6） COP9 signalosome complex subunit 1 × 1 （Q13098） COP9 signalosome complex subunit 3 × 1 （Q9UNS2） COP9 signalosome complex subunit 5 × 1 （Q92905） COP9 signalosome complex subunit 6 × 1 （Q7L5N1） COP9 signalosome complex subunit 8 × 1 （Q99627） Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） S-phase kinase-associated protein 1 × 1 （P63208） S-phase kinase-associated protein 2 × 1 （Q13309） IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.26 Å

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 9QO0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4D10 Crystal structure of the COP9 signalosome Deposited 2014-04-30 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 J 1–443（443 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4, 10 MM UREA.
Resolution 3.80 Å R-free 0.228
4D10 Crystal structure of the COP9 signalosome Deposited 2014-04-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–443（443 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4, 10 MM UREA.
Resolution 3.80 Å R-free 0.228
4D18 Crystal structure of the COP9 signalosome Deposited 2014-05-01 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–443（443 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTAL GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4. CRYSTAL DEHYDRATED OVERNIGHT WITH 20% PEG 6000 IN WELL
Resolution 4.08 Å R-free 0.253
4D18 Crystal structure of the COP9 signalosome Deposited 2014-05-01 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain J 1–443（443 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTAL GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4. CRYSTAL DEHYDRATED OVERNIGHT WITH 20% PEG 6000 IN WELL
Resolution 4.08 Å R-free 0.253
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–443（443 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain J 1–443（443 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain R 1–443（443 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain Z 1–443（443 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain h 1–443（443 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain p 1–443（443 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
6A73 Complex structure of CSN2 with IP6 Deposited 2018-07-02 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 Monomer；Protein × 1 PDB declaration: monomeric
Chain A 29–162（134 aa）
Mutation：C54T, C97A IHP INOSITOL HEXAKISPHOSPHATE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium sulfate ,100mM Bis-Tris pH 5.5, 25%PEG 3350.
Resolution 2.45 Å R-free 0.288
6A73 Complex structure of CSN2 with IP6 Deposited 2018-07-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain B 29–162（134 aa）
Mutation：C54T, C97A IHP INOSITOL HEXAKISPHOSPHATE × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M ammonium sulfate ,100mM Bis-Tris pH 5.5, 25%PEG 3350.
Resolution 2.45 Å R-free 0.288
6R6H Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain B 1–443（443 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5 100 mM NaCl 0.5 mM DTT 1% glycerol
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 8.40 Å
6R7F Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain B 1–443（443 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCL 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.20 Å
6R7H Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 30–443（414 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCl 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.80 Å
6R7I Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain B 1–443（443 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
6R7N Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 1–443（443 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCl 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.50 Å
8H38 Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(mutate) complex Deposited 2022-10-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain B 1–443（443 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
Resolution 4.25 Å
8H3A Cryo-EM Structure of the KBTBD2-CRL3~N8(removed)-CSN complex Deposited 2022-10-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 1–443（443 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.51 Å
8H3F Cryo-EM Structure of the KBTBD2-CRL3-CSN complex Deposited 2022-10-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 1–443（443 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.73 Å
9E5Z Cryo-EM structure of COP9 signalosome Deposited 2024-10-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–443（443 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9E77 Cryo-EM structure of CSN-N8 in complex with CSN5i-3 Deposited 2024-11-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain B 1–443（443 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9E81 Cryo-EM structure of COP9 signalosome in complex with CSN5i-3 Deposited 2024-11-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–443（443 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9EFM Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-1 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain B 1–443（443 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9EFQ Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-2 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain B 1–443（443 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.96 Å
9EFV Cryo-EM structure of CSN-N8CUL1 in complex with CSN5i-3 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain B 1–443（443 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
9EG1 COP9 signalosome deneddylation complex with cullin-5 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain B 1–443（443 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.52 Å
9EG8 Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-4A Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain B 1–443（443 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9EGL Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-3 Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain B 1–443（443 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
9PH4 Cryo-EM structure of COP9 signalosome in complex with CSN5i-1a Deposited 2025-07-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 1–443（443 aa）
Not recorded ZN ZINC ION × 1 A1CH3 6-[(4R,5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-carbonitrile × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9QO1 Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure Deposited 2025-03-25 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain B 1–443（443 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
9QO2 Dissociation-state-1 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain B 1–443（443 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9QO3 Dissociation-state-2 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: 13-meric
Chain B 1–443（443 aa）
Not recorded ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
9QO4 Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain B 1–443（443 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9QO5 Dissociation-state-4 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain B 1–443（443 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9QO6 9-subunit COP9 signalosome complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain B 1–443（443 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

28 other PDB entries and 36 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CSN2_HUMAN
Isoform —
PDB entities 7
Chains and sequence ranges Author chain B； PDBConstruct 1–443； UniProt 1–443

COP9 signalosome complex subunit 3

Homo sapiens

UniProt Q9UNS2

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 × 15 PDB declaration: 15-meric（15） Consistent with protein copy count Chain C； UniProt 1–423 Not recorded COP9 signalosome complex subunit 4 × 1 （Q9BT78） COP9 signalosome complex subunit 7b × 1 （Q9H9Q2） NEDD8 × 1 （Q15843） Cyclin-dependent kinases regulatory subunit 1 × 1 （P61024） COP9 signalosome complex subunit 9 × 1 （Q8WXC6） COP9 signalosome complex subunit 1 × 1 （Q13098） COP9 signalosome complex subunit 2 × 1 （P61201） COP9 signalosome complex subunit 5 × 1 （Q92905） COP9 signalosome complex subunit 6 × 1 （Q7L5N1） COP9 signalosome complex subunit 8 × 1 （Q99627） Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） S-phase kinase-associated protein 1 × 1 （P63208） S-phase kinase-associated protein 2 × 1 （Q13309） IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.26 Å

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 9QO0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4D10 Crystal structure of the COP9 signalosome Deposited 2014-04-30 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 K 1–423（423 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4, 10 MM UREA.
Resolution 3.80 Å R-free 0.228
4D10 Crystal structure of the COP9 signalosome Deposited 2014-04-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 1–423（423 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4, 10 MM UREA.
Resolution 3.80 Å R-free 0.228
4D18 Crystal structure of the COP9 signalosome Deposited 2014-05-01 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 1–423（423 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTAL GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4. CRYSTAL DEHYDRATED OVERNIGHT WITH 20% PEG 6000 IN WELL
Resolution 4.08 Å R-free 0.253
4D18 Crystal structure of the COP9 signalosome Deposited 2014-05-01 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain K 1–423（423 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTAL GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4. CRYSTAL DEHYDRATED OVERNIGHT WITH 20% PEG 6000 IN WELL
Resolution 4.08 Å R-free 0.253
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 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 1–423（423 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain K 1–423（423 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain S 1–423（423 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain a 1–423（423 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain i 1–423（423 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain q 1–423（423 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
6R6H Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain C 1–383（383 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5 100 mM NaCl 0.5 mM DTT 1% glycerol
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 8.40 Å
6R7F Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain C 1–403（403 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCL 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.20 Å
6R7H Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 1–403（403 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCl 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.80 Å
6R7I Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain C 3–403（401 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
6R7N Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain C 3–403（401 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCl 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.50 Å
8H38 Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(mutate) complex Deposited 2022-10-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain C 1–423（423 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
Resolution 4.25 Å
8H3A Cryo-EM Structure of the KBTBD2-CRL3~N8(removed)-CSN complex Deposited 2022-10-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 1–423（423 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.51 Å
8H3F Cryo-EM Structure of the KBTBD2-CRL3-CSN complex Deposited 2022-10-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 1–423（423 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.73 Å
9E5Z Cryo-EM structure of COP9 signalosome Deposited 2024-10-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 1–423（423 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9E77 Cryo-EM structure of CSN-N8 in complex with CSN5i-3 Deposited 2024-11-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain C 1–423（423 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9E81 Cryo-EM structure of COP9 signalosome in complex with CSN5i-3 Deposited 2024-11-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 1–423（423 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9EFM Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-1 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain C 1–423（423 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9EFQ Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-2 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain C 1–423（423 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.96 Å
9EFV Cryo-EM structure of CSN-N8CUL1 in complex with CSN5i-3 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain C 1–423（423 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
9EG1 COP9 signalosome deneddylation complex with cullin-5 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain C 1–423（423 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.52 Å
9EG8 Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-4A Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain C 1–423（423 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9EGL Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-3 Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain C 1–423（423 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
9PH4 Cryo-EM structure of COP9 signalosome in complex with CSN5i-1a Deposited 2025-07-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 1–423（423 aa）
Not recorded ZN ZINC ION × 1 A1CH3 6-[(4R,5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-carbonitrile × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9QO1 Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure Deposited 2025-03-25 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain C 1–423（423 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
9QO2 Dissociation-state-1 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain C 1–423（423 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9QO3 Dissociation-state-2 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: 13-meric
Chain C 1–423（423 aa）
Not recorded ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
9QO4 Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain C 1–423（423 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9QO5 Dissociation-state-4 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain C 1–423（423 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9QO6 9-subunit COP9 signalosome complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain C 1–423（423 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

