9A02 | pdb_00009a02

Integrative structure of the non-canonical human COP9 Signalosome


Integrative Structure Snapshot

  • Multi-Scale: Yes 
  • Multi-State: No 
  • Ordered-State: No 
  • Deposited Models: 1 
  • Representative Model: 1 

This is version 1.0 of the entry. See complete history


Literature

Structural dynamics of the human COP9 signalosome revealed by cross-linking mass spectrometry and integrative modeling.

Gutierrez CChemmama IEMao HYu CEcheverria IBlock SARychnovsky SDZheng NSali AHuang L

(2020) Proc Natl Acad Sci U S A 117: 4088-4098

  • DOI: https://doi.org/10.1073/pnas.1915542117
  • Primary Citation of Related Structures:  
    9A01, 9A02

  • PubMed Abstract: 

    The COP9 signalosome (CSN) is an evolutionarily conserved eight-subunit (CSN1-8) protein complex that controls protein ubiquitination by deneddylating Cullin-RING E3 ligases (CRLs). The activation and function of CSN hinges on its structural dynamics, which has been challenging to decipher by conventional tools. Here, we have developed a multichemistry cross-linking mass spectrometry approach enabled by three mass spectometry-cleavable cross-linkers to generate highly reliable cross-link data. We applied this approach with integrative structure modeling to determine the interaction and structural dynamics of CSN with the recently discovered ninth subunit, CSN9, in solution. Our results determined the localization of CSN9 binding sites and revealed CSN9-dependent structural changes of CSN. Together with biochemical analysis, we propose a structural model in which CSN9 binding triggers CSN to adopt a configuration that facilitates CSN-CRL interactions, thereby augmenting CSN deneddylase activity. Our integrative structure analysis workflow can be generalized to define in-solution architectures of dynamic protein complexes that remain inaccessible to other approaches.


  • Organizational Affiliation
    • Department of Physiology & Biophysics, University of California, Irvine, CA 92697.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CSN1491Homo sapiensMutation(s): 0 
Gene Names: GPS1
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Find proteins for Q13098 (Homo sapiens)
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PHAROS:  Q13098
GTEx:  ENSG00000169727 
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UniProt GroupQ13098
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CSN2443Homo sapiensMutation(s): 0 
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PHAROS:  P61201
GTEx:  ENSG00000166200 
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UniProt GroupP61201
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CSN3423Homo sapiensMutation(s): 0 
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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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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CSN4406Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000138663 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
CSN5334Homo sapiensMutation(s): 0 
EC: 3.4
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PHAROS:  Q92905
GTEx:  ENSG00000121022 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
CSN6327Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000168090 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
CSN7264Homo sapiensMutation(s): 0 
Gene Names: COPS7B
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GTEx:  ENSG00000144524 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
CSN8209Homo sapiensMutation(s): 0 
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GTEx:  ENSG00000198612 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
CSN957Homo sapiensMutation(s): 0 
Gene Names: COPS9
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GTEx:  ENSG00000172428 
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Experimental Data & Validation

Integrative Structure Snapshot

  • Multi-Scale: Yes 
  • Multi-State: No 
  • Ordered-State: No 
  • Deposited Models: 1 
  • Representative Model: 1 

Structure Validation

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View Summary Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-30
    Type: Initial release