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8h3a

Cryo-EM Structure of the KBTBD2-CRL3~N8(removed)-CSN complex

Method: ELECTRON MICROSCOPY Dmax: 211.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 × 12 PDB declaration: dodecameric（12） Consistent with protein copy count Chain E； UniProt 1–334 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 6 × 1 （Q7L5N1） COP9 signalosome complex subunit 7b × 1 （Q9H9Q2） COP9 signalosome complex subunit 8 × 1 （Q99627） Kelch repeat and BTB domain-containing protein 2 × 2 （Q8IY47） Cullin-3 × 1 （Q13618） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） ZN ZINC ION × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 7.51 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

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

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

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

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 × 12 PDB declaration: dodecameric（12） Consistent with protein copy count Chain A； UniProt 12–491 Not recorded COP9 signalosome complex subunit 5 × 1 （Q92905） 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 7b × 1 （Q9H9Q2） COP9 signalosome complex subunit 8 × 1 （Q99627） Kelch repeat and BTB domain-containing protein 2 × 2 （Q8IY47） Cullin-3 × 1 （Q13618） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） ZN ZINC ION × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 7.51 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

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

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

View Construct and Data Evidence
UniProt name CSN1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 52–527； UniProt 12–491

COP9 signalosome complex subunit 2

Homo sapiens

UniProt P61201

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count Chain B； UniProt 1–443 Not recorded COP9 signalosome complex subunit 5 × 1 （Q92905） 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 6 × 1 （Q7L5N1） COP9 signalosome complex subunit 7b × 1 （Q9H9Q2） COP9 signalosome complex subunit 8 × 1 （Q99627） Kelch repeat and BTB domain-containing protein 2 × 2 （Q8IY47） Cullin-3 × 1 （Q13618） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） ZN ZINC ION × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 7.51 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

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

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

View Construct and Data Evidence
UniProt name CSN2_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain B； PDBConstruct 1–443； UniProt 1–443

COP9 signalosome complex subunit 3

Homo sapiens

UniProt Q9UNS2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count Chain C； UniProt 1–423 Not recorded COP9 signalosome complex subunit 5 × 1 （Q92905） 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 6 × 1 （Q7L5N1） COP9 signalosome complex subunit 7b × 1 （Q9H9Q2） COP9 signalosome complex subunit 8 × 1 （Q99627） Kelch repeat and BTB domain-containing protein 2 × 2 （Q8IY47） Cullin-3 × 1 （Q13618） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） ZN ZINC ION × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 7.51 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

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

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

View Construct and Data Evidence
UniProt name CSN3_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain C； PDBConstruct 1–423； 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 × 12 PDB declaration: dodecameric（12） Consistent with protein copy count Chain D； UniProt 1–406 Not recorded COP9 signalosome complex subunit 5 × 1 （Q92905） COP9 signalosome complex subunit 1 × 1 （Q13098） COP9 signalosome complex subunit 2 × 1 （P61201） COP9 signalosome complex subunit 3 × 1 （Q9UNS2） COP9 signalosome complex subunit 6 × 1 （Q7L5N1） COP9 signalosome complex subunit 7b × 1 （Q9H9Q2） COP9 signalosome complex subunit 8 × 1 （Q99627） Kelch repeat and BTB domain-containing protein 2 × 2 （Q8IY47） Cullin-3 × 1 （Q13618） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） ZN ZINC ION × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 7.51 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

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

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

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

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 × 12 PDB declaration: dodecameric（12） Consistent with protein copy count Chain F； UniProt 1–327 Not recorded COP9 signalosome complex subunit 5 × 1 （Q92905） 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 7b × 1 （Q9H9Q2） COP9 signalosome complex subunit 8 × 1 （Q99627） Kelch repeat and BTB domain-containing protein 2 × 2 （Q8IY47） Cullin-3 × 1 （Q13618） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） ZN ZINC ION × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 7.51 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

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

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

View Construct and Data Evidence
UniProt name CSN6_HUMAN
Isoform —
PDB entities 6
Chains and sequence ranges Author chain F； PDBConstruct 1–327； UniProt 1–327

COP9 signalosome complex subunit 7b

Homo sapiens

UniProt Q9H9Q2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count Chain G； UniProt 1–264 Not recorded COP9 signalosome complex subunit 5 × 1 （Q92905） 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 8 × 1 （Q99627） Kelch repeat and BTB domain-containing protein 2 × 2 （Q8IY47） Cullin-3 × 1 （Q13618） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） ZN ZINC ION × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 7.51 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8H3A Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
6R6H Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-27 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain G 9–214（206 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5 100 mM NaCl 0.5 mM DTT 1% glycerol
cryo-EM vitrification conditions Cryogen NITROGEN
Resolution 8.40 Å
6R7F Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric
Chain G 8–215（208 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCL 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.20 Å
6R7H Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 8–215（208 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM HEPES pH 7.5 100 mM NaCl 0.5 mM DTT 1% Glycerol
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.80 Å
6R7I Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome Deposited 2019-03-28 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain G 1–215（215 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
8H38 Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(mutate) complex Deposited 2022-10-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain G 1–264（264 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
Resolution 4.25 Å
8H3F Cryo-EM Structure of the KBTBD2-CRL3-CSN complex Deposited 2022-10-08 Different construct Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain G 1–220（220 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.73 Å
9E5Z Cryo-EM structure of COP9 signalosome Deposited 2024-10-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain G 1–264（264 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
9E77 Cryo-EM structure of CSN-N8 in complex with CSN5i-3 Deposited 2024-11-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain G 1–264（264 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9E81 Cryo-EM structure of COP9 signalosome in complex with CSN5i-3 Deposited 2024-11-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain G 1–264（264 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
9EFM Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-1 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain G 1–264（264 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9EFQ Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-2 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain G 1–264（264 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.96 Å
9EFV Cryo-EM structure of CSN-N8CUL1 in complex with CSN5i-3 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain G 1–264（264 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
9EG1 COP9 signalosome deneddylation complex with cullin-5 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain G 1–264（264 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.52 Å
9EG8 Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-4A Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain G 1–264（264 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9EGL Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-3 Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain G 1–264（264 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
9PH4 Cryo-EM structure of COP9 signalosome in complex with CSN5i-1a Deposited 2025-07-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain G 1–264（264 aa）
Not recorded ZN ZINC ION × 1 A1CH3 6-[(4R,5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-carbonitrile × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
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 conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: 15-meric
Chain G 1–264（264 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.26 Å
9QO1 Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure Deposited 2025-03-25 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain G 1–264（264 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
9QO2 Dissociation-state-1 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain G 1–264（264 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9QO3 Dissociation-state-2 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: 13-meric
Chain G 1–264（264 aa）
Not recorded ZN ZINC ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
9QO4 Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain G 1–264（264 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9QO5 Dissociation-state-4 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain G 1–264（264 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9QO6 9-subunit COP9 signalosome complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain G 1–264（264 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