27 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CSN3_HUMAN
Isoform —
PDB entities 8
Chains and sequence ranges Author chain C； PDBConstruct 1–423； UniProt 1–423

COP9 signalosome complex subunit 5

Homo sapiens

UniProt Q92905

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 × 15 PDB declaration: 15-meric（15） Consistent with protein copy count Chain E； UniProt 1–334 Not recorded COP9 signalosome complex subunit 4 × 1 （Q9BT78） COP9 signalosome complex subunit 7b × 1 （Q9H9Q2） NEDD8 × 1 （Q15843） Cyclin-dependent kinases regulatory subunit 1 × 1 （P61024） COP9 signalosome complex subunit 9 × 1 （Q8WXC6） COP9 signalosome complex subunit 1 × 1 （Q13098） COP9 signalosome complex subunit 2 × 1 （P61201） COP9 signalosome complex subunit 3 × 1 （Q9UNS2） COP9 signalosome complex subunit 6 × 1 （Q7L5N1） COP9 signalosome complex subunit 8 × 1 （Q99627） Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） S-phase kinase-associated protein 1 × 1 （P63208） S-phase kinase-associated protein 2 × 1 （Q13309） IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.26 Å

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 9QO0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4D10 Crystal structure of the COP9 signalosome Deposited 2014-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain M 1–334（334 aa） Fragment：RESIDUES 1-423
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4, 10 MM UREA.
Resolution 3.80 Å R-free 0.228
4D10 Crystal structure of the COP9 signalosome Deposited 2014-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 1–334（334 aa） Fragment：RESIDUES 1-423
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4, 10 MM UREA.
Resolution 3.80 Å R-free 0.228
4D18 Crystal structure of the COP9 signalosome Deposited 2014-05-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 12–334（323 aa） Fragment：RESIDUES 12-334
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTAL GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4. CRYSTAL DEHYDRATED OVERNIGHT WITH 20% PEG 6000 IN WELL
Resolution 4.08 Å R-free 0.253
4D18 Crystal structure of the COP9 signalosome Deposited 2014-05-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain M 12–334（323 aa） Fragment：RESIDUES 12-334
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTAL GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4. CRYSTAL DEHYDRATED OVERNIGHT WITH 20% PEG 6000 IN WELL
Resolution 4.08 Å R-free 0.253
4F7O Crystal structure of CSN5 Deposited 2012-05-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1–257（257 aa） Fragment：UNP residues 1-257
Chain B 1–257（257 aa） Fragment：UNP residues 1-257
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 2 SCN THIOCYANATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG3350, KSCN, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.60 Å R-free 0.274
4F7O Crystal structure of CSN5 Deposited 2012-05-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–257（257 aa） Fragment：UNP residues 1-257
Chain B 1–257（257 aa） Fragment：UNP residues 1-257
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 4 SCN THIOCYANATE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG3350, KSCN, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.60 Å R-free 0.274
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 14–334（321 aa） Fragment：UNP residues 14-334
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain M 14–334（321 aa） Fragment：UNP residues 14-334
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain U 14–334（321 aa） Fragment：UNP residues 14-334
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain c 14–334（321 aa） Fragment：UNP residues 14-334
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain k 14–334（321 aa） Fragment：UNP residues 14-334
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain s 14–334（321 aa） Fragment：UNP residues 14-334
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
5JOG CRYSTAL STRUCTURE OF CSN5(2-257) IN COMPLEX WITH CNS5i-3 Deposited 2016-05-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–257（256 aa）
Not recorded ZN ZINC ION × 1 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；Protein solution: 18.9 mg/ml protein in 50mM NaCl, 50mM Mes/NaOH pH 6.0, 10uM ZnCl2, 0.5 mM TCEP with 1mM compound Crystallization solution: 35% MPD, 0.1M MES/NaOH pH 6.0, 0.2 M Li2SO4
Resolution 2.46 Å R-free 0.243
5JOH CRYSTAL STRUCTURE OF CSN5(2-257) IN COMPLEX WITH CNS5i-1b Deposited 2016-05-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–257（256 aa）
Not recorded ZN ZINC ION × 1 6M3 2'-chloro-6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-carbonitrile × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；Protein solution: 15 mg/ml CSN5 in 50mM NaCl, 50mM Mes/NaOH pH 6.0, 10uM ZnCl2, 0.5 mM TCEP with 1mM ligand Crystallization solution: 35% MPD, 0.2M LiSO4, 0.1 M MES/NaOH pH 6.0
Resolution 1.99 Å R-free 0.248
5M5Q COPS5(2-257) IN COMPLEX WITH A AZAINDOLE (COMPOUND 4) Deposited 2016-10-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–257（256 aa） Fragment：UNP residues 2-257
Not recorded ZN ZINC ION × 1 7K1 1-[(3~{R})-3-(1~{H}-benzimidazol-2-yl)morpholin-4-yl]-3-[2-(4-methyl-2-phenyl-phenyl)-1~{H}-pyrrolo[2,3-b]pyridin-3-yl]propan-1-one × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；277 K；35% MPD, 0.2M LiSO4, 0,1 M Mes pH 6.0
Resolution 2.20 Å R-free 0.219
6R6H Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5 100 mM NaCl 0.5 mM DTT 1% glycerol
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 8.40 Å
6R7F Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain E 24–334（311 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCL 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.20 Å
6R7H Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain E 24–334（311 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCl 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.80 Å
6R7I Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
8H38 Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(mutate) complex Deposited 2022-10-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain E 1–334（334 aa）
Mutation：H138A ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
Resolution 4.25 Å
8H3A Cryo-EM Structure of the KBTBD2-CRL3~N8(removed)-CSN complex Deposited 2022-10-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.51 Å
8H3F Cryo-EM Structure of the KBTBD2-CRL3-CSN complex Deposited 2022-10-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.73 Å
9E5Z Cryo-EM structure of COP9 signalosome Deposited 2024-10-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9E77 Cryo-EM structure of CSN-N8 in complex with CSN5i-3 Deposited 2024-11-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain E 1–334（334 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9E81 Cryo-EM structure of COP9 signalosome in complex with CSN5i-3 Deposited 2024-11-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 1–334（334 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9EFM Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-1 Deposited 2024-11-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain E 1–334（334 aa）
Mutation：E76A , D151N ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9EFQ Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-2 Deposited 2024-11-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain E 1–334（334 aa）
Mutation：E76A , D151N ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.96 Å
9EFV Cryo-EM structure of CSN-N8CUL1 in complex with CSN5i-3 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain E 1–334（334 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
9EG1 COP9 signalosome deneddylation complex with cullin-5 Deposited 2024-11-20 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain E 1–334（334 aa）
Mutation：E76A, D151N ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.52 Å
9EG8 Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-4A Deposited 2024-11-21 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain E 1–334（334 aa）
Mutation：E76A, D151N ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9EGL Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-3 Deposited 2024-11-21 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain E 1–334（334 aa）
Mutation：E76A, D151N ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
9PH4 Cryo-EM structure of COP9 signalosome in complex with CSN5i-1a Deposited 2025-07-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 1 A1CH3 6-[(4R,5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-carbonitrile × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9QO1 Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure Deposited 2025-03-25 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain E 1–334（334 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
9QO2 Dissociation-state-1 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain E 1–334（334 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9QO3 Dissociation-state-2 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: 13-meric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
9QO4 Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain E 1–334（334 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9QO5 Dissociation-state-4 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain E 1–334（334 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9QO6 9-subunit COP9 signalosome complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain E 1–334（334 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

30 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CSN5_HUMAN
Isoform —
PDB entities 9
Chains and sequence ranges Author chain E； PDBConstruct 1–334； UniProt 1–334

COP9 signalosome complex subunit 6

Homo sapiens

UniProt Q7L5N1

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 × 15 PDB declaration: 15-meric（15） Consistent with protein copy count Chain F； UniProt 1–327 Not recorded COP9 signalosome complex subunit 4 × 1 （Q9BT78） COP9 signalosome complex subunit 7b × 1 （Q9H9Q2） NEDD8 × 1 （Q15843） Cyclin-dependent kinases regulatory subunit 1 × 1 （P61024） COP9 signalosome complex subunit 9 × 1 （Q8WXC6） COP9 signalosome complex subunit 1 × 1 （Q13098） COP9 signalosome complex subunit 2 × 1 （P61201） COP9 signalosome complex subunit 3 × 1 （Q9UNS2） COP9 signalosome complex subunit 5 × 1 （Q92905） COP9 signalosome complex subunit 8 × 1 （Q99627） Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） S-phase kinase-associated protein 1 × 1 （P63208） S-phase kinase-associated protein 2 × 1 （Q13309） IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.26 Å

