4WSN

Crystal structure of the COP9 signalosome, a P1 crystal form

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.5 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.254 

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

  • 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 gen ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COP9 signalosome complex subunit 1
A, I, Q, Y, g, o
480Homo sapiensMutation(s): 0 
Gene Names: GPS1 (COPS1, CSN1)
Find proteins for Q13098 (Homo sapiens)
Go to Gene View: GPS1
Go to UniProtKB:  Q13098
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
COP9 signalosome complex subunit 2
B, J, R, Z, h, p
447Homo sapiensMutation(s): 0 
Gene Names: COPS2 (CSN2, TRIP15)
Find proteins for P61201 (Homo sapiens)
Go to Gene View: COPS2
Go to UniProtKB:  P61201
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
COP9 signalosome complex subunit 3
C, K, S, a, i, q
427Homo sapiensMutation(s): 0 
Gene Names: COPS3 (CSN3)
Find proteins for Q9UNS2 (Homo sapiens)
Go to Gene View: COPS3
Go to UniProtKB:  Q9UNS2
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
COP9 signalosome complex subunit 4
D, L, T, b, j, r
410Homo sapiensMutation(s): 0 
Gene Names: COPS4 (CSN4)
Find proteins for Q9BT78 (Homo sapiens)
Go to Gene View: COPS4
Go to UniProtKB:  Q9BT78
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
COP9 signalosome complex subunit 5
E, M, U, c, k, s
325Homo sapiensMutation(s): 0 
Gene Names: COPS5 (CSN5, JAB1)
EC: 3.4.-.-
Find proteins for Q92905 (Homo sapiens)
Go to Gene View: COPS5
Go to UniProtKB:  Q92905
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
COP9 signalosome complex subunit 6
F, N, V, d, l, t
331Homo sapiensMutation(s): 0 
Gene Names: COPS6 (CSN6, HVIP)
Find proteins for Q7L5N1 (Homo sapiens)
Go to Gene View: COPS6
Go to UniProtKB:  Q7L5N1
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
COP9 signalosome complex subunit 7a
G, O, W, e, m, u
222Homo sapiensMutation(s): 0 
Gene Names: COPS7A (CSN7A, DERP10)
Find proteins for Q9UBW8 (Homo sapiens)
Go to Gene View: COPS7A
Go to UniProtKB:  Q9UBW8
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
COP9 signalosome complex subunit 8
H, P, X, f, n, v
213Homo sapiensMutation(s): 0 
Gene Names: COPS8 (CSN8)
Find proteins for Q99627 (Homo sapiens)
Go to Gene View: COPS8
Go to UniProtKB:  Q99627
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
c, E, k, M, s, U
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 5.5 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.254 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 150.638α = 92.34
b = 150.983β = 92.62
c = 336.720γ = 119.88
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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