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 1.3 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: 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 ...

    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

    University of Basel, Petersplatz 10, 4003 Basel, Switzerland.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 1480Homo sapiensMutation(s): 0 
Gene Names: GPS1COPS1CSN1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13098 (Homo sapiens)
Explore Q13098 
Go to UniProtKB:  Q13098
PHAROS:  Q13098
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13098
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 2447Homo sapiensMutation(s): 0 
Gene Names: COPS2CSN2TRIP15
UniProt & NIH Common Fund Data Resources
Find proteins for P61201 (Homo sapiens)
Explore P61201 
Go to UniProtKB:  P61201
PHAROS:  P61201
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61201
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 3427Homo sapiensMutation(s): 0 
Gene Names: COPS3CSN3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNS2 (Homo sapiens)
Explore Q9UNS2 
Go to UniProtKB:  Q9UNS2
PHAROS:  Q9UNS2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UNS2
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 4410Homo sapiensMutation(s): 0 
Gene Names: COPS4CSN4
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BT78 (Homo sapiens)
Explore Q9BT78 
Go to UniProtKB:  Q9BT78
PHAROS:  Q9BT78
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BT78
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 5325Homo sapiensMutation(s): 0 
Gene Names: COPS5CSN5JAB1
EC: 3.4
UniProt & NIH Common Fund Data Resources
Find proteins for Q92905 (Homo sapiens)
Explore Q92905 
Go to UniProtKB:  Q92905
PHAROS:  Q92905
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92905
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 6331Homo sapiensMutation(s): 0 
Gene Names: COPS6CSN6HVIP
UniProt & NIH Common Fund Data Resources
Find proteins for Q7L5N1 (Homo sapiens)
Explore Q7L5N1 
Go to UniProtKB:  Q7L5N1
PHAROS:  Q7L5N1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7L5N1
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 7a222Homo sapiensMutation(s): 0 
Gene Names: COPS7ACSN7ADERP10
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBW8 (Homo sapiens)
Explore Q9UBW8 
Go to UniProtKB:  Q9UBW8
PHAROS:  Q9UBW8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBW8
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 8213Homo sapiensMutation(s): 0 
Gene Names: COPS8CSN8
UniProt & NIH Common Fund Data Resources
Find proteins for Q99627 (Homo sapiens)
Explore Q99627 
Go to UniProtKB:  Q99627
PHAROS:  Q99627
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99627
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
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