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 9QO0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4D10 Crystal structure of the COP9 signalosome Deposited 2014-04-30 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 N 1–327（327 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4, 10 MM UREA.
Resolution 3.80 Å R-free 0.228
4D10 Crystal structure of the COP9 signalosome Deposited 2014-04-30 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–327（327 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4, 10 MM UREA.
Resolution 3.80 Å R-free 0.228
4D18 Crystal structure of the COP9 signalosome Deposited 2014-05-01 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 F 1–327（327 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTAL GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4. CRYSTAL DEHYDRATED OVERNIGHT WITH 20% PEG 6000 IN WELL
Resolution 4.08 Å R-free 0.253
4D18 Crystal structure of the COP9 signalosome Deposited 2014-05-01 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain N 1–327（327 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTAL GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4. CRYSTAL DEHYDRATED OVERNIGHT WITH 20% PEG 6000 IN WELL
Resolution 4.08 Å R-free 0.253
4QFT Structure of COP9 signalosome complex subunit 6 Deposited 2014-05-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 31–211（181 aa） Fragment：unp residues 31-211
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.2 M Tri-Sodium citrate, 0.1 M Bis-Tris propane, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.76 Å R-free 0.206
4QFT Structure of COP9 signalosome complex subunit 6 Deposited 2014-05-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 31–211（181 aa） Fragment：unp residues 31-211
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；298 K；0.2 M Tri-Sodium citrate, 0.1 M Bis-Tris propane, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Resolution 1.76 Å R-free 0.206
4R14 Crystal structure of human CSN6 MPN domain Deposited 2014-08-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 38–210（173 aa） Fragment：MPN domain, UNP residues 38-210
Chain B 38–210（173 aa） Fragment：MPN domain, UNP residues 38-210
Not recorded HG MERCURY (II) ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.7；289 K；0.1M Tris pH 7.7, 26% (w/v) PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Resolution 2.60 Å R-free 0.259
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 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 F 1–327（327 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain N 1–327（327 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain V 1–327（327 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain d 1–327（327 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain l 1–327（327 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain t 1–327（327 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
6R6H Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain F 20–327（308 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5 100 mM NaCl 0.5 mM DTT 1% glycerol
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 8.40 Å
6R7F Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain F 29–316（288 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCL 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.20 Å
6R7H Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 29–316（288 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCl 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.80 Å
6R7I Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain F 1–327（327 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
8H38 Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(mutate) complex Deposited 2022-10-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain F 1–327（327 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
Resolution 4.25 Å
8H3A Cryo-EM Structure of the KBTBD2-CRL3~N8(removed)-CSN complex Deposited 2022-10-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 1–327（327 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.51 Å
8H3F Cryo-EM Structure of the KBTBD2-CRL3-CSN complex Deposited 2022-10-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 1–327（327 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.73 Å
9E5Z Cryo-EM structure of COP9 signalosome Deposited 2024-10-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–327（327 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9E77 Cryo-EM structure of CSN-N8 in complex with CSN5i-3 Deposited 2024-11-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain F 1–327（327 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9E81 Cryo-EM structure of COP9 signalosome in complex with CSN5i-3 Deposited 2024-11-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–327（327 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9EFM Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-1 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain F 1–327（327 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9EFQ Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-2 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain F 1–327（327 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.96 Å
9EFV Cryo-EM structure of CSN-N8CUL1 in complex with CSN5i-3 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain F 1–327（327 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
9EG1 COP9 signalosome deneddylation complex with cullin-5 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain F 1–327（327 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.52 Å
9EG8 Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-4A Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain F 1–327（327 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9EGL Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-3 Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain F 1–327（327 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
9PH4 Cryo-EM structure of COP9 signalosome in complex with CSN5i-1a Deposited 2025-07-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain F 1–327（327 aa）
Not recorded ZN ZINC ION × 1 A1CH3 6-[(4R,5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-carbonitrile × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9QO1 Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure Deposited 2025-03-25 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain F 1–327（327 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
9QO2 Dissociation-state-1 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain F 1–327（327 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9QO3 Dissociation-state-2 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: 13-meric
Chain F 1–327（327 aa）
Not recorded ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
9QO4 Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain F 1–327（327 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9QO5 Dissociation-state-4 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain F 1–327（327 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9QO6 9-subunit COP9 signalosome complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain F 1–327（327 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

28 other PDB entries and 36 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CSN6_HUMAN
Isoform —
PDB entities 10
Chains and sequence ranges Author chain F； PDBConstruct 1–327； UniProt 1–327

COP9 signalosome complex subunit 8

Homo sapiens

UniProt Q99627

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 × 15 PDB declaration: 15-meric（15） Consistent with protein copy count Chain H； UniProt 1–209 Not recorded COP9 signalosome complex subunit 4 × 1 （Q9BT78） COP9 signalosome complex subunit 7b × 1 （Q9H9Q2） NEDD8 × 1 （Q15843） Cyclin-dependent kinases regulatory subunit 1 × 1 （P61024） COP9 signalosome complex subunit 9 × 1 （Q8WXC6） COP9 signalosome complex subunit 1 × 1 （Q13098） COP9 signalosome complex subunit 2 × 1 （P61201） COP9 signalosome complex subunit 3 × 1 （Q9UNS2） COP9 signalosome complex subunit 5 × 1 （Q92905） COP9 signalosome complex subunit 6 × 1 （Q7L5N1） Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） S-phase kinase-associated protein 1 × 1 （P63208） S-phase kinase-associated protein 2 × 1 （Q13309） IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.26 Å

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 9QO0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4D10 Crystal structure of the COP9 signalosome Deposited 2014-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain P 2–209（208 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4, 10 MM UREA.
Resolution 3.80 Å R-free 0.228
4D10 Crystal structure of the COP9 signalosome Deposited 2014-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain H 2–209（208 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4, 10 MM UREA.
Resolution 3.80 Å R-free 0.228
4D18 Crystal structure of the COP9 signalosome Deposited 2014-05-01 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 H 1–209（209 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTAL GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4. CRYSTAL DEHYDRATED OVERNIGHT WITH 20% PEG 6000 IN WELL
Resolution 4.08 Å R-free 0.253
4D18 Crystal structure of the COP9 signalosome Deposited 2014-05-01 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain P 1–209（209 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 5.4；CRYSTAL GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4. CRYSTAL DEHYDRATED OVERNIGHT WITH 20% PEG 6000 IN WELL
Resolution 4.08 Å R-free 0.253
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 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 H 1–209（209 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain P 1–209（209 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain X 1–209（209 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain f 1–209（209 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain n 1–209（209 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain v 1–209（209 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；273 K；CRYSTALS GROWN BY VAPOR DIFFUSION BY MIXING 9.3 MG/ML PROTEIN IN 50 MM HEPES PH 7.4, 200 MM NACL, 2 MM EQUALLY WITH 12% PEG 6000, 100 MM TRISODIUM CITRATE PH 5.4, 0.1 M LI2SO4.
Resolution 5.50 Å R-free 0.282
6R6H Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain H 1–209（209 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5 100 mM NaCl 0.5 mM DTT 1% glycerol
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 8.40 Å
6R7F Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain H 1–209（209 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCL 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.20 Å
6R7H Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain H 11–209（199 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCl 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.80 Å
6R7I Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain H 1–209（209 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
6R7N Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain H 11–209（199 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCl 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.50 Å
8H38 Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(mutate) complex Deposited 2022-10-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain H 1–209（209 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
Resolution 4.25 Å
8H3A Cryo-EM Structure of the KBTBD2-CRL3~N8(removed)-CSN complex Deposited 2022-10-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain H 1–209（209 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.51 Å
8H3F Cryo-EM Structure of the KBTBD2-CRL3-CSN complex Deposited 2022-10-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain H 1–209（209 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.73 Å
9E5Z Cryo-EM structure of COP9 signalosome Deposited 2024-10-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain H 1–209（209 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9E77 Cryo-EM structure of CSN-N8 in complex with CSN5i-3 Deposited 2024-11-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain H 1–209（209 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9E81 Cryo-EM structure of COP9 signalosome in complex with CSN5i-3 Deposited 2024-11-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain H 1–209（209 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9EFM Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-1 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain H 1–209（209 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9EFQ Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-2 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain H 1–209（209 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.96 Å
9EFV Cryo-EM structure of CSN-N8CUL1 in complex with CSN5i-3 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain H 1–209（209 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
9EG1 COP9 signalosome deneddylation complex with cullin-5 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain H 1–209（209 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.52 Å
9EG8 Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-4A Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain H 1–209（209 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9EGL Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-3 Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain H 1–209（209 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
9PH4 Cryo-EM structure of COP9 signalosome in complex with CSN5i-1a Deposited 2025-07-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain H 1–209（209 aa）
Not recorded ZN ZINC ION × 1 A1CH3 6-[(4R,5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-carbonitrile × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
9QO1 Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure Deposited 2025-03-25 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain H 1–209（209 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
9QO2 Dissociation-state-1 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain H 1–209（209 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9QO3 Dissociation-state-2 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: 13-meric
Chain H 1–209（209 aa）
Not recorded ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
9QO4 Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain H 1–209（209 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9QO5 Dissociation-state-4 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain H 1–209（209 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9QO6 9-subunit COP9 signalosome complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain H 1–209（209 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

27 other PDB entries and 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CSN8_HUMAN
Isoform —
PDB entities 11
Chains and sequence ranges Author chain H； PDBConstruct 1–209； UniProt 1–209