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

View Construct and Data Evidence
UniProt name CSN7B_HUMAN
Isoform —
PDB entities 7
Chains and sequence ranges Author chain G； PDBConstruct 1–264； UniProt 1–264

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 × 12 PDB declaration: dodecameric（12） Consistent with protein copy count Chain H； UniProt 1–209 Not recorded COP9 signalosome complex subunit 5 × 1 （Q92905） 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 7b × 1 （Q9H9Q2） Kelch repeat and BTB domain-containing protein 2 × 2 （Q8IY47） Cullin-3 × 1 （Q13618） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） ZN ZINC ION × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 7.51 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

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

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

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

Kelch repeat and BTB domain-containing protein 2

Homo sapiens

UniProt Q8IY47

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 × 12 PDB declaration: dodecameric（12） Consistent with protein copy count Chain I； UniProt 1–623 Chain M； UniProt 1–623 Mutation：S252D COP9 signalosome complex subunit 5 × 1 （Q92905） 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 7b × 1 （Q9H9Q2） COP9 signalosome complex subunit 8 × 1 （Q99627） Cullin-3 × 1 （Q13618） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） ZN ZINC ION × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 7.51 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8H3A Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
8GQ6 Cryo-EM Structure of the KBTBD2-CUL3-Rbx1 dimeric complex Deposited 2022-08-29 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–623（623 aa）
Chain B 1–623（623 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.96 Å
8H33 Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 tetrameric complex Deposited 2022-10-07 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain A 1–623（623 aa）
Chain B 1–623（623 aa）
Chain G 1–623（623 aa）
Chain J 1–623（623 aa）
Not recorded ZN ZINC ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.86 Å
8H34 Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 hexameric complex Deposited 2022-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain A 1–623（623 aa）
Chain B 1–623（623 aa）
Chain G 1–623（623 aa）
Chain J 1–623（623 aa）
Chain N 1–623（623 aa）
Chain P 1–623（623 aa）
Not recorded ZN ZINC ION × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.99 Å
8H35 Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 octameric complex Deposited 2022-10-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain A 1–623（623 aa）
Chain B 1–623（623 aa）
Chain G 1–623（623 aa）
Chain J 1–623（623 aa）
Chain N 1–623（623 aa）
Chain P 1–623（623 aa）
Chain S 1–623（623 aa）
Chain U 1–623（623 aa）
Not recorded ZN ZINC ION × 24 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.41 Å
8H36 Cryo-EM Structure of the KBTBD2-CUL3-Rbx1-p85a dimeric complex Deposited 2022-10-08 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 1–623（623 aa）
Chain B 1–623（623 aa）
Mutation：S252D Mutation：S252D ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8H37 Cryo-EM Structure of the KBTBD2-CUL3-Rbx1-p85a tetrameric complex Deposited 2022-10-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain A 1–623（623 aa）
Chain B 1–623（623 aa）
Chain N 1–623（623 aa）
Chain P 1–623（623 aa）
Mutation：S252D Mutation：S252D Mutation：S252D Mutation：S252D ZN ZINC ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.52 Å
8H38 Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(mutate) complex Deposited 2022-10-08 Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain I 1–623（623 aa）
Chain M 1–623（623 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
Resolution 4.25 Å
8H3F Cryo-EM Structure of the KBTBD2-CRL3-CSN complex Deposited 2022-10-08 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain I 1–623（623 aa）
Chain M 1–623（623 aa）
Mutation：S252D Mutation：S252D ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.73 Å
8H3R Cryo-EM Structure of the KBTBD2-CRL3~N8 dimeric complex Deposited 2022-10-09 Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 1–623（623 aa）
Chain B 1–623（623 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.36 Å

9 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name KBTB2_HUMAN
Isoform —
PDB entities 9
Chains and sequence ranges Author chain I； PDBConstruct 1–623； UniProt 1–623 Author chain M； PDBConstruct 1–623； UniProt 1–623

