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4d18

Crystal structure of the COP9 signalosome

Method: X-RAY DIFFRACTION Dmax: 208.9 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 52–527 Fragment：RESIDUES 52-527 COP9 SIGNALOSOME COMPLEX SUBUNIT 2 × 1 （P61201） COP9 SIGNALOSOME COMPLEX SUBUNIT 3 × 1 （Q9UNS2） COP9 SIGNALOSOME COMPLEX SUBUNIT 4 × 1 （Q9BT78） COP9 SIGNALOSOME COMPLEX SUBUNIT 5 × 1 （Q92905） COP9 SIGNALOSOME COMPLEX SUBUNIT 6 × 1 （Q7L5N1） COP9 SIGNALOSOME COMPLEX SUBUNIT 7A × 1 （Q9UBW8） COP9 SIGNALOSOME COMPLEX SUBUNIT 8 × 1 （Q99627） 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
2 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain I； UniProt 52–527 Fragment：RESIDUES 52-527 COP9 SIGNALOSOME COMPLEX SUBUNIT 2 × 1 （P61201） COP9 SIGNALOSOME COMPLEX SUBUNIT 3 × 1 （Q9UNS2） COP9 SIGNALOSOME COMPLEX SUBUNIT 4 × 1 （Q9BT78） COP9 SIGNALOSOME COMPLEX SUBUNIT 5 × 1 （Q92905） COP9 SIGNALOSOME COMPLEX SUBUNIT 6 × 1 （Q7L5N1） COP9 SIGNALOSOME COMPLEX SUBUNIT 7A × 1 （Q9UBW8） COP9 SIGNALOSOME COMPLEX SUBUNIT 8 × 1 （Q99627） 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

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 4D18 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 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 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
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different construct 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 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 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 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 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 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 construct Different oligomeric state Different experimental method 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 method 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 method 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 method 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain 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 method 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 method 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 method 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 construct Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain A 1–491（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 construct 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 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct 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 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
9QO0 Pre-activated 9-subunit COP9 signalosome and neddylated SCF (Skp1-Skp2-Cks1) complex structure Deposited 2025-03-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: 15-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 3.26 Å
9QO1 Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure Deposited 2025-03-25 Different construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 construct Different oligomeric state Different experimental method 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 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 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CSN1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–480； UniProt 52–527 Author chain I； PDBConstruct 5–480； UniProt 52–527

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain B； UniProt 1–443 Not recorded COP9 SIGNALOSOME COMPLEX SUBUNIT 1 × 1 （Q13098） COP9 SIGNALOSOME COMPLEX SUBUNIT 3 × 1 （Q9UNS2） COP9 SIGNALOSOME COMPLEX SUBUNIT 4 × 1 （Q9BT78） COP9 SIGNALOSOME COMPLEX SUBUNIT 5 × 1 （Q92905） COP9 SIGNALOSOME COMPLEX SUBUNIT 6 × 1 （Q7L5N1） COP9 SIGNALOSOME COMPLEX SUBUNIT 7A × 1 （Q9UBW8） COP9 SIGNALOSOME COMPLEX SUBUNIT 8 × 1 （Q99627） 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
2 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain J； UniProt 1–443 Not recorded COP9 SIGNALOSOME COMPLEX SUBUNIT 1 × 1 （Q13098） COP9 SIGNALOSOME COMPLEX SUBUNIT 3 × 1 （Q9UNS2） COP9 SIGNALOSOME COMPLEX SUBUNIT 4 × 1 （Q9BT78） COP9 SIGNALOSOME COMPLEX SUBUNIT 5 × 1 （Q92905） COP9 SIGNALOSOME COMPLEX SUBUNIT 6 × 1 （Q7L5N1） COP9 SIGNALOSOME COMPLEX SUBUNIT 7A × 1 （Q9UBW8） COP9 SIGNALOSOME COMPLEX SUBUNIT 8 × 1 （Q99627） 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

