6R7N

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.50 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:  
    6R6H, 6R7N, 6R7F, 6R7H, 6R7I

  • 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 deneddylated CSN-CRL2 complexes by combining single-particle cryo-electron microscopy (cryo-EM) with chemical cross-linking mass spectrometry (XL-MS) ...

    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

    Department of Chemistry, King's College London, 7 Trinity Street, London, SE1 1DB, UK. argyris.politis@kcl.ac.uk.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 1A491Homo sapiensMutation(s): 0 
Gene Names: GPS1COPS1CSN1
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 4B [auth D]406Homo sapiensMutation(s): 0 
Gene Names: COPS4CSN4
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Find proteins for Q9BT78 (Homo sapiens)
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PHAROS:  Q9BT78
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 8C [auth H]199Homo sapiensMutation(s): 0 
Gene Names: COPS8CSN8
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Find proteins for Q99627 (Homo sapiens)
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Elongin-BD [auth P]104Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
Elongin-CE [auth Q]112Homo sapiensMutation(s): 0 
Gene Names: ELOCTCEB1
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
RBX1 E3 ubiquitin-protein ligaseF [auth R]86Homo sapiensMutation(s): 0 
Gene Names: RBX1RNF75ROC1
EC: 2.3.2.27 (UniProt), 2.3.2.32 (UniProt)
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 3G [auth C]401Homo sapiensMutation(s): 0 
Gene Names: COPS3CSN3
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
CSN7B_HUMANH [auth G]215Homo sapiensMutation(s): 0 
Gene Names: COPS7BCSN7B
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
Cullin-2I [auth O]745Homo sapiensMutation(s): 0 
Gene Names: CUL2
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 2J [auth B]443Homo sapiensMutation(s): 0 
Gene Names: COPS2CSN2TRIP15
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited Kingdom--

Revision History  (Full details and data files)

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