Cullin-3

Homo sapiens

UniProt Q13618

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 × 12 PDB declaration: dodecameric（12） Consistent with protein copy count Chain L； UniProt 1–768 Not recorded COP9 signalosome complex subunit 5 × 1 （Q92905） 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 7b × 1 （Q9H9Q2） COP9 signalosome complex subunit 8 × 1 （Q99627） Kelch repeat and BTB domain-containing protein 2 × 2 （Q8IY47） E3 ubiquitin-protein ligase RBX1 × 1 （P62877） ZN ZINC ION × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 7.51 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8H3A Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2MYL Cullin3 - BTB interface: a novel target for stapled peptides Deposited 2015-01-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 49–68（20 aa） Fragment：UNP residues 49-68
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 3；298 K；Pressure ambient
NMR sample composition 1 mM Cul349-68EN, trifluoroethanol/water | trifluoroethanol/water
Resolution not provided
2MYM Cullin3 - BTB interface: a novel target for stapled peptides Deposited 2015-01-27 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 49–68（20 aa） Fragment：UNP residues 49-68
Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 3；298 K；Pressure ambient
NMR sample composition 1 mM Cul349-68LA, trifluoroethanol/water | trifluoroethanol/water
Resolution not provided
4AP2 Crystal structure of the human KLHL11-Cul3 complex at 2.8A resolution Deposited 2012-03-30 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–388（388 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 1-388
Mutation：YES EDO 1,2-ETHANEDIOL × 4 IOD IODIDE ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 25% PEG3350, 0.15M NAI, 8% ETHGLY
Resolution 2.80 Å R-free 0.236
4APF Crystal structure of the human KLHL11-Cul3 complex at 3.1A resolution Deposited 2012-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 23–388（366 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 23-388
Mutation：YES No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions 0.12 M K CITRATE; 17% PEG 3350; 10% ETHYLENE GLYCOL; PH 6.5 BIS TRIS PROPANE
Resolution 3.10 Å R-free 0.222
4EOZ Crystal structure of the SPOP BTB domain complexed with the Cul3 N-terminal domain Deposited 2012-04-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 20–381（362 aa） Fragment：N-terminal domain from Cul3, unp residue 20-381
Chain D 20–381（362 aa） Fragment：N-terminal domain from Cul3, unp residue 20-381
Mutation：I342R, L346D Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：I342R, L346D Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.025M Hepes pH 6.5, 0.1M MgCl2, 13% PEG 2000, 11% 2,4-Methyl-2-Pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.263
4EOZ Crystal structure of the SPOP BTB domain complexed with the Cul3 N-terminal domain Deposited 2012-04-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 20–381（362 aa） Fragment：N-terminal domain from Cul3, unp residue 20-381
Mutation：I342R, L346D Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.025M Hepes pH 6.5, 0.1M MgCl2, 13% PEG 2000, 11% 2,4-Methyl-2-Pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.263
4EOZ Crystal structure of the SPOP BTB domain complexed with the Cul3 N-terminal domain Deposited 2012-04-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 20–381（362 aa） Fragment：N-terminal domain from Cul3, unp residue 20-381
Mutation：I342R, L346D Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.025M Hepes pH 6.5, 0.1M MgCl2, 13% PEG 2000, 11% 2,4-Methyl-2-Pentanediol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 2.40 Å R-free 0.263
4HXI Crystal structure of KLHL3/Cul3 complex Deposited 2012-11-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 20–381（362 aa） Fragment：NTD
Mutation：K274R, I342R, L346D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.2M ammonium tartrate, 14% PEG 3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Resolution 3.51 Å R-free 0.278
5NLB Crystal structure of human CUL3 N-terminal domain bound to KEAP1 BTB and 3-box Deposited 2017-04-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 26–381（356 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；15% PEG3350, 10% ethylene glycol, 0.2M potassium citrate tribasic
Resolution 3.45 Å R-free 0.288
6I2M Crystal structure of vaccinia virus protein A55 BTB-Back domain in complex with human Cullin-3 N-terminus Deposited 2018-11-01 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 23–388（366 aa）
Mutation：I342R and L346D No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；3.29% tacsimate pH 6.5, 9.92% PEG3350
Resolution 2.30 Å R-free 0.282
8GQ6 Cryo-EM Structure of the KBTBD2-CUL3-Rbx1 dimeric complex Deposited 2022-08-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–768（768 aa）
Chain F 1–768（768 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.96 Å
8H33 Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 tetrameric complex Deposited 2022-10-07 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain C 1–768（768 aa）
Chain F 1–768（768 aa）
Chain H 1–768（768 aa）
Chain I 1–768（768 aa）
Not recorded ZN ZINC ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.86 Å
8H34 Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 hexameric complex Deposited 2022-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain C 1–768（768 aa）
Chain F 1–768（768 aa）
Chain H 1–768（768 aa）
Chain I 1–768（768 aa）
Chain M 1–768（768 aa）
Chain O 1–768（768 aa）
Not recorded ZN ZINC ION × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.99 Å
8H35 Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 octameric complex Deposited 2022-10-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain C 1–768（768 aa）
Chain F 1–768（768 aa）
Chain H 1–768（768 aa）
Chain I 1–768（768 aa）
Chain M 1–768（768 aa）
Chain O 1–768（768 aa）
Chain T 1–768（768 aa）
Chain V 1–768（768 aa）
Not recorded ZN ZINC ION × 24 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.41 Å
8H36 Cryo-EM Structure of the KBTBD2-CUL3-Rbx1-p85a dimeric complex Deposited 2022-10-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain C 1–768（768 aa）
Chain F 1–768（768 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8H37 Cryo-EM Structure of the KBTBD2-CUL3-Rbx1-p85a tetrameric complex Deposited 2022-10-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain C 1–768（768 aa）
Chain F 1–768（768 aa）
Chain M 1–768（768 aa）
Chain O 1–768（768 aa）
Not recorded ZN ZINC ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.52 Å
8H38 Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(mutate) complex Deposited 2022-10-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain L 1–768（768 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
Resolution 4.25 Å
8H3F Cryo-EM Structure of the KBTBD2-CRL3-CSN complex Deposited 2022-10-08 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain L 1–768（768 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.73 Å
8H3Q Cryo-EM Structure of the CAND1-Cul3-Rbx1 complex Deposited 2022-10-09 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–768（768 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.76 Å
8H3R Cryo-EM Structure of the KBTBD2-CRL3~N8 dimeric complex Deposited 2022-10-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–768（768 aa）
Chain F 1–768（768 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.36 Å
8I79 Cryo-EM structure of KCTD7 in complex with Cullin3 Deposited 2023-01-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 22–388（367 aa）
Chain C 22–388（367 aa）
Chain E 22–388（367 aa）
Chain H 22–388（367 aa）
Chain J 22–388（367 aa）
Mutation：I342R, L346D Mutation：I342R, L346D Mutation：I342R, L346D Mutation：I342R, L346D Mutation：I342R, L346D No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8K8T Structure of CUL3-RBX1-KLHL22 complex Deposited 2023-07-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–768（768 aa）
Chain D 1–768（768 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8K9I Structure of CUL3-RBX1-KLHL22 complex without CUL3 NA motif Deposited 2023-08-01 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 25–768（744 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8KHP CULLIN3-KLHL22-RBX1 E3 ligase Deposited 2023-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–768（768 aa）
Chain D 1–768（768 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.67 Å
8U80 KCTD5/Cullin3/Gbeta1gamma2 Complex: Local Refinment of KCTD5(BTB)/Cullin3(NTD) Deposited 2023-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain C1 1–381（381 aa）
Chain C2 1–381（381 aa）
Chain C3 1–381（381 aa）
Chain C4 1–381（381 aa）
Chain C5 1–381（381 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
8U81 KCTD5/Cullin3/Gbeta1gamma2 Complex: State A From Composite RELION Multi-body Refinement Map Deposited 2023-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain C1 1–381（381 aa）
Chain C2 1–381（381 aa）
Chain C3 1–381（381 aa）
Chain C4 1–381（381 aa）
Chain C5 1–381（381 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.82 Å
8U82 KCTD5/Cullin3/Gbeta1gamma2 Complex: State B From Composite RELION Multi-body Refinement Map Deposited 2023-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain C1 2–381（380 aa）
Chain C2 2–381（380 aa）
Chain C3 2–381（380 aa）
Chain C4 2–381（380 aa）
Chain C5 2–381（380 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.84 Å
8U83 KCTD5/Cullin3/Gbeta1gamma2 Complex: State C From Composite RELION Multi-body Refinement Map Deposited 2023-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain C1 1–381（381 aa） Fragment：UNP residues 1-381
Chain C2 1–381（381 aa） Fragment：UNP residues 1-381
Chain C3 1–381（381 aa） Fragment：UNP residues 1-381
Chain C4 1–381（381 aa） Fragment：UNP residues 1-381
Chain C5 1–381（381 aa） Fragment：UNP residues 1-381
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.98 Å
8U84 KCTD5/Cullin3/Gbeta1gamma2 Complex: State D From Composite RELION Multi-body Refinement Map Deposited 2023-09-15 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric
Chain C1 1–381（381 aa）
Chain C2 1–381（381 aa）
Chain C3 1–381（381 aa）
Chain C4 1–381（381 aa）
Chain C5 1–381（381 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.88 Å
9EGL Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-3 Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain J 1–768（768 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
9RWZ ZSWIM8-CUL3 complex bound to AGO2-miR-7-CYRANO Deposited 2025-07-10 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 9 PDB declaration: 11-meric
Chain H 1–390（390 aa）
Chain I 1–390（390 aa）
Mutation：I342R, L346D Mutation：I342R, L346D ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8；25 mM HEPES, 50 mM NaCl, 1 mM TCEP, pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å

