4WSN

Crystal structure of the COP9 signalosome, a P1 crystal form


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.50 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Cullin-RING ubiquitin E3 ligase regulation by the COP9 signalosome.

Cavadini, S.Fischer, E.S.Bunker, R.D.Potenza, A.Lingaraju, G.M.Goldie, K.N.Mohamed, W.I.Faty, M.Petzold, G.Beckwith, R.E.Tichkule, R.B.Hassiepen, U.Abdulrahman, W.Pantelic, R.S.Matsumoto, S.Sugasawa, K.Stahlberg, H.Thoma, N.H.

(2016) Nature 531: 598-603

  • DOI: https://doi.org/10.1038/nature17416
  • Primary Citation of Related Structures:  
    4WSN

  • PubMed Abstract: 

    The cullin-RING ubiquitin E3 ligase (CRL) family comprises over 200 members in humans. The COP9 signalosome complex (CSN) regulates CRLs by removing their ubiquitin-like activator NEDD8. The CUL4A-RBX1-DDB1-DDB2 complex (CRL4A(DDB2)) monitors the genome for ultraviolet-light-induced DNA damage. CRL4A(DBB2) is inactive in the absence of damaged DNA and requires CSN to regulate the repair process. The structural basis of CSN binding to CRL4A(DDB2) and the principles of CSN activation are poorly understood. Here we present cryo-electron microscopy structures for CSN in complex with neddylated CRL4A ligases to 6.4 Å resolution. The CSN conformers defined by cryo-electron microscopy and a novel apo-CSN crystal structure indicate an induced-fit mechanism that drives CSN activation by neddylated CRLs. We find that CSN and a substrate cannot bind simultaneously to CRL4A, favouring a deneddylated, inactive state for substrate-free CRL4 complexes. These architectural and regulatory principles appear conserved across CRL families, allowing global regulation by CSN.


  • Organizational Affiliation

    Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 1480Homo sapiensMutation(s): 0 
Gene Names: GPS1COPS1CSN1
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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 2447Homo sapiensMutation(s): 0 
Gene Names: COPS2CSN2TRIP15
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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 3427Homo sapiensMutation(s): 0 
Gene Names: COPS3CSN3
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Find proteins for Q9UNS2 (Homo sapiens)
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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 4410Homo sapiensMutation(s): 0 
Gene Names: COPS4CSN4
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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 5325Homo sapiensMutation(s): 0 
Gene Names: COPS5CSN5JAB1
EC: 3.4
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GTEx:  ENSG00000121022 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 6331Homo sapiensMutation(s): 0 
Gene Names: COPS6CSN6HVIP
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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 7a222Homo sapiensMutation(s): 0 
Gene Names: COPS7ACSN7ADERP10
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Find proteins for Q9UBW8 (Homo sapiens)
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PHAROS:  Q9UBW8
GTEx:  ENSG00000111652 
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UniProt GroupQ9UBW8
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 8213Homo sapiensMutation(s): 0 
Gene Names: COPS8CSN8
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Find proteins for Q99627 (Homo sapiens)
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PHAROS:  Q99627
GTEx:  ENSG00000198612 
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UniProt GroupQ99627
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.50 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.254 
  • R-Value Observed: 0.255 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 150.638α = 92.34
b = 150.983β = 92.62
c = 336.72γ = 119.88
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-23
    Type: Initial release
  • Version 1.1: 2016-04-06
    Changes: Database references
  • Version 1.2: 2016-04-13
    Changes: Database references
  • Version 1.3: 2019-03-27
    Changes: Data collection, Source and taxonomy
  • Version 1.4: 2024-01-10
    Changes: Data collection, Database references, Refinement description