Cullin-1

Homo sapiens

UniProt Q13616

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 × 15 PDB declaration: 15-meric（15） Consistent with protein copy count Chain I； UniProt 1–776 Not recorded COP9 signalosome complex subunit 4 × 1 （Q9BT78） COP9 signalosome complex subunit 7b × 1 （Q9H9Q2） NEDD8 × 1 （Q15843） Cyclin-dependent kinases regulatory subunit 1 × 1 （P61024） COP9 signalosome complex subunit 9 × 1 （Q8WXC6） COP9 signalosome complex subunit 1 × 1 （Q13098） COP9 signalosome complex subunit 2 × 1 （P61201） COP9 signalosome complex subunit 3 × 1 （Q9UNS2） COP9 signalosome complex subunit 5 × 1 （Q92905） COP9 signalosome complex subunit 6 × 1 （Q7L5N1） COP9 signalosome complex subunit 8 × 1 （Q99627） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） S-phase kinase-associated protein 1 × 1 （P63208） S-phase kinase-associated protein 2 × 1 （Q13309） IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.26 Å

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 9QO0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1LDJ Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex Deposited 2002-04-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 17–776（760 aa） Fragment：Residues 17-776
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；10% Ethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.288
1LDK Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex Deposited 2002-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 15–410（396 aa） Fragment：RESIDUES 15-410
Chain B 411–776（366 aa） Fragment：RESIDUES 411-776
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；peg4k, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.331
1LDK Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex Deposited 2002-04-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain A 15–410（396 aa） Fragment：RESIDUES 15-410
Chain B 411–776（366 aa） Fragment：RESIDUES 411-776
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；peg4k, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.331
1U6G Crystal Structure of The Cand1-Cul1-Roc1 Complex Deposited 2004-07-29 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–776（776 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；PEG 8000, sodium chloride, DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.317
29HG Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO22 SCF ubiquition ligase in complex with NSD2 via UNC10088 Deposited 2026-03-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–776（776 aa）
Not recorded A1J20 ~{N}-cyclopropyl-~{N}-[[4-[[2-(6-oxidanylhexanoyl)-1~{H}-isoquinolin-6-yl]carbamoyl]phenyl]methyl]-3-oxidanylidene-4~{H}-1,4-benzoxazine-7-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
29HH Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO22 SCF ubiquition ligase in complex with NSD2, UNC10088 and Bach1 Deposited 2026-03-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 1–776（776 aa）
Not recorded A1J20 ~{N}-cyclopropyl-~{N}-[[4-[[2-(6-oxidanylhexanoyl)-1~{H}-isoquinolin-6-yl]carbamoyl]phenyl]methyl]-3-oxidanylidene-4~{H}-1,4-benzoxazine-7-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
29HI Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO22 SCF ubiquition ligase in complex with NSD2 via UNC10415667 Deposited 2026-03-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–776（776 aa）
Not recorded A1J21 4-[[cyclopropyl-[(~{Z})-2-methyl-4-(5-oxidanylidene-2~{H}-1,4-oxazin-3-yl)but-3-enoyl]amino]methyl]-~{N}-[3-[2-[[4-(hydroxymethyl)phenyl]carbonyl-methyl-amino]ethyl]phenyl]benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
3RTR A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases Deposited 2011-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 411–776（366 aa） Fragment：UNP residues 411-776
Mutation：L421E, V451E, V452K, Y455K ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；17% PEG 3350, 100 mM Tris pH 7.5, 200 mM Sodium/Postassium Tartrate, 2% Benzamidine Hydrochloride, 1% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.21 Å R-free 0.282
3RTR A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases Deposited 2011-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 411–776（366 aa） Fragment：UNP residues 411-776
Mutation：L421E, V451E, V452K, Y455K ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；17% PEG 3350, 100 mM Tris pH 7.5, 200 mM Sodium/Postassium Tartrate, 2% Benzamidine Hydrochloride, 1% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.21 Å R-free 0.282
3RTR A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases Deposited 2011-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 411–776（366 aa） Fragment：UNP residues 411-776
Mutation：L421E, V451E, V452K, Y455K ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；17% PEG 3350, 100 mM Tris pH 7.5, 200 mM Sodium/Postassium Tartrate, 2% Benzamidine Hydrochloride, 1% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.21 Å R-free 0.282
3RTR A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases Deposited 2011-05-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 411–776（366 aa） Fragment：UNP residues 411-776
Mutation：L421E, V451E, V452K, Y455K ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；17% PEG 3350, 100 mM Tris pH 7.5, 200 mM Sodium/Postassium Tartrate, 2% Benzamidine Hydrochloride, 1% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.21 Å R-free 0.282
3TDU N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex: Structure of a human Cul1WHB-Dcn1P-acetylated Ubc12N complex Deposited 2011-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 702–776（75 aa） Fragment：unp residues 702-776
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；276 K；27% PEG1500, 0.1M MIB, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 276K
Resolution 1.50 Å R-free 0.232
3TDU N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex: Structure of a human Cul1WHB-Dcn1P-acetylated Ubc12N complex Deposited 2011-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 702–776（75 aa） Fragment：unp residues 702-776
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4；276 K；27% PEG1500, 0.1M MIB, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 276K
Resolution 1.50 Å R-free 0.232
3TDZ N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex: Structure of a human Cul1WHB-Dcn1P-stapled acetylated Ubc12N complex Deposited 2011-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 702–776（75 aa） Fragment：unp residues 702-776
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；21% PEG3350, 0.2M KCl, pH Unbuffered, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.00 Å R-free 0.224
3TDZ N-terminal acetylation acts as an avidity enhancer within an interconnected multiprotein complex: Structure of a human Cul1WHB-Dcn1P-stapled acetylated Ubc12N complex Deposited 2011-08-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 702–776（75 aa） Fragment：unp residues 702-776
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；21% PEG3350, 0.2M KCl, pH Unbuffered, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.00 Å R-free 0.224
4F52 Structure of a Glomulin-RBX1-CUL1 complex Deposited 2012-05-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 411–690（280 aa） Fragment：C-terminal domain, delta WHB domain, UNP residues 411-690
Mutation：L421E, V451E, V452K, Y455K ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；18-21% PEG3350, 0.3-0.45M ammonium citrate, 10mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.00 Å R-free 0.289
4F52 Structure of a Glomulin-RBX1-CUL1 complex Deposited 2012-05-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 411–690（280 aa） Fragment：C-terminal domain, delta WHB domain, UNP residues 411-690
Mutation：L421E, V451E, V452K, Y455K ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；18-21% PEG3350, 0.3-0.45M ammonium citrate, 10mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.00 Å R-free 0.289
4P5O Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action Deposited 2014-03-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 411–776（366 aa）
Mutation：L421E, V451E, V452K, Y455K, K720R ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；11% PEG3350, 0.2M ammonium citrate, 10mM ATP
Resolution 3.11 Å R-free 0.284
4P5O Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action Deposited 2014-03-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 411–776（366 aa）
Mutation：L421E, V451E, V452K, Y455K, K720R ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；11% PEG3350, 0.2M ammonium citrate, 10mM ATP
Resolution 3.11 Å R-free 0.284
5V89 Structure of DCN4 PONY domain bound to CUL1 WHB Deposited 2017-03-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain C 702–776（75 aa） Fragment：WHB subdomain residues 702-776
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；25% PEG3350, 0.2M LiSO4, 10mM TCEP, 10mM Bis-Tris Propane
Resolution 1.55 Å R-free 0.194
6TTU Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 Deposited 2019-12-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 1–776（776 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.70 Å
6WCQ Structure of a substrate-bound DQC ubiquitin ligase Deposited 2020-03-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–434（434 aa） Fragment：residues 1-434
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 8.50 Å
7B5L Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27-UBE2L3~Ub~ARIH1. Transition State 1 Deposited 2020-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 1–776（776 aa）
Not recorded ZN ZINC ION × 9 SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7B5M Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1. Transition State 2 Deposited 2020-12-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 1–776（776 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.91 Å
7B5N Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1. Deposited 2020-12-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–776（776 aa）
Not recorded ZN ZINC ION × 9 SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7B5R Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27 Deposited 2020-12-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 1–776（776 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7B5S Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-ARIH1 Ariadne. Transition State 1 Deposited 2020-12-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–776（776 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7Z8R CAND1-CUL1-RBX1 Deposited 2022-03-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–776（776 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7Z8T CAND1-SCF-SKP2 CAND1 engaged SCF rocked Deposited 2022-03-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–776（776 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7Z8V CAND1-SCF-SKP2 (SKP1deldel) CAND1 engaged SCF rocked Deposited 2022-03-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–776（776 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7ZBW CAND1-SCF-SKP2 CAND1 rolling-2 SCF engaged Deposited 2022-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–776（776 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7ZBZ CAND1 delhairpin-SCF-SKP2 CAND1 partly engaged SCF partly rocked Deposited 2022-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–776（776 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8CAF N8C_Fab3b in complex with NEDD8-CUL1(WHB) Deposited 2023-01-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain H 698–776（79 aa） Fragment：UNP residues 677-776
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2.0-2.1M Ammonium Sulfate, 0.1M Citrate pH 6.0, 10mM TCEP
Resolution 2.66 Å R-free 0.263
8CAF N8C_Fab3b in complex with NEDD8-CUL1(WHB) Deposited 2023-01-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain E 698–776（79 aa） Fragment：UNP residues 677-776
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；2.0-2.1M Ammonium Sulfate, 0.1M Citrate pH 6.0, 10mM TCEP
Resolution 2.66 Å R-free 0.263
8CDJ CAND1 b-hairpin++-SCF-SKP2 CAND1 rolling SCF engaged Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–776（776 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8CDK CAND1 b-hairpin++-SCF-SKP2 CAND1 partly engaged SCF partly rocked Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–776（776 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
8OR0 CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2 Deposited 2023-04-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 1–776（776 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8OR2 CAND1-CUL1-RBX1-DCNL1 Deposited 2023-04-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–776（776 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8OR3 CAND1-CUL1-RBX1-SKP1-SKP2-DCNL1 Deposited 2023-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–776（776 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8OR4 Partially dissociated CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2 Deposited 2023-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain A 1–776（776 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8UA6 Cryo-EM Structure of SCF-FBOX22-BACH1BTB Deposited 2023-09-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 13–776（764 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8UBT Structure of SCF-FBXL17-BACH1BTB E3 ligase complex Deposited 2023-09-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 13–776（764 aa） Fragment：UNP residues 310-701
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8UBU Cryo-EM structure of dimeric SCF-FBXL17-BACH1BTB E3 ligase complex close conformation Deposited 2023-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain A 13–776（764 aa）
Chain H 13–776（764 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8VVY Human Cullin-1 in complex with CAND2 Deposited 2024-01-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 13–776（764 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.49 Å
9EFM Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-1 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain J 1–776（776 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9EFV Cryo-EM structure of CSN-N8CUL1 in complex with CSN5i-3 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain J 1–776（776 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
9JKB Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO4 SCF ubiquition ligase complex Deposited 2024-09-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain A 2–776（775 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
9KBD Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO3 SCF ubiquition ligase complex Deposited 2024-10-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–776（776 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9QO1 Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure Deposited 2025-03-25 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain I 1–776（776 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
9QO2 Dissociation-state-1 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain I 1–776（776 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9QO3 Dissociation-state-2 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: 13-meric
Chain I 1–776（776 aa）
Not recorded ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
9QO4 Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain I 1–776（776 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9QO5 Dissociation-state-4 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain I 1–776（776 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9XZJ Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex and a 3-way DNA fork (consensus structure) Deposited 2025-08-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain C 1–776（776 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
9XZK Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex and a 3-way DNA fork (head structure) Deposited 2025-08-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–776（776 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.91 Å
9XZL Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex and a 3-way DNA fork (body structure) Deposited 2025-08-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain C 1–776（776 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

