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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 1 AIQYgo480Homo sapiensMutation(s): 0 
Gene Names: GPS1COPS1CSN1
Find proteins for Q13098 (Homo sapiens)
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PHAROS:  Q13098
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 2 BJRZhp447Homo sapiensMutation(s): 0 
Gene Names: COPS2CSN2TRIP15
Find proteins for P61201 (Homo sapiens)
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PHAROS:  P61201
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 3 CKSaiq427Homo sapiensMutation(s): 0 
Gene Names: COPS3CSN3
Find proteins for Q9UNS2 (Homo sapiens)
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PHAROS:  Q9UNS2
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 4 DLTbjr410Homo sapiensMutation(s): 0 
Gene Names: COPS4CSN4
Find proteins for Q9BT78 (Homo sapiens)
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PHAROS:  Q9BT78
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 5 EMUcks325Homo sapiensMutation(s): 0 
Gene Names: COPS5CSN5JAB1
EC: 3.4
Find proteins for Q92905 (Homo sapiens)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 6 FNVdlt331Homo sapiensMutation(s): 0 
Gene Names: COPS6CSN6HVIP
Find proteins for Q7L5N1 (Homo sapiens)
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PHAROS:  Q7L5N1
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 7a GOWemu222Homo sapiensMutation(s): 0 
Gene Names: COPS7ACSN7ADERP10
Find proteins for Q9UBW8 (Homo sapiens)
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PHAROS:  Q9UBW8
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 8 HPXfnv213Homo sapiensMutation(s): 0 
Gene Names: COPS8CSN8
Find proteins for Q99627 (Homo sapiens)
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PHAROS:  Q99627
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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

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Entry History 

Deposition Data

Revision History 

  • 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