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: 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 p ...

    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, remoteĀ 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.


    Related Citations: 
    • Parkin-phosphoubiquitin complex reveals cryptic ubiquitin-binding site required for RBR ligase activity.
      Kumar, A., Chaugule, V.K., Condos, T.E.C., Barber, K.R., Johnson, C., Toth, R., Sundaramoorthy, R., Knebel, A., Shaw, G.S., Walden, H.
      (2017) Nat Struct Mol Biol 24: 475

    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase parkinB322Homo sapiensMutation(s): 1 
Gene Names: PRKNPARK2
EC: 2.3.2.31
Find proteins for O60260 (Homo sapiens)
Explore O60260 
Go to UniProtKB:  O60260
NIH Common Fund Data Resources
PHAROS  O60260
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ubiquitinD76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
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PHAROS  P0CG47
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 L3C156Homo sapiensMutation(s): 3 
Gene Names: UBE2L3UBCE7UBCH7
EC: 2.3.2.23
Find proteins for P68036 (Homo sapiens)
Explore P68036 
Go to UniProtKB:  P68036
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PHAROS  P68036
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
phosphoubiquitinA76Homo sapiensMutation(s): 0 
Gene Names: UBC
Find proteins for P0CG48 (Homo sapiens)
Explore P0CG48 
Go to UniProtKB:  P0CG48
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PHAROS  P0CG48
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP
AL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 1000 
  • Conformers Submitted: 10 
  • Selection Criteria: structures with the lowest energy 
  • OLDERADO: 6N13 Olderado

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 

  • 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