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 A, I, Q, Y, g, o480Homo sapiensMutation(s): 0 
Gene Names: GPS1, COPS1, CSN1
Find proteins for Q13098 (Homo sapiens)
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Go to UniProtKB:  Q13098
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PHAROS:  Q13098
GTEx:  ENSG00000169727
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 2 B, J, R, Z, h, p447Homo sapiensMutation(s): 0 
Gene Names: COPS2, CSN2, TRIP15
Find proteins for P61201 (Homo sapiens)
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PHAROS:  P61201
GTEx:  ENSG00000166200
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 3 C, K, S, a, i, q427Homo sapiensMutation(s): 0 
Gene Names: COPS3, CSN3
Find proteins for Q9UNS2 (Homo sapiens)
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GTEx:  ENSG00000141030
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 4 D, L, T, b, j, r410Homo sapiensMutation(s): 0 
Gene Names: COPS4, CSN4
Find proteins for Q9BT78 (Homo sapiens)
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PHAROS:  Q9BT78
GTEx:  ENSG00000138663
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 5 E, M, U, c, k, s325Homo sapiensMutation(s): 0 
Gene Names: COPS5, CSN5, JAB1
EC: 3.4
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GTEx:  ENSG00000121022
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 6 F, N, V, d, l, t331Homo sapiensMutation(s): 0 
Gene Names: COPS6, CSN6, HVIP
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GTEx:  ENSG00000168090
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 7a G, O, W, e, m, u222Homo sapiensMutation(s): 0 
Gene Names: COPS7A, CSN7A, DERP10
Find proteins for Q9UBW8 (Homo sapiens)
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GTEx:  ENSG00000111652
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 8 H, P, X, f, n, v213Homo sapiensMutation(s): 0 
Gene Names: COPS8, CSN8
Find proteins for Q99627 (Homo sapiens)
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GTEx:  ENSG00000198612
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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