29 other PDB entries and 31 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CUL3_HUMAN
Isoform —
PDB entities 10
Chains and sequence ranges Author chain L； PDBConstruct 1–768； UniProt 1–768

E3 ubiquitin-protein ligase RBX1

Homo sapiens

UniProt P62877

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 12 PDB declaration: dodecameric（12） Consistent with protein copy count Chain R； UniProt 1–108 Not recorded COP9 signalosome complex subunit 5 × 1 （Q92905） 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 7b × 1 （Q9H9Q2） COP9 signalosome complex subunit 8 × 1 （Q99627） Kelch repeat and BTB domain-containing protein 2 × 2 （Q8IY47） Cullin-3 × 1 （Q13618） ZN ZINC ION × 4 ELECTRON MICROSCOPY cryo-EM buffer：pH 7.8 cryo-EM vitrification conditions：Cryogen ETHANE Resolution 7.51 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 8H3A Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1LDJ Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex Deposited 2002-04-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 19–108（90 aa） Fragment：Residues 19-108
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；10% Ethanol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.288
1LDK Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex Deposited 2002-04-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain C 19–108（90 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；peg4k, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.331
1LDK Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex Deposited 2002-04-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain C 19–108（90 aa）
Not recorded ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；peg4k, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.331
1U6G Crystal Structure of The Cand1-Cul1-Roc1 Complex Deposited 2004-07-29 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 1–108（108 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；PEG 8000, sodium chloride, DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.317
29HG Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO22 SCF ubiquition ligase in complex with NSD2 via UNC10088 Deposited 2026-03-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–108（108 aa）
Not recorded A1J20 ~{N}-cyclopropyl-~{N}-[[4-[[2-(6-oxidanylhexanoyl)-1~{H}-isoquinolin-6-yl]carbamoyl]phenyl]methyl]-3-oxidanylidene-4~{H}-1,4-benzoxazine-7-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
29HH Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO22 SCF ubiquition ligase in complex with NSD2, UNC10088 and Bach1 Deposited 2026-03-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain E 1–108（108 aa）
Not recorded A1J20 ~{N}-cyclopropyl-~{N}-[[4-[[2-(6-oxidanylhexanoyl)-1~{H}-isoquinolin-6-yl]carbamoyl]phenyl]methyl]-3-oxidanylidene-4~{H}-1,4-benzoxazine-7-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
29HI Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO22 SCF ubiquition ligase in complex with NSD2 via UNC10415667 Deposited 2026-03-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain E 1–108（108 aa）
Not recorded A1J21 4-[[cyclopropyl-[(~{Z})-2-methyl-4-(5-oxidanylidene-2~{H}-1,4-oxazin-3-yl)but-3-enoyl]amino]methyl]-~{N}-[3-[2-[[4-(hydroxymethyl)phenyl]carbonyl-methyl-amino]ethyl]phenyl]benzamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.90 Å
2HYE Crystal Structure of the DDB1-Cul4A-Rbx1-SV5V Complex Deposited 2006-08-05 Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain D 1–108（108 aa）
Not recorded ZN ZINC ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；100mM NaHEPES, 7-9% PEG4000, 10% iso-propanol, 5mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.10 Å R-free 0.316
2LGV Rbx1 Deposited 2011-08-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 12–108（97 aa） Fragment：sequence database residues 12-108
Mutation：W27S, V30S, L32Q, W33S ZN ZINC ION × 3 SOLUTION NMR
NMR measurement conditions pH 7.5；298 K；Ionic strength (raw mmCIF value) 0.120；Pressure ambient
NMR sample composition 20 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 700 uM [U-98% 15N] protein, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 20 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 700 uM [U-98% 13C; U-98% 15N] protein, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 20 mM sodium phosphate, 100 mM sodium chloride, 1 mM DTT, 700 uM [U-98% 13C; U-98% 15N] protein, 100% D2O | 100% D2O
Resolution not provided
3DPL Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation. Deposited 2008-07-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain R 5–108（104 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；277 K；2% PEG 3350, 0.1M HEPES, 0.2M L-proline, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 2.60 Å R-free 0.277
3DQV Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation Deposited 2008-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain R 5–108（104 aa） Fragment：Rbx1 residues 5-108
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；with ~19% PEG3350, 275mM (NH4)2PO4, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.299
3DQV Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation Deposited 2008-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain Y 5–108（104 aa） Fragment：Rbx1 residues 5-108
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；with ~19% PEG3350, 275mM (NH4)2PO4, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.299
3DQV Structural Insights into NEDD8 Activation of Cullin-RING Ligases: Conformational Control of Conjugation Deposited 2008-07-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 5–108（104 aa） Fragment：Rbx1 residues 5-108
Chain Y 5–108（104 aa） Fragment：Rbx1 residues 5-108
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions 277 K；with ~19% PEG3350, 275mM (NH4)2PO4, 5mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 3.00 Å R-free 0.299
3RTR A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases Deposited 2011-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain H 5–108（104 aa） Fragment：UNP residues 5-108
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；17% PEG 3350, 100 mM Tris pH 7.5, 200 mM Sodium/Postassium Tartrate, 2% Benzamidine Hydrochloride, 1% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.21 Å R-free 0.282
3RTR A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases Deposited 2011-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 5–108（104 aa） Fragment：UNP residues 5-108
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；17% PEG 3350, 100 mM Tris pH 7.5, 200 mM Sodium/Postassium Tartrate, 2% Benzamidine Hydrochloride, 1% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.21 Å R-free 0.282
3RTR A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases Deposited 2011-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 5–108（104 aa） Fragment：UNP residues 5-108
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；17% PEG 3350, 100 mM Tris pH 7.5, 200 mM Sodium/Postassium Tartrate, 2% Benzamidine Hydrochloride, 1% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.21 Å R-free 0.282
3RTR A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases Deposited 2011-05-03 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain F 5–108（104 aa） Fragment：UNP residues 5-108
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；17% PEG 3350, 100 mM Tris pH 7.5, 200 mM Sodium/Postassium Tartrate, 2% Benzamidine Hydrochloride, 1% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.21 Å R-free 0.282
4F52 Structure of a Glomulin-RBX1-CUL1 complex Deposited 2012-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 5–108（104 aa） Fragment：UNP residues 5-108