47 other PDB entries and 56 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CUL1_HUMAN
Isoform —
PDB entities 12
Chains and sequence ranges Author chain I； PDBConstruct 1–776； UniProt 1–776

E3 ubiquitin-protein ligase RBX1

Homo sapiens

UniProt P62877

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 15 PDB declaration: 15-meric（15） Consistent with protein copy count Chain J； UniProt 1–108 Not recorded COP9 signalosome complex subunit 4 × 1 （Q9BT78） COP9 signalosome complex subunit 7b × 1 （Q9H9Q2） NEDD8 × 1 （Q15843） Cyclin-dependent kinases regulatory subunit 1 × 1 （P61024） COP9 signalosome complex subunit 9 × 1 （Q8WXC6） COP9 signalosome complex subunit 1 × 1 （Q13098） COP9 signalosome complex subunit 2 × 1 （P61201） COP9 signalosome complex subunit 3 × 1 （Q9UNS2） COP9 signalosome complex subunit 5 × 1 （Q92905） COP9 signalosome complex subunit 6 × 1 （Q7L5N1） COP9 signalosome complex subunit 8 × 1 （Q99627） Cullin-1 × 1 （Q13616） S-phase kinase-associated protein 1 × 1 （P63208） S-phase kinase-associated protein 2 × 1 （Q13309） IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.26 Å

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

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

View Construct and Data Evidence
UniProt name RBX1_HUMAN
Isoform —
PDB entities 13
Chains and sequence ranges Author chain J； PDBConstruct 1–108； UniProt 1–108

S-phase kinase-associated protein 1

Homo sapiens

UniProt P63208

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 × 15 PDB declaration: 15-meric（15） Consistent with protein copy count Chain L； UniProt 1–163 Not recorded COP9 signalosome complex subunit 4 × 1 （Q9BT78） COP9 signalosome complex subunit 7b × 1 （Q9H9Q2） NEDD8 × 1 （Q15843） Cyclin-dependent kinases regulatory subunit 1 × 1 （P61024） COP9 signalosome complex subunit 9 × 1 （Q8WXC6） COP9 signalosome complex subunit 1 × 1 （Q13098） COP9 signalosome complex subunit 2 × 1 （P61201） COP9 signalosome complex subunit 3 × 1 （Q9UNS2） COP9 signalosome complex subunit 5 × 1 （Q92905） COP9 signalosome complex subunit 6 × 1 （Q7L5N1） COP9 signalosome complex subunit 8 × 1 （Q99627） Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） S-phase kinase-associated protein 2 × 1 （Q13309） IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.26 Å