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 4D18 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 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 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
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 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 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 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 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 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 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 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 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 experimental method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 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 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 method 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 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 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 method 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 method 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 method 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 method 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 method 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 method 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 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 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
9QO0 Pre-activated 9-subunit COP9 signalosome and neddylated SCF (Skp1-Skp2-Cks1) complex structure Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: 15-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 3.26 Å
9QO1 Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different experimental method 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 ligand/ion Different experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 experimental method 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 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 CSN2_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 5–447； UniProt 1–443 Author chain J； PDBConstruct 5–447； 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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain C； UniProt 1–423 Not recorded COP9 SIGNALOSOME COMPLEX SUBUNIT 1 × 1 （Q13098） COP9 SIGNALOSOME COMPLEX SUBUNIT 2 × 1 （P61201） COP9 SIGNALOSOME COMPLEX SUBUNIT 4 × 1 （Q9BT78） COP9 SIGNALOSOME COMPLEX SUBUNIT 5 × 1 （Q92905） COP9 SIGNALOSOME COMPLEX SUBUNIT 6 × 1 （Q7L5N1） COP9 SIGNALOSOME COMPLEX SUBUNIT 7A × 1 （Q9UBW8） COP9 SIGNALOSOME COMPLEX SUBUNIT 8 × 1 （Q99627） 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
2 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain K； UniProt 1–423 Not recorded COP9 SIGNALOSOME COMPLEX SUBUNIT 1 × 1 （Q13098） COP9 SIGNALOSOME COMPLEX SUBUNIT 2 × 1 （P61201） COP9 SIGNALOSOME COMPLEX SUBUNIT 4 × 1 （Q9BT78） COP9 SIGNALOSOME COMPLEX SUBUNIT 5 × 1 （Q92905） COP9 SIGNALOSOME COMPLEX SUBUNIT 6 × 1 （Q7L5N1） COP9 SIGNALOSOME COMPLEX SUBUNIT 7A × 1 （Q9UBW8） COP9 SIGNALOSOME COMPLEX SUBUNIT 8 × 1 （Q99627） 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

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 4D18 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 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 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
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 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 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 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 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 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 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 experimental method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 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 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 method 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 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 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 method 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 method 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 method 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 method 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 method 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 method 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 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 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
9QO0 Pre-activated 9-subunit COP9 signalosome and neddylated SCF (Skp1-Skp2-Cks1) complex structure Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: 15-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 3.26 Å
9QO1 Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different experimental method 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 ligand/ion Different experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 experimental method 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 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 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CSN3_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 5–427； UniProt 1–423 Author chain K； PDBConstruct 5–427； UniProt 1–423

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain D； UniProt 1–406 Not recorded 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 7A × 1 （Q9UBW8） COP9 SIGNALOSOME COMPLEX SUBUNIT 8 × 1 （Q99627） 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
2 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain L； UniProt 1–406 Not recorded 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 7A × 1 （Q9UBW8） COP9 SIGNALOSOME COMPLEX SUBUNIT 8 × 1 （Q99627） 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

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 4D18 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 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 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 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
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 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 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 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 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 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 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 experimental method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 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 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 method 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 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 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 method 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 method 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 method 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 method 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 method 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 method 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 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 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
9QO0 Pre-activated 9-subunit COP9 signalosome and neddylated SCF (Skp1-Skp2-Cks1) complex structure Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: 15-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 3.26 Å
9QO1 Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different experimental method 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 ligand/ion Different experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 experimental method 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 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 34 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CSN4_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain D； PDBConstruct 5–410； UniProt 1–406 Author chain L； PDBConstruct 5–410； UniProt 1–406

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain E； UniProt 12–334 Fragment：RESIDUES 12-334 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 4 × 1 （Q9BT78） COP9 SIGNALOSOME COMPLEX SUBUNIT 6 × 1 （Q7L5N1） COP9 SIGNALOSOME COMPLEX SUBUNIT 7A × 1 （Q9UBW8） COP9 SIGNALOSOME COMPLEX SUBUNIT 8 × 1 （Q99627） 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
2 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain M； UniProt 12–334 Fragment：RESIDUES 12-334 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 4 × 1 （Q9BT78） COP9 SIGNALOSOME COMPLEX SUBUNIT 6 × 1 （Q7L5N1） COP9 SIGNALOSOME COMPLEX SUBUNIT 7A × 1 （Q9UBW8） COP9 SIGNALOSOME COMPLEX SUBUNIT 8 × 1 （Q99627） 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