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；18-21% PEG3350, 0.3-0.45M ammonium citrate, 10mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.00 Å R-free 0.289
4F52 Structure of a Glomulin-RBX1-CUL1 complex Deposited 2012-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain D 5–108（104 aa） Fragment：UNP residues 5-108
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；18-21% PEG3350, 0.3-0.45M ammonium citrate, 10mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Resolution 3.00 Å R-free 0.289
4P5O Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action Deposited 2014-03-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain B 3–108（106 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；11% PEG3350, 0.2M ammonium citrate, 10mM ATP
Resolution 3.11 Å R-free 0.284
4P5O Structure of an RBX1-UBC12~NEDD8-CUL1-DCN1 complex: a RING-E3-E2~ubiquitin-like protein-substrate intermediate trapped in action Deposited 2014-03-18 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain D 3–108（106 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；11% PEG3350, 0.2M ammonium citrate, 10mM ATP
Resolution 3.11 Å R-free 0.284
5N4W Crystal structure of the Cul2-Rbx1-EloBC-VHL ubiquitin ligase complex Deposited 2017-02-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 1–102（102 aa）
Not recorded ZN ZINC ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.6；293 K；0.1 M Tris pH 7.6, 0.15 M ammonium sulphate, 15% polyethyleneglycol 4000 and 3% 1,4-dioxane or 4% acetonitrile. The sample was crystallised in the presence of a 19-mer peptide mimicking the substrate HIF-1alpha - residues 559-577 (DEALAPYIPMDDDFQLRSF, with the mutations L559D and M561A and P564 is hydroxyproline).
Resolution 3.90 Å R-free 0.346
6TTU Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2 Deposited 2019-12-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.70 Å
7B5L Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-SKP1-SKP2-CKSHS1-Cyclin A-CDK2-p27-UBE2L3~Ub~ARIH1. Transition State 1 Deposited 2020-12-04 Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 9 SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7B5M Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-SKP1-SKP2-CKSHS1-p27~Ub~ARIH1. Transition State 2 Deposited 2020-12-05 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.91 Å
7B5N Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: NEDD8-CUL1-RBX1-UBE2L3~Ub~ARIH1. Deposited 2020-12-05 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 9 SY8 5-azanylpentan-2-one × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7B5S Ubiquitin ligation to F-box protein substrates by SCF-RBR E3-E3 super-assembly: CUL1-RBX1-ARIH1 Ariadne. Transition State 1 Deposited 2020-12-07 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.60 Å
7OKQ Cryo-EM Structure of the DDB1-DCAF1-CUL4A-RBX1 Complex Deposited 2021-05-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: Hexadecameric
Chain D 1–108（108 aa）
Chain H 1–108（108 aa）
Chain L 1–108（108 aa）
Chain P 1–108（108 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 8.40 Å
7PLO H. sapiens replisome-CUL2/LRR1 complex Deposited 2021-09-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 24 PDB declaration: 26-meric
Chain T 1–108（108 aa）
Not recorded ZN ZINC ION × 8 MG MAGNESIUM ION × 3 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 3 SO4 SULFATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7Z8B Structure of CRL7FBXW8 reveals coupling with CUL1-RBX1/ROC1 for multi-cullin-RING E3-catalyzed ubiquitin ligation Deposited 2022-03-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
7Z8R CAND1-CUL1-RBX1 Deposited 2022-03-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain R 5–108（104 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7Z8T CAND1-SCF-SKP2 CAND1 engaged SCF rocked Deposited 2022-03-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 5–108（104 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
7Z8V CAND1-SCF-SKP2 (SKP1deldel) CAND1 engaged SCF rocked Deposited 2022-03-18 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 5–108（104 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7ZBW CAND1-SCF-SKP2 CAND1 rolling-2 SCF engaged Deposited 2022-03-24 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 5–108（104 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8B3G C(N)RL4CSA-UVSSA-E2-ubiquitin complex. Deposited 2022-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8B3I CRL4CSA-E2-Ub (state 2) Deposited 2022-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8CDJ CAND1 b-hairpin++-SCF-SKP2 CAND1 rolling SCF engaged Deposited 2023-01-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 5–108（104 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8CDK CAND1 b-hairpin++-SCF-SKP2 CAND1 partly engaged SCF partly rocked Deposited 2023-01-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 5–108（104 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.32 Å
8GQ6 Cryo-EM Structure of the KBTBD2-CUL3-Rbx1 dimeric complex Deposited 2022-08-29 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 1–108（108 aa）
Chain E 1–108（108 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.96 Å
8H33 Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 tetrameric complex Deposited 2022-10-07 Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain D 1–108（108 aa）
Chain E 1–108（108 aa）
Chain K 1–108（108 aa）
Chain L 1–108（108 aa）
Not recorded ZN ZINC ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.86 Å
8H34 Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 hexameric complex Deposited 2022-10-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric
Chain D 1–108（108 aa）
Chain E 1–108（108 aa）
Chain K 1–108（108 aa）
Chain L 1–108（108 aa）
Chain Q 1–108（108 aa）
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 18 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.99 Å
8H35 Cryo-EM Structure of the KBTBD2-Cul3-Rbx1 octameric complex Deposited 2022-10-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 24 PDB declaration: 24-meric
Chain D 1–108（108 aa）
Chain E 1–108（108 aa）
Chain K 1–108（108 aa）
Chain L 1–108（108 aa）
Chain Q 1–108（108 aa）
Chain R 1–108（108 aa）
Chain W 1–108（108 aa）
Chain X 1–108（108 aa）
Not recorded ZN ZINC ION × 24 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.41 Å
8H36 Cryo-EM Structure of the KBTBD2-CUL3-Rbx1-p85a dimeric complex Deposited 2022-10-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain D 1–108（108 aa）
Chain E 1–108（108 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8H37 Cryo-EM Structure of the KBTBD2-CUL3-Rbx1-p85a tetrameric complex Deposited 2022-10-08 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 16 PDB declaration: hexadecameric
Chain D 1–108（108 aa）
Chain E 1–108（108 aa）
Chain Q 1–108（108 aa）
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 12 ELECTRON MICROSCOPY
cryo-EM buffer pH 8.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.52 Å
8H38 Cryo-EM Structure of the KBTBD2-CRL3~N8-CSN(mutate) complex Deposited 2022-10-08 Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
Resolution 4.25 Å
8H3F Cryo-EM Structure of the KBTBD2-CRL3-CSN complex Deposited 2022-10-08 Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.73 Å
8H3Q Cryo-EM Structure of the CAND1-Cul3-Rbx1 complex Deposited 2022-10-09 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.76 Å
8H3R Cryo-EM Structure of the KBTBD2-CRL3~N8 dimeric complex Deposited 2022-10-09 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain D 1–108（108 aa）
Chain E 1–108（108 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.36 Å
