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 6R7H | pdb_00006r7h

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 6R7H

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 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: 
    • Division of Structural Biology, The Institute of Cancer Research, London, SW3 6JB, UK.

Macromolecule Content 

  • Total Structure Weight: 414.39 kDa 
  • Atom Count: 28,843 
  • Modeled Residue Count: 3,592 
  • Deposited Residue Count: 3,622 
  • Unique protein chains: 12

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 1433Homo sapiensMutation(s): 0 
Gene Names: GPS1, COPS1, CSN1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13098 (Homo sapiens)
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PHAROS:  Q13098
GTEx:  ENSG00000169727 
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UniProt GroupQ13098
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongin-CB [auth Q]112Homo sapiensMutation(s): 0 
Gene Names: ELOC, TCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens)
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PHAROS:  Q15369
GTEx:  ENSG00000154582 
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UniProt GroupQ15369
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Cullin-2C [auth O]654Homo sapiensMutation(s): 0 
Gene Names: CUL2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13617 (Homo sapiens)
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PHAROS:  Q13617
GTEx:  ENSG00000108094 
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UniProt GroupQ13617
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RBX1D [auth R]90Homo sapiensMutation(s): 0 
EC: 2.3.2.32 (UniProt), 2.3.2.27 (UniProt)
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Find proteins for P62877 (Homo sapiens)
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GTEx:  ENSG00000100387 
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UniProt GroupP62877
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 2E [auth B]414Homo sapiensMutation(s): 0 
Gene Names: COPS2, CSN2, TRIP15
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GTEx:  ENSG00000166200 
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Reference Sequence
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 3F [auth C]403Homo sapiensMutation(s): 0 
Gene Names: COPS3, CSN3
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Find proteins for Q9UNS2 (Homo sapiens)
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PHAROS:  Q9UNS2
GTEx:  ENSG00000141030 
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UniProt GroupQ9UNS2
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 4G [auth D]406Homo sapiensMutation(s): 0 
Gene Names: COPS4, CSN4
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Find proteins for Q9BT78 (Homo sapiens)
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GTEx:  ENSG00000138663 
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Reference Sequence
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 5H [auth E]311Homo sapiensMutation(s): 0 
Gene Names: COPS5, CSN5, JAB1
EC: 3.4
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Find proteins for Q92905 (Homo sapiens)
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GTEx:  ENSG00000121022 
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Reference Sequence
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 6I [auth F]288Homo sapiensMutation(s): 0 
Gene Names: COPS6, CSN6, HVIP
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Find proteins for Q7L5N1 (Homo sapiens)
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GTEx:  ENSG00000168090 
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Reference Sequence
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 7bJ [auth G]208Homo sapiensMutation(s): 0 
Gene Names: COPS7B, CSN7B
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Find proteins for Q9H9Q2 (Homo sapiens)
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GTEx:  ENSG00000144524 
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Reference Sequence
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
COP9 signalosome complex subunit 8K [auth H]199Homo sapiensMutation(s): 0 
Gene Names: COPS8, CSN8
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Find proteins for Q99627 (Homo sapiens)
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GTEx:  ENSG00000198612 
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Reference Sequence
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Elongin-BL [auth P]104Homo sapiensMutation(s): 0 
Gene Names: ELOB, TCEB2
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Find proteins for Q15370 (Homo sapiens)
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GTEx:  ENSG00000103363 
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 8.80 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: 2024-05-22
    Changes: Data collection, Database references