9PH4 | pdb_00009ph4

Cryo-EM structure of COP9 signalosome in complex with CSN5i-1a

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history. 


Literature

Cryo-EM structure of COP9 signalosome in complex with CSN5i-1a

Shi, H., Zheng, N.

To be published.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 1491Homo sapiensMutation(s): 0 
Gene Names: GPS1, COPS1, CSN1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13098 (Homo sapiens)
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PHAROS:  Q13098
GTEx:  ENSG00000169727 
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UniProt GroupQ13098
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 2443Homo sapiensMutation(s): 0 
Gene Names: COPS2, CSN2, TRIP15
UniProt & NIH Common Fund Data Resources
Find proteins for P61201 (Homo sapiens)
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PHAROS:  P61201
GTEx:  ENSG00000166200 
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UniProt GroupP61201
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 3423Homo sapiensMutation(s): 0 
Gene Names: COPS3, CSN3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNS2 (Homo sapiens)
Explore Q9UNS2 
Go to UniProtKB:  Q9UNS2
PHAROS:  Q9UNS2
GTEx:  ENSG00000141030 
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UniProt GroupQ9UNS2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 4406Homo sapiensMutation(s): 0 
Gene Names: COPS4, CSN4
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Find proteins for Q9BT78 (Homo sapiens)
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PHAROS:  Q9BT78
GTEx:  ENSG00000138663 
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UniProt GroupQ9BT78
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 5334Homo sapiensMutation(s): 0 
Gene Names: COPS5, CSN5, JAB1
EC: 3.4
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Find proteins for Q92905 (Homo sapiens)
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PHAROS:  Q92905
GTEx:  ENSG00000121022 
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UniProt GroupQ92905
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 6327Homo sapiensMutation(s): 0 
Gene Names: COPS6, CSN6, HVIP
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Find proteins for Q7L5N1 (Homo sapiens)
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PHAROS:  Q7L5N1
GTEx:  ENSG00000168090 
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UniProt GroupQ7L5N1
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 7b264Homo sapiensMutation(s): 0 
Gene Names: COPS7B, CSN7B
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H9Q2 (Homo sapiens)
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PHAROS:  Q9H9Q2
GTEx:  ENSG00000144524 
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UniProt GroupQ9H9Q2
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 8209Homo sapiensMutation(s): 0 
Gene Names: COPS8, CSN8
UniProt & NIH Common Fund Data Resources
Find proteins for Q99627 (Homo sapiens)
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PHAROS:  Q99627
GTEx:  ENSG00000198612 
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UniProt GroupQ99627
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1CH3 (Subject of Investigation/LOI)
Query on A1CH3
Download Ideal Coordinates CCD File 
J [auth E]6-[(4R,5S,6S)-6-hydroxy-6,7,8,9-tetrahydro-5H-imidazo[1,5-a]azepin-5-yl][1,1'-biphenyl]-3-carbonitrile
C21 H19 N3 O
YJXOYLFTOJVXJZ-SFTDATJTSA-N
ZN (Subject of Investigation/LOI)
Query on ZN
Download Ideal Coordinates CCD File 
I [auth E]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

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View more in-depth experimental data
Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-12-03
    Type: Initial release