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 9QO0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–162（162 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.314
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 1–162（162 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.314
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 1–162（162 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.314
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 1–162（162 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.314
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain J 1–162（162 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.314
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain L 1–162（162 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.314
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain N 1–162（162 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.314
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain P 1–162（162 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.314
1FS1 INSIGHTS INTO SCF UBIQUITIN LIGASES FROM THE STRUCTURE OF THE SKP1-SKP2 COMPLEX Deposited 2000-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–147（147 aa） Fragment：RESIDUES 1-147
Chain D 1–147（147 aa） Fragment：RESIDUES 1-147
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；PEG 1500, sodium acetate, ammonium acetate, DTT, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.274
1FS2 INSIGHTS INTO SCF UBIQUITIN LIGASES FROM THE STRUCTURE OF THE SKP1-SKP2 COMPLEX Deposited 2000-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–146（146 aa） Fragment：RESIDUES 1-37; 43-147
Chain D 1–146（146 aa） Fragment：RESIDUES 1-37; 43-147
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.90 Å R-free 0.287
1LDK Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex Deposited 2002-04-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 1–139（139 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；peg4k, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.331
1LDK Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex Deposited 2002-04-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain D 1–139（139 aa）
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；peg4k, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.331
1P22 Structure of a beta-TrCP1-Skp1-beta-catenin complex: destruction motif binding and lysine specificity on the SCFbeta-TrCP1 ubiquitin ligase Deposited 2003-04-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–162（162 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.8；298 K；PEG4000, sodium citrate, Bis-Tris Propane, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 2.95 Å R-free 0.286
29HG Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO22 SCF ubiquition ligase in complex with NSD2 via UNC10088 Deposited 2026-03-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–163（163 aa）
Not recorded A1J20 ~{N}-cyclopropyl-~{N}-[[4-[[2-(6-oxidanylhexanoyl)-1~{H}-isoquinolin-6-yl]carbamoyl]phenyl]methyl]-3-oxidanylidene-4~{H}-1,4-benzoxazine-7-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
29HH Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO22 SCF ubiquition ligase in complex with NSD2, UNC10088 and Bach1 Deposited 2026-03-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain C 1–163（163 aa）
Not recorded A1J20 ~{N}-cyclopropyl-~{N}-[[4-[[2-(6-oxidanylhexanoyl)-1~{H}-isoquinolin-6-yl]carbamoyl]phenyl]methyl]-3-oxidanylidene-4~{H}-1,4-benzoxazine-7-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
29HI Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO22 SCF ubiquition ligase in complex with NSD2 via UNC10415667 Deposited 2026-03-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 1–163（163 aa）
Not recorded A1J21 4-[[cyclopropyl-[(~{Z})-2-methyl-4-(5-oxidanylidene-2~{H}-1,4-oxazin-3-yl)but-3-enoyl]amino]methyl]-~{N}-[3-[2-[[4-(hydroxymethyl)phenyl]carbonyl-methyl-amino]ethyl]phenyl]benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
2ASS Crystal structure of the Skp1-Skp2-Cks1 complex Deposited 2005-08-24 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 A 1–159（159 aa）
Mutation：P1A PO4 PHOSPHATE ION × 3 BEN BENZAMIDINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；BTP, sodium/potassium phosphate, benzamidine, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.242
2ASS Crystal structure of the Skp1-Skp2-Cks1 complex Deposited 2005-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–159（159 aa）
Mutation：P1A PO4 PHOSPHATE ION × 6 BEN BENZAMIDINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；BTP, sodium/potassium phosphate, benzamidine, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.242
2ASS Crystal structure of the Skp1-Skp2-Cks1 complex Deposited 2005-08-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–159（159 aa）
Mutation：P1A PO4 PHOSPHATE ION × 6 BEN BENZAMIDINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；BTP, sodium/potassium phosphate, benzamidine, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.242
2AST Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide Deposited 2005-08-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–159（159 aa）
Not recorded BEN BENZAMIDINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG8K, 5% benzamidine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.30 Å R-free 0.221
2AST Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide Deposited 2005-08-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–159（159 aa）
Not recorded BEN BENZAMIDINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG8K, 5% benzamidine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.30 Å R-free 0.221
2AST Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide Deposited 2005-08-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–159（159 aa）
Not recorded BEN BENZAMIDINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG8K, 5% benzamidine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.30 Å R-free 0.221
2E31 Structural basis for selection of glycosylated substrate by SCFFbs1 ubiquitin ligase Deposited 2006-11-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 0–162（163 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.7；293 K；2.0M ammonium sulphate, 0.1M sodium citrate, 30mM chitobiose, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 2.40 Å R-free 0.291
2E32 Structural basis for selection of glycosylated substrate by SCFFbs1 ubiquitin ligase Deposited 2006-11-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 0–162（163 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.7；293 K；2.0M ammonium sulphate, 0.1M sodium citrate, 30mM chitobiose, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.52 Å R-free 0.299
2E32 Structural basis for selection of glycosylated substrate by SCFFbs1 ubiquitin ligase Deposited 2006-11-20 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 0–162（163 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.7；293 K；2.0M ammonium sulphate, 0.1M sodium citrate, 30mM chitobiose, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Resolution 3.52 Å R-free 0.299
2OVP Structure of the Skp1-Fbw7 complex Deposited 2007-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–163（163 aa） Fragment：residues 1-147
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1 M HEPES-Na, 1.2 M Li2SO4, 7.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.90 Å R-free 0.268
2OVP Structure of the Skp1-Fbw7 complex Deposited 2007-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–163（163 aa） Fragment：residues 1-147
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1 M HEPES-Na, 1.2 M Li2SO4, 7.5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.90 Å R-free 0.268
2OVQ Structure of the Skp1-Fbw7-CyclinEdegC complex Deposited 2007-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–163（163 aa） Fragment：residues 1-147
Not recorded SO4 SULFATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；294 K；0.1 M Bicine, 1.4 M Li2SO4, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.60 Å R-free 0.266
2OVQ Structure of the Skp1-Fbw7-CyclinEdegC complex Deposited 2007-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–163（163 aa） Fragment：residues 1-147
Not recorded SO4 SULFATE ION × 32 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；294 K；0.1 M Bicine, 1.4 M Li2SO4, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.60 Å R-free 0.266
2OVR Structure of the Skp1-Fbw7-CyclinEdegN complex Deposited 2007-02-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–163（163 aa） Fragment：residues 1-147
Not recorded SO4 SULFATE ION × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；294 K；0.1 M Hepes-Na, 1.12 M Li2SO4, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Resolution 2.50 Å R-free 0.251
3L2O Structure-Based Mechanism of Dimerization-Dependent Ubiquitination by the SCFFbx4 Ubiquitin Ligase Deposited 2009-12-15 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–163（163 aa）
Mutation：deletion: 38-43, 70-81; P2A; insertion: GGSG between 69 and 82 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；1.5-2 M sodium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.80 Å R-free 0.295
3L2O Structure-Based Mechanism of Dimerization-Dependent Ubiquitination by the SCFFbx4 Ubiquitin Ligase Deposited 2009-12-15 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–163（163 aa）
Mutation：deletion: 38-43, 70-81; P2A; insertion: GGSG between 69 and 82 No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；1.5-2 M sodium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 2.80 Å R-free 0.295
3WSO Crystal structure of the Skp1-FBG3 complex Deposited 2014-03-18 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–163（163 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；288 K；8% 2-propanol, 16% PEG4000, 0.1M Na PIPES , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.60 Å R-free 0.266
4I6J A ubiquitin ligase-substrate complex Deposited 2012-11-29 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 1–163（163 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；0.2M ammonium citrate, 13-14% PEG3350 7% Acetonitrile, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.70 Å R-free 0.265
5IBK Skp1-F-box in complex with a ubiquitin variant Deposited 2016-02-22 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 A 1–69（69 aa） Fragment：;UNP resdiues 1-61(deletion 37-42) and 70-163 linked by LINKER GGSG,UNP resdiues 1-61(deletion 37-42) and 70-163 linked by LINKER GGSG ;
Chain A 82–163（82 aa） Fragment：;UNP resdiues 1-61(deletion 37-42) and 70-163 linked by LINKER GGSG,UNP resdiues 1-61(deletion 37-42) and 70-163 linked by LINKER GGSG ;
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；100 mM Acetate pH 4.5, 12% PEG 4000, 15% glyerol
Resolution 2.50 Å R-free 0.240
5IBK Skp1-F-box in complex with a ubiquitin variant Deposited 2016-02-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–69（69 aa） Fragment：;UNP resdiues 1-61(deletion 37-42) and 70-163 linked by LINKER GGSG,UNP resdiues 1-61(deletion 37-42) and 70-163 linked by LINKER GGSG ;
Chain D 82–163（82 aa） Fragment：;UNP resdiues 1-61(deletion 37-42) and 70-163 linked by LINKER GGSG,UNP resdiues 1-61(deletion 37-42) and 70-163 linked by LINKER GGSG ;
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；100 mM Acetate pH 4.5, 12% PEG 4000, 15% glyerol
Resolution 2.50 Å R-free 0.240
5JH5 Structural Basis for the Hierarchical Assembly of the Core of PRC1.1 Deposited 2016-04-20 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 2–163（162 aa） Fragment：Residues 2-163
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.25；298 K；100 mM HEPES, 10 % 2-methyl-2,4-pentanediol, 10 mM NaCl
Resolution 2.55 Å R-free 0.257
5K35 Structure of the Legionella effector, AnkB, in complex with human Skp1 Deposited 2016-05-19 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–163（163 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.2 M trimethylamine N-oxide, 0.1 M Tris pH 8.5, 20% (w/v) PEG 2000 MME
Resolution 2.85 Å R-free 0.275
5V4B Crystal structure of the Skp1-FBXW7-DISC1 complex Deposited 2017-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–69（69 aa）
Chain A 82–163（82 aa）
Not recorded SO4 SULFATE ION × 9 IMD IMIDAZOLE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；277.15 K；100 mM Hepes, 1.2M lithium sulfate
Resolution 2.60 Å R-free 0.219
5V4B Crystal structure of the Skp1-FBXW7-DISC1 complex Deposited 2017-03-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–69（69 aa）
Chain A 82–163（82 aa）
Not recorded SO4 SULFATE ION × 36 IMD IMIDAZOLE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.4；277.15 K；100 mM Hepes, 1.2M lithium sulfate
Resolution 2.60 Å R-free 0.219
5VZT Crystal structure of the Skp1-FBXO31 complex Deposited 2017-05-29 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–163（163 aa）
Mutation：P2A ZN ZINC ION × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 PO4 PHOSPHATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；277 K；100 mM sodium citrate (pH 5.3), 0.27 M ammonium acetate, 13-17% MPD, 0.02 M CaCl2
Resolution 2.70 Å R-free 0.242
5VZT Crystal structure of the Skp1-FBXO31 complex Deposited 2017-05-29 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 1–163（163 aa）
Mutation：P2A ZN ZINC ION × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 PO4 PHOSPHATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；277 K；100 mM sodium citrate (pH 5.3), 0.27 M ammonium acetate, 13-17% MPD, 0.02 M CaCl2
Resolution 2.70 Å R-free 0.242
5VZU Crystal structure of the Skp1-FBXO31-cyclin D1 complex Deposited 2017-05-29 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–163（163 aa）
Mutation：P2A ZN ZINC ION × 1 PO4 PHOSPHATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；277 K；100 mM sodium citrate (pH 5.3), 0.27 M ammonium acetate, 13-17% MPD, 0.02 M CaCl2