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 4D18 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 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 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
4F7O Crystal structure of CSN5 Deposited 2012-05-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 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 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 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 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 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 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 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 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 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 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 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 construct Different oligomeric state Different experimental method 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 method 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 method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 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 × 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain 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 construct 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 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 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 × 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 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 × 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 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 × 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 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 × 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 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 × 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 construct 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 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
9QO0 Pre-activated 9-subunit COP9 signalosome and neddylated SCF (Skp1-Skp2-Cks1) complex structure Deposited 2025-03-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: 15-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 3.26 Å
9QO1 Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure Deposited 2025-03-25 Different construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions 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 construct Different oligomeric state Different experimental method 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 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 37 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CSN5_HUMAN
Isoform —
PDB entities 5
Chains and sequence ranges Author chain E； PDBConstruct 5–327； UniProt 12–334 Author chain M； PDBConstruct 5–327； UniProt 12–334

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain F； UniProt 1–327 Not recorded 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 4 × 1 （Q9BT78） COP9 SIGNALOSOME COMPLEX SUBUNIT 5 × 1 （Q92905） COP9 SIGNALOSOME COMPLEX SUBUNIT 7A × 1 （Q9UBW8） COP9 SIGNALOSOME COMPLEX SUBUNIT 8 × 1 （Q99627） 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
2 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain N； UniProt 1–327 Not recorded 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 4 × 1 （Q9BT78） COP9 SIGNALOSOME COMPLEX SUBUNIT 5 × 1 （Q92905） COP9 SIGNALOSOME COMPLEX SUBUNIT 7A × 1 （Q9UBW8） COP9 SIGNALOSOME COMPLEX SUBUNIT 8 × 1 （Q99627） 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

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 4D18 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 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 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
4QFT Structure of COP9 signalosome complex subunit 6 Deposited 2014-05-21 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 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 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 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 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 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 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 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 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 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 experimental method 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 method 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 method 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 method 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 method 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 method 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 method 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 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 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 method 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 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 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 method 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 method 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 method 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 method 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 method 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 method 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 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 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
9QO0 Pre-activated 9-subunit COP9 signalosome and neddylated SCF (Skp1-Skp2-Cks1) complex structure Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: 15-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 3.26 Å
9QO1 Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different experimental method 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 ligand/ion Different experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 experimental method 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 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 CSN6_HUMAN
Isoform —
PDB entities 6
Chains and sequence ranges Author chain F； PDBConstruct 5–331； UniProt 1–327 Author chain N； PDBConstruct 5–331； UniProt 1–327

COP9 SIGNALOSOME COMPLEX SUBUNIT 7A

HOMO SAPIENS

UniProt Q9UBW8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain G； UniProt 1–218 Fragment：RESIDUES 1-218 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 4 × 1 （Q9BT78） COP9 SIGNALOSOME COMPLEX SUBUNIT 5 × 1 （Q92905） COP9 SIGNALOSOME COMPLEX SUBUNIT 6 × 1 （Q7L5N1） COP9 SIGNALOSOME COMPLEX SUBUNIT 8 × 1 （Q99627） 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
2 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain O； UniProt 1–218 Fragment：RESIDUES 1-218 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 4 × 1 （Q9BT78） COP9 SIGNALOSOME COMPLEX SUBUNIT 5 × 1 （Q92905） COP9 SIGNALOSOME COMPLEX SUBUNIT 6 × 1 （Q7L5N1） COP9 SIGNALOSOME COMPLEX SUBUNIT 8 × 1 （Q99627） 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