8IJ1 Protomer 1 and 2 of the asymmetry trimer of the Cul2-Rbx1-EloBC-FEM1B ubiquitin ligase complex Deposited 2023-02-24 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 5 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8JAQ Structure of CRL2APPBP2 bound with RxxGP degron (tetramer) Deposited 2023-05-06 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric
Chain R 1–108（108 aa）
Chain V 1–108（108 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.26 Å
8JAS Structure of CRL2APPBP2 bound with RxxGPAA degron (tetramer) Deposited 2023-05-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 21 PDB declaration: 21-meric
Chain R 1–108（108 aa）
Chain V 1–108（108 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
8JAV Structure of CRL2APPBP2 bound with the C-degron of MRPL28 (tetramer) Deposited 2023-05-07 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric
Chain R 1–108（108 aa）
Chain V 1–108（108 aa）
Not recorded ZN ZINC ION × 8 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å
8JE1 An asymmetry dimer of the Cul2-Rbx1-EloBC-FEM1B ubiquitin ligase complexed with BEX2 Deposited 2023-05-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.95 Å
8K9I Structure of CUL3-RBX1-KLHL22 complex without CUL3 NA motif Deposited 2023-08-01 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 1–108（108 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
8KHP CULLIN3-KLHL22-RBX1 E3 ligase Deposited 2023-08-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 1–108（108 aa）
Chain F 1–108（108 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.67 Å
8OR0 CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2 Deposited 2023-04-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain B 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8OR2 CAND1-CUL1-RBX1-DCNL1 Deposited 2023-04-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8OR3 CAND1-CUL1-RBX1-SKP1-SKP2-DCNL1 Deposited 2023-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8OR4 Partially dissociated CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2 Deposited 2023-04-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric
Chain B 1–108（108 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
8PQL K48-linked ubiquitin chain formation with a cullin-RING E3 ligase and Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2-donor UB-acceptor UB-SIL1 peptide Deposited 2023-07-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: nonameric
Chain K 1–108（108 aa）
Not recorded SY8 5-azanylpentan-2-one × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.76 Å
8Q7E Structure of CUL9-RBX1 ubiquitin E3 ligase complex - hexameric assembly Deposited 2023-08-16 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain C 1–108（108 aa）
Chain D 1–108（108 aa）
Chain G 1–108（108 aa）
Chain H 1–108（108 aa）
Chain K 1–108（108 aa）
Chain L 1–108（108 aa）
Mutation：p.M1_A4del Mutation：p.M1_A4del Mutation：p.M1_A4del Mutation：p.M1_A4del Mutation：p.M1_A4del Mutation：p.M1_A4del No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
8Q7H Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylated and neddylated conformation - focused cullin dimer Deposited 2023-08-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain C 1–108（108 aa）
Chain D 1–108（108 aa）
Mutation：p.M1_A4del Mutation：p.M1_A4del ZN ZINC ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.10 Å
8Q7R Ubiquitin ligation to substrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-FEM1C with trapped UBE2R2~donor UB-Sil1 peptide Deposited 2023-08-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain R 1–108（108 aa）
Not recorded U9O 5-azanyl-1-oxidanyl-pentan-2-one × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.71 Å
8QU8 PROTAC-mediated complex of KRAS with VHL/Elongin-B/Elongin-C/Cullin-2/Rbx1 Deposited 2023-10-14 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain E 2–108（107 aa）
Not recorded ZN ZINC ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 1 WYL (2S,4R)-1-[(2S)-2-[4-[4-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butoxy]-1,2,3-triazol-1-yl]-3-methyl-butanoyl]-N-[(1R)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-2-oxidanyl-ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
8R5H Ubiquitin ligation to neosubstrate by a cullin-RING E3 ligase & Cdc34: NEDD8-CUL2-RBX1-ELOB/C-VHL-MZ1 with trapped UBE2R2~donor UB-BRD4 BD2 Deposited 2023-11-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain R 5–108（104 aa）
Not recorded ZN ZINC ION × 3 SY8 5-azanylpentan-2-one × 1 759 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.44 Å
8RHZ Structure of CUL9-RBX1 ubiquitin E3 ligase complex in unneddylated conformation - symmetry expanded unneddylated dimer Deposited 2023-12-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–108（108 aa）
Chain D 1–108（108 aa）
Mutation：p.M1_A4del Mutation：p.M1_A4del ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.37 Å
8RWZ Open non-crosslinked structure Brd4BD2-MZ1-(NEDD8)-CRL2VHL Deposited 2024-02-05 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 16–108（93 aa）
Not recorded 759 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
8RX0 (NEDD8)-CRL2VHL-MZ1-Brd4BD2-Ub(G76S, K48C)-UBE2R1(C93K, S138C, C191S, C223S)-Ub Deposited 2024-02-05 Different construct Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain R 16–108（93 aa）
Not recorded 759 (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-chlorophenyl)-4,5,13-trimethyl-3-thia-1,8,11,12-tetrazatricyclo[8.3.0.0^{2,6}]trideca-2(6),4,7,10,12-pentaen-9-yl]ethanoylamino]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-2,3-dihydro-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8UBU Cryo-EM structure of dimeric SCF-FBXL17-BACH1BTB E3 ligase complex close conformation Deposited 2023-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain B 16–108（93 aa）
Chain I 16–108（93 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.60 Å
8WDK The complex structure of Cul2-VCB-Protac-Wee1 Deposited 2023-09-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 21–102（82 aa）
Not recorded W6U (2S,4R)-1-[(2S)-3,3-dimethyl-2-[3-[4-[4-[4-[[3-oxidanylidene-1-[6-(2-oxidanylpropan-2-yl)pyridin-2-yl]-2-prop-2-enyl-pyrazolo[3,4-d]pyrimidin-6-yl]amino]phenyl]piperazin-1-yl]butoxy]propanoylamino]butanoyl]-N-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.64 Å
8WQA Cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89 (conformation 1) Deposited 2023-10-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain I 16–108（93 aa）
Chain J 16–108（93 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
8WQB Cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89 (conformation 2) Deposited 2023-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain E 16–108（93 aa）
Chain I 16–108（93 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.37 Å
8WQC cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CDK5R1 Deposited 2023-10-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 16–108（93 aa）
Chain J 16–108（93 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.54 Å
8WQE Cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CUX1 (conformation 1) Deposited 2023-10-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain I 16–108（93 aa）
Chain J 16–108（93 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.38 Å
8WQF cryo-EM structure of CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CUX1 (conformation 2) Deposited 2023-10-11 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain E 16–108（93 aa）
Chain I 16–108（93 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.27 Å
8WQG cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89 (conformation 1) Deposited 2023-10-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain F 16–108（93 aa）
Chain J 16–108（93 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.09 Å
