6R7F

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 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: https://doi.org/10.1038/s41467-019-11772-y
  • Primary Citation of Related Structures:  
    6R6H, 6R7F, 6R7H, 6R7I, 6R7N

  • 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). 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.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 1433Homo sapiensMutation(s): 0 
Gene Names: GPS1COPS1CSN1
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GTEx:  ENSG00000169727 
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UniProt GroupQ13098
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 2443Homo sapiensMutation(s): 0 
Gene Names: COPS2CSN2TRIP15
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GTEx:  ENSG00000166200 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 3403Homo sapiensMutation(s): 0 
Gene Names: COPS3CSN3
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GTEx:  ENSG00000141030 
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UniProt GroupQ9UNS2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 4406Homo sapiensMutation(s): 0 
Gene Names: COPS4CSN4
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GTEx:  ENSG00000138663 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 5311Homo sapiensMutation(s): 0 
Gene Names: COPS5CSN5JAB1
EC: 3.4
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GTEx:  ENSG00000121022 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 6288Homo sapiensMutation(s): 0 
Gene Names: COPS6CSN6HVIP
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GTEx:  ENSG00000168090 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 8G [auth H]209Homo sapiensMutation(s): 0 
Gene Names: COPS8CSN8
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GTEx:  ENSG00000198612 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 7bH [auth G]208Homo sapiensMutation(s): 0 
Gene Names: COPS7BCSN7B
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PHAROS:  Q9H9Q2
GTEx:  ENSG00000144524 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
von Hippel-Lindau disease tumor suppressorI [auth V]160Homo sapiensMutation(s): 0 
Gene Names: VHL
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GTEx:  ENSG00000134086 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-BJ [auth P]118Homo sapiensMutation(s): 0 
Gene Names: ELOBTCEB2
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GTEx:  ENSG00000103363 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Elongin-CK [auth Q]112Homo sapiensMutation(s): 0 
Gene Names: ELOCTCEB1
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GTEx:  ENSG00000154582 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Cullin-2L [auth O]745Homo sapiensMutation(s): 0 
Gene Names: CUL2
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GTEx:  ENSG00000108094 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RBX1M [auth R]90Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000100387 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
NEDD876Homo sapiensMutation(s): 0 
Gene Names: NEDD8
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GTEx:  ENSG00000129559 
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UniProt GroupQ15843
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.20 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
  • Version 1.2: 2019-10-09
    Changes: Advisory, Data collection, Derived calculations