Resolution 2.70 Å R-free 0.233
5VZU Crystal structure of the Skp1-FBXO31-cyclin D1 complex Deposited 2017-05-29 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–163（163 aa）
Mutation：P2A ZN ZINC ION × 1 PO4 PHOSPHATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.3；277 K；100 mM sodium citrate (pH 5.3), 0.27 M ammonium acetate, 13-17% MPD, 0.02 M CaCl2
Resolution 2.70 Å R-free 0.233
5XYL Solution Structure of Skp1 from Homo sapiens Deposited 2017-07-09 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–163（163 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 20 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 20 mM sodium phosphate, 100 mM sodium chloride, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 20 mM sodium phosphate, 100 mM sodium chloride, 100% D2O | 100% D2O
Resolution not provided
6BVA Ubiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragment complex. Deposited 2017-12-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 1–163（163 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes pH 7.5, 0.2 M calcium chloride, 18% (w/v) PEG 6000
Resolution 2.66 Å R-free 0.263
6BVA Ubiquitin Variant (UbV.Fl10.1) bound to a human Skp1-Fbl10 fragment complex. Deposited 2017-12-12 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–163（163 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes pH 7.5, 0.2 M calcium chloride, 18% (w/v) PEG 6000
Resolution 2.66 Å R-free 0.263
6BYH Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2017-12-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–163（163 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M PCTP buffer pH6, 25% (w/v) PEG 1500
Resolution 2.61 Å R-free 0.294
6BYH Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2017-12-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–163（163 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M PCTP buffer pH6, 25% (w/v) PEG 1500
Resolution 2.61 Å R-free 0.294
6BYH Ubiquitin Variant (UbV.Fl11.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2017-12-20 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain G 1–163（163 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；0.1 M PCTP buffer pH6, 25% (w/v) PEG 1500
Resolution 2.61 Å R-free 0.294
6C16 Ubiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2018-01-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–163（163 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1 M malic acid pH 4.5, 0.15 M sodium chloride, 27% (w/v) PEG3350
Resolution 3.27 Å R-free 0.317
6C16 Ubiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragment complex. Deposited 2018-01-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–163（163 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；0.1 M malic acid pH 4.5, 0.15 M sodium chloride, 27% (w/v) PEG3350
Resolution 3.27 Å R-free 0.317
6M90 Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2776 ternary complex Deposited 2018-08-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–163（162 aa）
Not recorded J91 2-(2-fluorophenoxy)-3-{[2-oxo-6-(trifluoromethyl)-1,2-dihydropyridine-3-carbonyl]amino}benzoic acid × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% PEG 4000 0.1M BTP pH 5.5
Resolution 2.05 Å R-free 0.212
6M91 Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-103094 ternary complex Deposited 2018-08-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–163（162 aa）
Not recorded J97 3-({4-[(2,6-dichlorophenyl)sulfanyl]-2-oxo-6-(trifluoromethyl)-1,2-dihydropyridine-3-carbonyl}amino)benzoic acid × 1 PO4 PHOSPHATE ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% PEG 4000 0.1M BTP pH 5.5
Resolution 2.40 Å R-free 0.216
6M92 Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-2663 ternary complex Deposited 2018-08-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–163（162 aa）
Not recorded J8V 3-{[2-oxo-4-phenoxy-6-(trifluoromethyl)-1,2-dihydropyridine-3-carbonyl]amino}benzoic acid × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% PEG 4000 0.1M BTP pH 5.5
Resolution 2.35 Å R-free 0.221
6M93 Monophosphorylated pSer33 b-Catenin peptide, b-TrCP/Skp1, NRX-1933 ternary complex Deposited 2018-08-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–163（162 aa）
Not recorded J8Y 2-oxo-N-[3-(1H-tetrazol-5-yl)phenyl]-6-(trifluoromethyl)-1,2-dihydropyridine-3-carboxamide × 1 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% PEG 4000 0.1M BTP pH 5.5
Resolution 2.50 Å R-free 0.230
6M94 Monophosphorylated pSer33 b-Catenin peptide bound to b-TrCP/Skp1 Complex Deposited 2018-08-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 2–163（162 aa）
Not recorded PO4 PHOSPHATE ION × 1 DMS DIMETHYL SULFOXIDE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；8% PEG 4000 0.1M BTP pH5.5
Resolution 2.70 Å R-free 0.238
6O60 Crystal structure of GGTase3-FBXL2-SKP1 complex Deposited 2019-03-04 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–163（163 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M MES pH6.0, 20%-22% (v/v) PEG 400
Resolution 2.50 Å R-free 0.247
6TTU Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 Deposited 2019-12-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain S 1–163（163 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.70 Å
6VCD Cryo-EM structure of IRP2-FBXL5-SKP1 complex Deposited 2019-12-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–163（163 aa）
Not recorded FES FE2/S2 (INORGANIC) CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
6W66 The structure of the F64A, S172A mutant Keap1-BTB domain in complex with SKP1-FBXL17 Deposited 2020-03-16 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 1–163（163 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；well solution 37.5 ul of 50 mM MgCl2, 100 mM HEPES pH 7.5, 30% (v/v) PEG MME 550 (E7 Hampton Index) + 12.5ul H2O mixed 1:1 with complex at 15mg/ml in 150 mM NaCl, 25 mM Tris/HCl pH 8.0
Resolution 3.21 Å R-free 0.290
6WCQ Structure of a substrate-bound DQC ubiquitin ligase Deposited 2020-03-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–163（163 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 8.50 Å
6WNX FBXW11-SKP1 in complex with a pSer33/pSer37 Beta-Catenin peptide Deposited 2020-04-23 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 1–163（163 aa）
Not recorded GOL GLYCEROL × 4 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.12M Ethylene Glycol, 0.1M Morpheus Buffer 1 pH 6.5, 30.0% GOL_P4K
Resolution 2.50 Å R-free 0.251
6WNX FBXW11-SKP1 in complex with a pSer33/pSer37 Beta-Catenin peptide Deposited 2020-04-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–163（163 aa）
Not recorded GOL GLYCEROL × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.12M Ethylene Glycol, 0.1M Morpheus Buffer 1 pH 6.5, 30.0% GOL_P4K
Resolution 2.50 Å R-free 0.251
6WNX FBXW11-SKP1 in complex with a pSer33/pSer37 Beta-Catenin peptide Deposited 2020-04-23 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain H 1–163（163 aa）
Not recorded GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.12M Ethylene Glycol, 0.1M Morpheus Buffer 1 pH 6.5, 30.0% GOL_P4K
Resolution 2.50 Å R-free 0.251
7B5L Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27-UBE2L3~Ub~ARIH1. Transition State 1 Deposited 2020-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain S 1–163（163 aa）
Not recorded ZN ZINC ION × 9 SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7B5M Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1. Transition State 2 Deposited 2020-12-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain S 1–163（163 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.91 Å
7B5R Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27 Deposited 2020-12-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain S 1–163（163 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7T1Y Structure of the Fbw7-Skp1-MycCdegron complex Deposited 2021-12-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–163（162 aa）
Not recorded SO4 SULFATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298.15 K；0.1 M Bicine pH6.5, 1.6 M Li2SO4
Resolution 2.55 Å R-free 0.268
7T1Z Structure of the Fbw7-Skp1-MycNdegron complex Deposited 2021-12-02 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 2–163（162 aa）
Not recorded SO4 SULFATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298.15 K；0.1 M Bicine pH6.5, 1.6 M Li2SO4
Resolution 2.77 Å R-free 0.248
7Z8B Structure of CRL7FBXW8 reveals coupling with CUL1-RBX1/ROC1 for multi-cullin-RING E3-catalyzed ubiquitin ligation Deposited 2022-03-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain S 1–163（163 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7Z8T CAND1-SCF-SKP2 CAND1 engaged SCF rocked Deposited 2022-03-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain S 1–163（163 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7Z8V CAND1-SCF-SKP2 (SKP1deldel) CAND1 engaged SCF rocked Deposited 2022-03-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain S 1–163（163 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7ZBW CAND1-SCF-SKP2 CAND1 rolling-2 SCF engaged Deposited 2022-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain S 1–163（163 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7ZBZ CAND1 delhairpin-SCF-SKP2 CAND1 partly engaged SCF partly rocked Deposited 2022-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain S 1–163（163 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8BYA Cryo-EM structure of SKP1-SKP2-CKS1-CDK2-CyclinA-p27KIP1 Complex Deposited 2022-12-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 1–163（163 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å
8BYL Cryo-EM structure of SKP1-SKP2-CKS1 from the SCFSKP2 E3 ligase complex Deposited 2022-12-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–163（163 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8CDJ CAND1 b-hairpin++-SCF-SKP2 CAND1 rolling SCF engaged Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain S 1–163（163 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8CDK CAND1 b-hairpin++-SCF-SKP2 CAND1 partly engaged SCF partly rocked Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain S 1–163（163 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
8OR0 CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2 Deposited 2023-04-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 1–163（163 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8OR3 CAND1-CUL1-RBX1-SKP1-SKP2-DCNL1 Deposited 2023-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 1–163（163 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8OR4 Partially dissociated CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2 Deposited 2023-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain D 1–163（163 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8S7D Cryo-EM structure of SKP1-FBXO22 in complex with a BACH1 BTB dimer at 3.2A resolution Deposited 2024-02-29 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–163（163 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8S7E Cryo-EM structure of SKP1-FBXO22 Deposited 2024-02-29 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 2–163（162 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8UA6 Cryo-EM Structure of SCF-FBOX22-BACH1BTB Deposited 2023-09-20 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–160（160 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
8UBT Structure of SCF-FBXL17-BACH1BTB E3 ligase complex Deposited 2023-09-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–163（163 aa） Fragment：BTB domain (UNP residues 7-128)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8UBU Cryo-EM structure of dimeric SCF-FBXL17-BACH1BTB E3 ligase complex close conformation Deposited 2023-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain C 1–163（163 aa）
Chain G 1–163（163 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
9CB3 E2F1-Cyclin F Interface Deposited 2024-06-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–163（163 aa） Fragment：BTB domain (UNP residues 7-128)
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.47 Å
9JKB Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO4 SCF ubiquition ligase complex Deposited 2024-09-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 1–163（163 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
9KBD Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO3 SCF ubiquition ligase complex Deposited 2024-10-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–163（163 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9KBF Cryo-EM structure of the SKP1-FBXO3 complex Deposited 2024-10-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–163（163 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.74 Å
9QO2 Dissociation-state-1 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain L 1–163（163 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9QO3 Dissociation-state-2 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: 13-meric
Chain L 1–163（163 aa）
Not recorded ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
9QO4 Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain L 1–163（163 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9QO5 Dissociation-state-4 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain L 1–163（163 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9XZJ Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex and a 3-way DNA fork (consensus structure) Deposited 2025-08-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain S 1–163（163 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
9XZL Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex and a 3-way DNA fork (body structure) Deposited 2025-08-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain S 1–163（163 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

