4D10

Crystal structure of the COP9 signalosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


This is version 1.4 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:  
    4D0P, 4D18, 4D10

  • 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 attached activator, NEDD8 ...

    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.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 SIGNALOSOME COMPLEX SUBUNIT 1A, I480Homo sapiensMutation(s): 0 
Gene Names: GPS1COPS1CSN1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 SIGNALOSOME COMPLEX SUBUNIT 2B, J447Homo sapiensMutation(s): 0 
Gene Names: COPS2CSN2TRIP15
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 SIGNALOSOME COMPLEX SUBUNIT 3C, K423Homo sapiensMutation(s): 0 
Gene Names: COPS3CSN3
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 SIGNALOSOME COMPLEX SUBUNIT 4D, L410Homo sapiensMutation(s): 0 
Gene Names: COPS4CSN4
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 SIGNALOSOME COMPLEX SUBUNIT 5E, M334Homo sapiensMutation(s): 0 
Gene Names: COPS5CSN5JAB1
EC: 3.4
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 SIGNALOSOME COMPLEX SUBUNIT 6F, N331Homo sapiensMutation(s): 0 
Gene Names: COPS6CSN6HVIP
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 SIGNALOSOME COMPLEX SUBUNIT 7AG, O222Homo sapiensMutation(s): 0 
Gene Names: COPS7ACSN7ADERP10
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 SIGNALOSOME COMPLEX SUBUNIT 8H, P212Homo sapiensMutation(s): 0 
Gene Names: COPS8CSN8
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
Q [auth E], R [auth M]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 31
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 151.615α = 90
b = 151.615β = 90
c = 343.069γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
SHARPphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2014-07-30
    Changes: Database references
  • Version 1.2: 2014-08-20
    Changes: Database references
  • Version 1.3: 2019-03-06
    Changes: Data collection, Experimental preparation, Other
  • Version 1.4: 2019-03-27
    Changes: Data collection, Source and taxonomy