6N13

UbcH7-Ub Complex with R0RBR Parkin and phosphoubiquitin


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 1000 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Synergistic recruitment of UbcH7~Ub and phosphorylated Ubl domain triggers parkin activation.

Condos, T.E.Dunkerley, K.M.Freeman, E.A.Barber, K.R.Aguirre, J.D.Chaugule, V.K.Xiao, Y.Konermann, L.Walden, H.Shaw, G.S.

(2018) EMBO J 37

  • DOI: https://doi.org/10.15252/embj.2018100014
  • Primary Citation of Related Structures:  
    6N13

  • PubMed Abstract: 

    The E3 ligase parkin ubiquitinates outer mitochondrial membrane proteins during oxidative stress and is linked to early-onset Parkinson's disease. Parkin is autoinhibited but is activated by the kinase PINK1 that phosphorylates ubiquitin leading to parkin recruitment, and stimulates phosphorylation of parkin's N-terminal ubiquitin-like (pUbl) domain. How these events alter the structure of parkin to allow recruitment of an E2~Ub conjugate and enhanced ubiquitination is an unresolved question. We present a model of an E2~Ub conjugate bound to the phospho-ubiquitin-loaded C-terminus of parkin, derived from NMR chemical shift perturbation experiments. We show the UbcH7~Ub conjugate binds in the open state whereby conjugated ubiquitin binds to the RING1/IBR interface. Further, NMR and mass spectrometry experiments indicate the RING0/RING2 interface is re-modelled, remote from the E2 binding site, and this alters the reactivity of the RING2(Rcat) catalytic cysteine, needed for ubiquitin transfer. Our experiments provide evidence that parkin phosphorylation and E2~Ub recruitment act synergistically to enhance a weak interaction of the pUbl domain with the RING0 domain and rearrange the location of the RING2(Rcat) domain to drive parkin activity.


  • Organizational Affiliation

    Department of Biochemistry, The University of Western Ontario, London, ON, Canada gshaw1@uwo.ca.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase parkinA [auth B]322Homo sapiensMutation(s): 1 
Gene Names: PRKNPARK2
EC: 2.3.2.31
UniProt & NIH Common Fund Data Resources
Find proteins for O60260 (Homo sapiens)
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Go to UniProtKB:  O60260
PHAROS:  O60260
GTEx:  ENSG00000185345 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO60260
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ubiquitinB [auth D]76Homo sapiensMutation(s): 0 
Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
PHAROS:  P0CG47
GTEx:  ENSG00000170315 
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UniProt GroupP0CG47
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 L3156Homo sapiensMutation(s): 3 
Gene Names: UBE2L3UBCE7UBCH7
EC: 2.3.2.23
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Find proteins for P68036 (Homo sapiens)
Explore P68036 
Go to UniProtKB:  P68036
PHAROS:  P68036
GTEx:  ENSG00000185651 
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UniProt GroupP68036
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
phosphoubiquitinD [auth A]76Homo sapiensMutation(s): 0 
Gene Names: UBC
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Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
PHAROS:  P0CG48
GTEx:  ENSG00000150991 
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UniProt GroupP0CG48
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 1000 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Canadian Institutes of Health Research (CIHR)CanadaMOP-14606

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-28
    Type: Initial release
  • Version 1.1: 2018-12-12
    Changes: Data collection, Database references
  • Version 1.2: 2020-01-08
    Changes: Author supporting evidence, Data collection, Database references