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 4D18 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 experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain O 1–218（218 aa） Fragment：RESIDUES 1-218
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 experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain G 1–218（218 aa） Fragment：RESIDUES 1-218
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
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain G 1–218（218 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 construct Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain O 1–218（218 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 construct Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain W 1–218（218 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 construct Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain e 1–218（218 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 construct Different experimental conditions Different structure-quality metrics Assembly 5 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain m 1–218（218 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 construct Different experimental conditions Different structure-quality metrics Assembly 6 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain u 1–218（218 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

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

View Construct and Data Evidence
UniProt name CSN7A_HUMAN
Isoform —
PDB entities 7
Chains and sequence ranges Author chain G； PDBConstruct 5–222； UniProt 1–218 Author chain O； PDBConstruct 5–222； UniProt 1–218

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain H； UniProt 1–209 Not recorded 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 4 × 1 （Q9BT78） COP9 SIGNALOSOME COMPLEX SUBUNIT 5 × 1 （Q92905） COP9 SIGNALOSOME COMPLEX SUBUNIT 6 × 1 （Q7L5N1） COP9 SIGNALOSOME COMPLEX SUBUNIT 7A × 1 （Q9UBW8） 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
2 Protein heterocomplex Heteromer Protein × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain P； UniProt 1–209 Not recorded 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 4 × 1 （Q9BT78） COP9 SIGNALOSOME COMPLEX SUBUNIT 5 × 1 （Q92905） COP9 SIGNALOSOME COMPLEX SUBUNIT 6 × 1 （Q7L5N1） COP9 SIGNALOSOME COMPLEX SUBUNIT 7A × 1 （Q9UBW8） 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

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 4D18 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 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 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
4WSN Crystal structure of the COP9 signalosome, a P1 crystal form Deposited 2014-10-28 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 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 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 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 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 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 experimental method 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 method 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 method 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 method 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 method 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 method 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 method 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 method 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 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 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 method 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 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 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 method 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 method 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 method 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 method 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 method 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 method 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 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 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
9QO0 Pre-activated 9-subunit COP9 signalosome and neddylated SCF (Skp1-Skp2-Cks1) complex structure Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: 15-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 3.26 Å
9QO1 Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different experimental method 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 ligand/ion Different experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 experimental method Different experimental conditions 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 experimental method 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 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 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CSN8_HUMAN
Isoform —
PDB entities 8
Chains and sequence ranges Author chain H； PDBConstruct 5–213； UniProt 1–209 Author chain P； PDBConstruct 5–213； UniProt 1–209

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 4d18

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4d18
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4d18
Deposition date deposition_date2014-05-01
Structure title titleCrystal structure of the COP9 signalosome
Keywords keywordsSIGNALING PROTEIN, PCI COMPLEX, CSN, SGN, MPN DOMAIN; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier63.23 Å
Radius of gyration Rg (electron density) rg_electron62.73 Å
Forward intensity I(0) i04772810000.00
Molecular weight molecular_weight589460.0 kDa
Excluded volume excluded_volume740630 ų
Envelope volume envelope_volume1147300 ų
Hydration-shell volume shell_volume148930 ų
Envelope diameter envelope_diameter225.4 Å
Shell Rg shell_rg66.83 Å
Envelope Rg envelope_rg61.35 Å
Shape Rg shape_rg62.72 Å
Total Rg total_rg62.86 Å
Total atoms total_atoms41422
Residues n_residues5178
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 dmax208.9 Å
Rg (real space) rg_real62.86 Å
Rg uncertainty (real space) rg_real_error1.86 Å
I(0) (real space) i0_real4.7730e+09
I(0) uncertainty (real space) i0_real_error9.6610e+07
Rg (reciprocal space) rg_reciprocal63.51 Å
I(0) (reciprocal space) i0_reciprocal4778000000.0000
Solution quality estimate total_estimate0.6355
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary83.5 Å
Skewness Skewness skewness0.167
Kurtosis Kurtosis kurtosis-0.356
Angular range angular_range— – 0.1250 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha333200000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.835; Stabil: 1.000; Sysdev: 0.000; Positv: 1.000; Valcen: 0.944; Smooth: 0.809
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

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8. Citations (1)

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9. Files and Curves (10)