4D18

Crystal structure of the COP9 signalosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.08 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.236 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of the Human Cop9 Signalosome

Lingaraju, G.M.Bunker, R.D.Cavadini, S.Hess, D.Hassiepen, U.Renatus, M.Fischer, E.S.Thoma, N.H.

(2014) Nature 512: 161

  • DOI: 10.1038/nature13566
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Ubiquitination is a crucial cellular signalling process, and is controlled on multiple levels. Cullin-RING E3 ubiquitin ligases (CRLs) are regulated by the eight-subunit COP9 signalosome (CSN). CSN inactivates CRLs by removing their covalently attach ...

    Ubiquitination is a crucial cellular signalling process, and is controlled on multiple levels. Cullin-RING E3 ubiquitin ligases (CRLs) are regulated by the eight-subunit COP9 signalosome (CSN). CSN inactivates CRLs by removing their covalently attached activator, NEDD8. NEDD8 cleavage by CSN is catalysed by CSN5, a Zn(2+)-dependent isopeptidase that is inactive in isolation. Here we present the crystal structure of the entire ∼350-kDa human CSN holoenzyme at 3.8 Å resolution, detailing the molecular architecture of the complex. CSN has two organizational centres: a horseshoe-shaped ring created by its six proteasome lid-CSN-initiation factor 3 (PCI) domain proteins, and a large bundle formed by the carboxy-terminal α-helices of every subunit. CSN5 and its dimerization partner, CSN6, are intricately embedded at the core of the helical bundle. In the substrate-free holoenzyme, CSN5 is autoinhibited, which precludes access to the active site. We find that neddylated CRL binding to CSN is sensed by CSN4, and communicated to CSN5 with the assistance of CSN6, resulting in activation of the deneddylase.


    Organizational Affiliation

    1] Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland [2] University of Basel, Petersplatz 10, 4003 Basel, Switzerland [3].




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COP9 SIGNALOSOME COMPLEX SUBUNIT 1
A, I
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
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
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
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
327Homo 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
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
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
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 
E, M
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.08 Å
  • R-Value Free: 0.253 
  • R-Value Work: 0.236 
  • Space Group: P 31
Unit Cell:
Length (Å)Angle (°)
a = 147.680α = 90.00
b = 147.680β = 90.00
c = 317.850γ = 120.00
Software Package:
Software NamePurpose
BUSTERrefinement
SHARPphasing
XDSdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2014-07-30
    Type: Database references
  • Version 1.2: 2014-08-20
    Type: Database references