8WQH cryo-EM structure of neddylated CUL2-RBX1-ELOB-ELOC-FEM1B bound with the C-degron of CCDC89 (conformation 2) Deposited 2023-10-11 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: dodecameric
Chain B 16–108（93 aa）
Chain J 16–108（93 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.44 Å
9BJ8 human CRL2-ZYG11B complex Deposited 2024-04-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.78 Å
9BJ9 Human CRL-2 ZYG11B binding to human NLRP1 Gly/N degron Deposited 2024-04-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain R 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.2
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.20 Å
9EFM Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-1 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain K 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.16 Å
9EFQ Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-2 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain K 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.96 Å
9EFV Cryo-EM structure of CSN-N8CUL1 in complex with CSN5i-3 Deposited 2024-11-20 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain K 1–108（108 aa）
Not recorded 6LT 3-(difluoromethyl)-N-{6-[(5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-yl}-1-(propan-2-yl)-1H-pyrazole-5-carboxamide × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
9EG8 Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-4A Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain K 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.39 Å
9EGL Cryo-EM structure of COP9 signalosome precatalytic state with neddylated cullin-3 Deposited 2024-11-21 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: undecameric
Chain K 1–108（108 aa）
Not recorded ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
9J63 Cryo-EM structure of neddylated Cul2-Rbx1-EloBC-FEM1B homodimer Deposited 2024-08-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain E 1–108（108 aa）
Chain H 1–108（108 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
9J64 Cryo-EM structure of neddylated Cul2-Rbx1-EloBC-FEM1B homodimer complexed with FNIP1 degron Deposited 2024-08-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Insufficient information Heteromer；Protein × 8 PDB declaration: octameric
Chain E 1–108（108 aa）
Chain H 1–108（108 aa）
Not recorded ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.28 Å
9J77 Cryo-EM structure of CRL2-FEM1B (dimer 1) Deposited 2024-08-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain E 16–108（93 aa）
Chain I 16–108（93 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.56 Å
9J78 Cryo-EM structure of CRL2-FEM1B (dimer 2) Deposited 2024-08-18 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain E 16–108（93 aa）
Chain I 16–108（93 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.88 Å
9J79 Cryo-EM structure of CRL2-FEM1B bound with TOM20(tetramer) Deposited 2024-08-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 19 PDB declaration: 19-meric
Chain I 16–108（93 aa）
Chain N 16–108（93 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.08 Å
9JKB Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO4 SCF ubiquition ligase complex Deposited 2024-09-15 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric
Chain R 16–108（93 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
9KBD Cryo-EM structure of the CUL1-RBX1-SKP1-FBXO3 SCF ubiquition ligase complex Deposited 2024-10-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain R 1–108（108 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
9LKY Dimer of CRL2-FEM1B bound with PLD6 Deposited 2025-01-17 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 11 PDB declaration: 11-meric
Chain E 16–108（93 aa）
Chain I 16–108（93 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.93 Å
9LWI The head region of HBx-Smc5/6 ubiquitination complex Deposited 2025-02-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 9 PDB declaration: nonameric
Chain H 1–108（108 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9LWJ The head-arm region of HBx-Smc5/6 ubiquitination complex Deposited 2025-02-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain H 1–108（108 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.19 Å
9LWL HBx-Smc5/6 ubiquitination complex Deposited 2025-02-15 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain H 1–108（108 aa）
Not recorded ZN ZINC ION × 6 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 7.25 Å
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 conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 15 PDB declaration: 15-meric
Chain J 1–108（108 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.26 Å
9QO1 Activated 9-subunit COP9 signalosome and neddylated SCF (SKP1-SKP2-CKS1) complex structure Deposited 2025-03-25 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 12 PDB declaration: 12-meric
Chain J 1–108（108 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
9QO2 Dissociation-state-1 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain J 1–108（108 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
9QO4 Dissociation-state-3 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain J 1–108（108 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.95 Å
9QO5 Dissociation-state-4 of 9-subunit CSN and SCF (SKP1-SKP2-CKS1) complex Deposited 2025-03-25 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: 14-meric
Chain J 1–108（108 aa）
Not recorded IHP INOSITOL HEXAKISPHOSPHATE × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5；15 mM Hepes pH 7.5, 120 mM NaCl, 0.5 mM DTT
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
9T32 The Cullin 2 RING VHL E3 ligase dimerised by the homoPROTAC CM11 Deposited 2025-10-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric
Chain R 20–108（89 aa）
Chain S 20–108（89 aa）
Not recorded A1JTC (2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[2-[2-[[(2~{S})-3,3-dimethyl-1-[(2~{S},4~{R})-2-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methylcarbamoyl]-4-oxidanyl-pyrrolidin-1-yl]-1-oxidanylidene-butan-2-yl]amino]-2-oxidanylidene-ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethoxy]ethanoylamino]-3,3-dimethyl-butanoyl]-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-4-oxidanyl-pyrrolidine-2-carboxamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 6.90 Å
9UUM Cryo-EM structure of mezigdomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain R 2–108（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.41 Å
9V0A Cryo-EM structure of pomalidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain R 2–108（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.69 Å
9V0B Cryo-EM structure of avadomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain R 2–108（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.54 Å
9V0F Cryo-EM structure of cemsidomide-organized CRL4-DDB1-CRBN-IKZF3(ZF2-ZF3)-UbcH5a-Ub ubiquitylation assembly Deposited 2025-05-17 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain R 2–108（107 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY mmCIF provides none of the parsed conditions Resolution 3.71 Å
9XZJ Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex and a 3-way DNA fork (consensus structure) Deposited 2025-08-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: octameric
Chain R 1–108（108 aa）
Not recorded AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.13 Å
9XZK Cryo-EM structure of F-box helicase 1 (FBH1) bound to an SCF ubiquitin ligase complex and a 3-way DNA fork (head structure) Deposited 2025-08-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain R 1–108（108 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.91 Å

