5D0K

Structure of UbE2D2:RNF165:Ub complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Secondary ubiquitin-RING docking enhances Arkadia and Ark2C E3 ligase activity.

Wright, J.D.Mace, P.D.Day, C.L.

(2016) Nat Struct Mol Biol 23: 45-52

  • DOI: https://doi.org/10.1038/nsmb.3142
  • Primary Citation of Related Structures:  
    5D0I, 5D0K, 5D0M

  • PubMed Abstract: 

    RING-domain E3 ligases enhance transfer of ubiquitin to substrate proteins by stabilizing the RING-bound thioester-linked E2∼ubiquitin conjugate in a defined conformation that primes the active site for nucleophilic attack. Here we report that the monomeric RING domains from the human E3 ligases Arkadia and Ark2C bind directly to free ubiquitin with an affinity comparable to that of other dedicated ubiquitin-binding domains. Further work showed that the Ark-like RING domain and the noncovalently bound ubiquitin molecule coordinately stabilize the E2-conjugated ubiquitin (donor ubiquitin) in the 'closed' conformation. Our studies identify the RING domain of Arkadia as a ubiquitin-binding domain and provide insight into a new ubiquitin-dependent mechanism used by monomeric RING domains to activate ubiquitin transfer. This study also suggests how substrates that have been monoubiquitinated could be favored for further ubiquitination.


  • Organizational Affiliation

    Biochemistry Department, University of Otago, Dunedin, New Zealand.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 D2A,
C [auth D],
E [auth G],
G [auth J]
152Homo sapiensMutation(s): 4 
Gene Names: UBE2D2PUBC1UBC4UBC5BUBCH4UBCH5B
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.24 (UniProt), 2.3.2.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P62837 (Homo sapiens)
Explore P62837 
Go to UniProtKB:  P62837
PHAROS:  P62837
GTEx:  ENSG00000131508 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62837
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RING finger protein 165B [auth C],
D [auth F],
F [auth I],
H [auth L]
92Homo sapiensMutation(s): 0 
Gene Names: RNF165
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q6ZSG1 (Homo sapiens)
Explore Q6ZSG1 
Go to UniProtKB:  Q6ZSG1
PHAROS:  Q6ZSG1
GTEx:  ENSG00000141622 
Entity Groups  
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UniProt GroupQ6ZSG1
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Polyubiquitin-BI [auth B],
J [auth E],
K [auth H],
L [auth K]
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 
Entity Groups  
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UniProt GroupP0CG47
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 113.046α = 90
b = 113.046β = 90
c = 135.667γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-12-09
    Type: Initial release
  • Version 1.1: 2015-12-16
    Changes: Derived calculations
  • Version 1.2: 2015-12-30
    Changes: Database references
  • Version 1.3: 2016-01-20
    Changes: Database references
  • Version 1.4: 2024-03-06
    Changes: Data collection, Database references, Derived calculations