5N2W

WT-Parkin and pUB complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

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: 475-483

  • DOI: 10.1038/nsmb.3400
  • Primary Citation of Related Structures:  
    5N2W, 5N38

  • PubMed Abstract: 

    • RING-between-RING (RBR) E3 ligases are a class of ubiquitin ligases distinct from RING or HECT E3 ligases. An important RBR ligase is Parkin, mutations in which lead to early-onset hereditary Parkinsonism. Parkin and other RBR ligases share a catalyt ...

    RING-between-RING (RBR) E3 ligases are a class of ubiquitin ligases distinct from RING or HECT E3 ligases. An important RBR ligase is Parkin, mutations in which lead to early-onset hereditary Parkinsonism. Parkin and other RBR ligases share a catalytic RBR module but are usually autoinhibited and activated via distinct mechanisms. Recent insights into Parkin regulation predict large, unknown conformational changes during Parkin activation. However, current data on active RBR ligases reflect the absence of regulatory domains. Therefore, it remains unclear how individual RBR ligases are activated, and whether they share a common mechanism. We now report the crystal structure of a human Parkin-phosphoubiquitin complex, which shows that phosphoubiquitin binding induces movement in the 'in-between RING' (IBR) domain to reveal a cryptic ubiquitin-binding site. Mutation of this site negatively affects Parkin's activity. Furthermore, ubiquitin binding promotes cooperation between Parkin molecules, which suggests a role for interdomain association in the RBR ligase mechanism.

    Organizational Affiliation: 

    MRC Protein Phosphorylation and Ubiquitylation Unit, College of Life Sciences, University of Dundee, Dundee, UK.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase parkin,E3 ubiquitin-protein ligase parkinA405Homo sapiensMutation(s): 0 
Gene Names: PARK2, PRKN
EC: 2.3.2 (PDB Primary Data), 2.3.2.31 (UniProt)
Find proteins for O60260 (Homo sapiens)
Explore O60260 
Go to UniProtKB:  O60260
NIH Common Fund Data Resources
PHAROS  O60260
GTEx  ENSG00000185345
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-BB76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
NIH Common Fund Data Resources
PHAROS  P0CG47
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TMO
Query on TMO
Download CCD File 
A
trimethylamine oxide
C3 H9 N O
UYPYRKYUKCHHIB-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
CL
Query on CL
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A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
SEP
Query on SEP		BL-PEPTIDE LINKINGC3 H8 N O6 PSER
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.68 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.29α = 90
b = 147.29β = 90
c = 87.49γ = 120
Software Package:
Software NamePurpose
BUSTERrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Cancer Research UKUnited Kingdom17739
Medical Research Council (United Kingdom)United KingdomMC_UU_12016/12

Revision History 

  • Version 1.0: 2017-04-19
    Type: Initial release
  • Version 1.1: 2017-04-26
    Changes: Database references
  • Version 1.2: 2017-05-17
    Changes: Database references
  • Version 1.3: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.4: 2018-01-31
    Changes: Database references