8ZZQ | pdb_00008zzq

The proteasome-interacting Ecm29 protein disassembles the 26S proteasome in response to oxidative stress

Integrative structure models are generated using different types of input information, including varied experimental data, physical principles, statistical preferences, and other prior information.


Integrative Structure Snapshot

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

This is version 1.0 of the entry. See complete history

Literature

The proteasome-interacting Ecm29 protein disassembles the 26S proteasome in response to oxidative stress.

Wang, X.Chemmama, I.E.Yu, C.Huszagh, A.Xu, Y.Viner, R.Block, S.A.Cimermancic, P.Rychnovsky, S.D.Ye, Y.Sali, A.Huang, L.

(2017) J Biol Chem 292: 16310-16320

  • DOI: https://doi.org/10.1074/jbc.M117.803619
  • Primary Citation Related Structures: 
    8ZZQ

  • PubMed Abstract: 

    Oxidative stress has been implicated in multiple human neurological and other disorders. Proteasomes are multi-subunit proteases critical for the removal of oxidatively damaged proteins. To understand stress-associated human pathologies, it is important to uncover the molecular events underlying the regulation of proteasomes upon oxidative stress. To this end, we investigated H 2 O 2 stress-induced molecular changes of the human 26S proteasome and determined that stress-induced 26S proteasome disassembly is conserved from yeast to human. Moreover, we developed and employed a new proteomic approach, XAP ( in vivo cross-linking-assisted affinity purification), coupled with stable isotope labeling with amino acids in cell culture (SILAC)-based quantitative MS, to capture and quantify several weakly bound proteasome-interacting proteins and examine their roles in stress-mediated proteasomal remodeling. Our results indicate that the adapter protein Ecm29 is the main proteasome-interacting protein responsible for stress-triggered remodeling of the 26S proteasome in human cells. Importantly, using a disuccinimidyl sulfoxide-based cross-linking MS platform, we mapped the interactions of Ecm29 within itself and with proteasome subunits and determined the architecture of the Ecm29-proteasome complex with integrative structure modeling. These results enabled us to propose a structural model in which Ecm29 intrudes on the interaction between the 20S core particle and the 19S regulatory particle in the 26S proteasome, disrupting the proteasome structure in response to oxidative stress.


  • Organizational Affiliation
    • From the Department of Physiology and Biophysics, University of California, Irvine, California 92697.

Macromolecule Content 

  • Total Structure Weight: 1,282.91 kDa 
  • Modeled Residue Count: 9,839 
  • Deposited Residue Count: 9,839 
  • Unique protein chains: 19

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Rpt6406Homo sapiensMutation(s): 0 
Gene Names: PSMC5
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Find proteins for P62195 (Homo sapiens)
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PHAROS:  P62195
GTEx:  ENSG00000087191 
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UniProt GroupP62195
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Rpt4389Homo sapiensMutation(s): 0 
Gene Names: PSMC6
UniProt & NIH Common Fund Data Resources
Find proteins for P62333 (Homo sapiens)
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GTEx:  ENSG00000100519 
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UniProt GroupP62333
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Rpt5439Homo sapiensMutation(s): 0 
Gene Names: PSMC3
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GTEx:  ENSG00000165916 
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UniProt GroupP17980
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Rpt2440Homo sapiensMutation(s): 0 
Gene Names: PSMC1
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Find proteins for P62191 (Homo sapiens)
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GTEx:  ENSG00000100764 
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UniProt GroupP62191
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Rpt3418Homo sapiensMutation(s): 0 
Gene Names: PSMC4
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Find proteins for P43686 (Homo sapiens)
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GTEx:  ENSG00000013275 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Rpt1433Homo sapiensMutation(s): 0 
Gene Names: PSMC2
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GTEx:  ENSG00000161057 
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Rpn12350Homo sapiensMutation(s): 0 
Gene Names: PSMD8
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Find proteins for P48556 (Homo sapiens)
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GTEx:  ENSG00000099341 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Rpn10377Homo sapiensMutation(s): 0 
Gene Names: PSMD4
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Find proteins for P55036 (Homo sapiens)
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GTEx:  ENSG00000159352 
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Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Rpn11310Homo sapiensMutation(s): 0 
Gene Names: PSMD14
EC: 3.4.19.12
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GTEx:  ENSG00000115233 
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Entity ID: 10
MoleculeChains  Sequence LengthOrganismDetailsImage
Rpn1570Homo sapiensMutation(s): 0 
Gene Names: SEM1
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Find proteins for P60896 (Homo sapiens)
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GTEx:  ENSG00000127922 
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Entity ID: 11
MoleculeChains  Sequence LengthOrganismDetailsImage
Rpn1908Homo sapiensMutation(s): 0 
Gene Names: PSMD2
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GTEx:  ENSG00000175166 
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Entity ID: 12
MoleculeChains  Sequence LengthOrganismDetailsImage
Rpn2953Homo sapiensMutation(s): 0 
Gene Names: PSMD1
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Find proteins for Q99460 (Homo sapiens)
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GTEx:  ENSG00000173692 
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Entity ID: 13
MoleculeChains  Sequence LengthOrganismDetailsImage
Rpn3534Homo sapiensMutation(s): 0 
Gene Names: PSMD3
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GTEx:  ENSG00000108344 
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Entity ID: 14
MoleculeChains  Sequence LengthOrganismDetailsImage
Rpn5456Homo sapiensMutation(s): 0 
Gene Names: PSMD12
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GTEx:  ENSG00000197170 
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Entity ID: 15
MoleculeChains  Sequence LengthOrganismDetailsImage
Rpn6422Homo sapiensMutation(s): 0 
Gene Names: PSMD11
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GTEx:  ENSG00000108671 
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Entity ID: 16
MoleculeChains  Sequence LengthOrganismDetailsImage
Rpn7389Homo sapiensMutation(s): 0 
Gene Names: PSMD6
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Find proteins for Q15008 (Homo sapiens)
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GTEx:  ENSG00000163636 
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Entity ID: 17
MoleculeChains  Sequence LengthOrganismDetailsImage
Rpn8324Homo sapiensMutation(s): 0 
Gene Names: PSMD7
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Find proteins for P51665 (Homo sapiens)
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GTEx:  ENSG00000103035 
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Entity ID: 18
MoleculeChains  Sequence LengthOrganismDetailsImage
Rpn9376Homo sapiensMutation(s): 0 
Gene Names: PSMD13
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GTEx:  ENSG00000185627 
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Entity ID: 19
MoleculeChains  Sequence LengthOrganismDetailsImage
ecm291,845Homo sapiensMutation(s): 0 
Gene Names: ECPAS
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GTEx:  ENSG00000136813 
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Experimental Data & Validation

Integrative Structure Snapshot

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

Structure Validation

View Full Validation Report

View Summary Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-22
    Type: Initial release