71 other PDB entries and 97 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SKP1_HUMAN
Isoform —
PDB entities 14
Chains and sequence ranges Author chain L； PDBConstruct 1–163； UniProt 1–163

S-phase kinase-associated protein 2

Homo sapiens

UniProt Q13309

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 × 15 PDB declaration: 15-meric（15） Consistent with protein copy count Chain M； UniProt 1–424 Not recorded COP9 signalosome complex subunit 4 × 1 （Q9BT78） COP9 signalosome complex subunit 7b × 1 （Q9H9Q2） NEDD8 × 1 （Q15843） Cyclin-dependent kinases regulatory subunit 1 × 1 （P61024） COP9 signalosome complex subunit 9 × 1 （Q8WXC6） COP9 signalosome complex subunit 1 × 1 （Q13098） COP9 signalosome complex subunit 2 × 1 （P61201） COP9 signalosome complex subunit 3 × 1 （Q9UNS2） COP9 signalosome complex subunit 5 × 1 （Q92905） COP9 signalosome complex subunit 6 × 1 （Q7L5N1） COP9 signalosome complex subunit 8 × 1 （Q99627） Cullin-1 × 1 （Q13616） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） S-phase kinase-associated protein 1 × 1 （P63208） IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT cryo-EM vitrification conditions：Cryogen ETHANE Resolution 3.26 Å

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 9QO0 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 89–424（336 aa） Fragment：101-436
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.314
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 89–424（336 aa） Fragment：101-436
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.314
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain E 89–424（336 aa） Fragment：101-436
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.314
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain G 89–424（336 aa） Fragment：101-436
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.314
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain I 89–424（336 aa） Fragment：101-436
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.314
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain K 89–424（336 aa） Fragment：101-436
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.314
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain M 89–424（336 aa） Fragment：101-436
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.314
1FQV Insights into scf ubiquitin ligases from the structure of the skp1-skp2 complex Deposited 2000-09-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain O 89–424（336 aa） Fragment：101-436
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, Tris-Cl, ammonium acetate, DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.80 Å R-free 0.314
1FS1 INSIGHTS INTO SCF UBIQUITIN LIGASES FROM THE STRUCTURE OF THE SKP1-SKP2 COMPLEX Deposited 2000-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 101–153（53 aa） Fragment：RESIDUES 101-153
Chain C 101–153（53 aa） Fragment：RESIDUES 101-153
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；277 K；PEG 1500, sodium acetate, ammonium acetate, DTT, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.80 Å R-free 0.274
1FS2 INSIGHTS INTO SCF UBIQUITIN LIGASES FROM THE STRUCTURE OF THE SKP1-SKP2 COMPLEX Deposited 2000-09-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 89–398（310 aa） Fragment：RESIDUES 101-153; 193-410 (F-BOX + 8 LRRS)
Chain C 89–398（310 aa） Fragment：RESIDUES 101-153; 193-410 (F-BOX + 8 LRRS)
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 2.90 Å R-free 0.287
1LDK Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex Deposited 2002-04-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 97–137（41 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；peg4k, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.331
1LDK Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex Deposited 2002-04-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain E 97–137（41 aa）
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；peg4k, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.331
2ASS Crystal structure of the Skp1-Skp2-Cks1 complex Deposited 2005-08-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 89–424（336 aa）
Not recorded PO4 PHOSPHATE ION × 3 BEN BENZAMIDINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；BTP, sodium/potassium phosphate, benzamidine, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.242
2ASS Crystal structure of the Skp1-Skp2-Cks1 complex Deposited 2005-08-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 89–424（336 aa）
Not recorded PO4 PHOSPHATE ION × 6 BEN BENZAMIDINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；BTP, sodium/potassium phosphate, benzamidine, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.242
2ASS Crystal structure of the Skp1-Skp2-Cks1 complex Deposited 2005-08-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 89–424（336 aa）
Not recorded PO4 PHOSPHATE ION × 6 BEN BENZAMIDINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；277 K；BTP, sodium/potassium phosphate, benzamidine, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.242
2AST Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide Deposited 2005-08-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 89–424（336 aa）
Not recorded BEN BENZAMIDINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG8K, 5% benzamidine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.30 Å R-free 0.221
2AST Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide Deposited 2005-08-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 89–424（336 aa）
Not recorded BEN BENZAMIDINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG8K, 5% benzamidine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.30 Å R-free 0.221
2AST Crystal structure of Skp1-Skp2-Cks1 in complex with a p27 peptide Deposited 2005-08-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain B 89–424（336 aa）
Not recorded BEN BENZAMIDINE × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG8K, 5% benzamidine, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.30 Å R-free 0.221
7B5L Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27-UBE2L3~Ub~ARIH1. Transition State 1 Deposited 2020-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain T 1–424（424 aa）
Not recorded ZN ZINC ION × 9 SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7B5M Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1. Transition State 2 Deposited 2020-12-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain T 1–424（424 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.91 Å
7B5R Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27 Deposited 2020-12-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain T 1–424（424 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7LUO N-terminus of Skp2 bound to Cyclin A Deposited 2021-02-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain A 17–83（67 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；1.7 M Sodium-potassium phosphate
Resolution 3.17 Å R-free 0.277
7LUO N-terminus of Skp2 bound to Cyclin A Deposited 2021-02-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain C 17–83（67 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.2；293 K；1.7 M Sodium-potassium phosphate
Resolution 3.17 Å R-free 0.277
7Z8T CAND1-SCF-SKP2 CAND1 engaged SCF rocked Deposited 2022-03-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain F 1–424（424 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7Z8V CAND1-SCF-SKP2 (SKP1deldel) CAND1 engaged SCF rocked Deposited 2022-03-18 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain F 1–424（424 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7ZBW CAND1-SCF-SKP2 CAND1 rolling-2 SCF engaged Deposited 2022-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain F 1–424（424 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7ZBZ CAND1 delhairpin-SCF-SKP2 CAND1 partly engaged SCF partly rocked Deposited 2022-03-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain F 1–424（424 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8BYA Cryo-EM structure of SKP1-SKP2-CKS1-CDK2-CyclinA-p27KIP1 Complex Deposited 2022-12-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain E 1–424（424 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å
8BYL Cryo-EM structure of SKP1-SKP2-CKS1 from the SCFSKP2 E3 ligase complex Deposited 2022-12-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–424（424 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8CDJ CAND1 b-hairpin++-SCF-SKP2 CAND1 rolling SCF engaged Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain F 1–424（424 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8CDK CAND1 b-hairpin++-SCF-SKP2 CAND1 partly engaged SCF partly rocked Deposited 2023-01-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain F 1–424（424 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
8OR0 CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2 Deposited 2023-04-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain E 1–424（424 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8OR3 CAND1-CUL1-RBX1-SKP1-SKP2-DCNL1 Deposited 2023-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–424（424 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8OR4 Partially dissociated CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2 Deposited 2023-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain E 1–424（424 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9QO2 Dissociation-state-1 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain M 1–424（424 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9QO3 Dissociation-state-2 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: 13-meric
Chain M 1–424（424 aa）
Not recorded ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
9QO4 Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain M 1–424（424 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9QO5 Dissociation-state-4 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain M 1–424（424 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å

25 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SKP2_HUMAN
Isoform —
PDB entities 15
Chains and sequence ranges Author chain M； PDBConstruct 1–424； UniProt 1–424

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

SAXS scattering curve SAXS Profile

SAXS profile for 9qo0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9qo0
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9qo0
Deposition date deposition_date2025-03-25
Structure title titlePre-activated 9-subunit COP9 signalosome and neddylated SCF (Skp1-Skp2-Cks1) complex structure
Keywords keywordsE3 ligases, COP9 signalosome, LIGASE; LIGASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier59.90 Å
Radius of gyration Rg (electron density) rg_electron59.73 Å
Forward intensity I(0) i02435910000.00
Molecular weight molecular_weight417930.0 kDa
Excluded volume excluded_volume524770 ų
Envelope volume envelope_volume888830 ų
Hydration-shell volume shell_volume124800 ų
Envelope diameter envelope_diameter200.1 Å
Shell Rg shell_rg62.26 Å
Envelope Rg envelope_rg57.32 Å
Shape Rg shape_rg59.76 Å
Total Rg total_rg59.68 Å
Total atoms total_atoms29373
Residues n_residues3744
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax194.7 Å
Rg (real space) rg_real59.66 Å
Rg uncertainty (real space) rg_real_error1.89 Å
I(0) (real space) i0_real2.4360e+09
I(0) uncertainty (real space) i0_real_error5.2500e+07
Rg (reciprocal space) rg_reciprocal60.07 Å
I(0) (reciprocal space) i0_reciprocal2437000000.0000
Solution quality estimate total_estimate0.8718
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary74.9 Å
Skewness Skewness skewness0.188
Kurtosis Kurtosis kurtosis-0.425
Angular range angular_range— – 0.1300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha159100000.0000
Real-space data points n_real_points27
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.897; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.959; Smooth: 0.680
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (17)

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8. Citations (1)

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9. Files and Curves (10)