6R6H

Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis of Cullin 2 RING E3 ligase regulation by the COP9 signalosome.

Faull, S.V.Lau, A.M.C.Martens, C.Ahdash, Z.Hansen, K.Yebenes, H.Schmidt, C.Beuron, F.Cronin, N.B.Morris, E.P.Politis, A.

(2019) Nat Commun 10: 3814-3814

  • DOI: 10.1038/s41467-019-11772-y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cullin-Ring E3 Ligases (CRLs) regulate a multitude of cellular pathways through specific substrate receptors. The COP9 signalosome (CSN) deactivates CRLs by removing NEDD8 from activated Cullins. Here we present structures of the neddylated and dened ...

    Cullin-Ring E3 Ligases (CRLs) regulate a multitude of cellular pathways through specific substrate receptors. The COP9 signalosome (CSN) deactivates CRLs by removing NEDD8 from activated Cullins. Here we present structures of the neddylated and deneddylated CSN-CRL2 complexes by combining single-particle cryo-electron microscopy (cryo-EM) with chemical cross-linking mass spectrometry (XL-MS). These structures suggest a conserved mechanism of CSN activation, consisting of conformational clamping of the CRL2 substrate by CSN2/CSN4, release of the catalytic CSN5/CSN6 heterodimer and finally activation of the CSN5 deneddylation machinery. Using hydrogen-deuterium exchange (HDX)-MS we show that CRL2 activates CSN5/CSN6 in a neddylation-independent manner. The presence of NEDD8 is required to activate the CSN5 active site. Overall, by synergising cryo-EM with MS, we identify sensory regions of the CSN that mediate its stepwise activation and provide a framework for understanding the regulatory mechanism of other Cullin family members.


    Organizational Affiliation

    Centro de Investigaciones Biológicas, Consejo Superior de Investigaciones Científicas, Madrid, Spain.,Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK. argyris.politis@kcl.ac.uk.,Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK. ed.morris@icr.ac.uk.,Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK.,Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK.,Interdisciplinary Research Center HALOmem, Charles Tanford Protein Centre, Martin Luther University Halle-Wittenberg, Kurt-Mothes-Strasse 3a, 06120, Halle/Saale, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
COP9 signalosome complex subunit 1
A
491Homo 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
443Homo 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
403Homo 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
406Homo 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
334Homo 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
308Homo 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 8
H
209Homo sapiensMutation(s): 0 
Gene Names: COPS8 (CSN8)
Find proteins for Q99627 (Homo sapiens)
Go to Gene View: COPS8
Go to UniProtKB:  Q99627
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
Cullin-2
O
745Homo sapiensMutation(s): 0 
Gene Names: CUL2
Find proteins for Q13617 (Homo sapiens)
Go to Gene View: CUL2
Go to UniProtKB:  Q13617
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
Elongin-B
P
105Homo sapiensMutation(s): 0 
Gene Names: ELOB (TCEB2)
Find proteins for Q15370 (Homo sapiens)
Go to Gene View: ELOB
Go to UniProtKB:  Q15370
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
ELOC_HUMAN
Q
99Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ELC1
Find proteins for Q03071 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q03071
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
RBX1_HUMAN
R
86Homo sapiensMutation(s): 0 
Gene Names: RBX1 (RNF75, ROC1)
EC: 2.3.2.27, 2.3.2.32
Find proteins for P62877 (Homo sapiens)
Go to Gene View: RBX1
Go to UniProtKB:  P62877
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
von Hippel-Lindau disease tumor suppressor
V
150Homo sapiensMutation(s): 0 
Gene Names: VHL
Find proteins for P40337 (Homo sapiens)
Go to Gene View: VHL
Go to UniProtKB:  P40337
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
COP9 signalosome complex subunit 7b
G
206Homo sapiensMutation(s): 0 
Gene Names: COPS7B (CSN7B)
Find proteins for Q9H9Q2 (Homo sapiens)
Go to Gene View: COPS7B
Go to UniProtKB:  Q9H9Q2
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
E
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited Kingdom--

Revision History 

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2019-09-04
    Type: Data collection, Database references