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

View Construct and Data Evidence
UniProt name RBX1_HUMAN
Isoform —
PDB entities 11
Chains and sequence ranges Author chain R； PDBConstruct 1–108； UniProt 1–108

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 8h3a

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8h3a
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8h3a
Deposition date deposition_date2022-10-08
Structure title titleCryo-EM Structure of the KBTBD2-CRL3~N8(removed)-CSN complex
Keywords keywordsligase, complex; LIGASE
Experimental Method methodELECTRON MICROSCOPY
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier63.99 Å
Radius of gyration Rg (electron density) rg_electron63.65 Å
Forward intensity I(0) i03800790000.00
Molecular weight molecular_weight522860.0 kDa
Excluded volume excluded_volume655540 ų
Envelope volume envelope_volume1065500 ų
Hydration-shell volume shell_volume138470 ų
Envelope diameter envelope_diameter205.9 Å
Shell Rg shell_rg67.08 Å
Envelope Rg envelope_rg60.72 Å
Shape Rg shape_rg63.66 Å
Total Rg total_rg63.68 Å
Total atoms total_atoms36704
Residues n_residues4560
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 dmax211.0 Å
Rg (real space) rg_real63.63 Å
Rg uncertainty (real space) rg_real_error1.75 Å
I(0) (real space) i0_real3.8010e+09
I(0) uncertainty (real space) i0_real_error7.4440e+07
Rg (reciprocal space) rg_reciprocal64.26 Å
I(0) (reciprocal space) i0_reciprocal3805000000.0000
Solution quality estimate total_estimate0.8798
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary84.4 Å
Skewness Skewness skewness0.115
Kurtosis Kurtosis kurtosis-0.508
Angular range angular_range— – 0.1250 Å−1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha208700000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.883; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.825
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (12)

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8. Citations (1)

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9. Files and Curves (10)