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 1.3 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: 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 monome ...

    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
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 D2 A, D, G, J152Homo sapiensMutation(s): 4 
Gene Names: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B
EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt), 2.3.2.24 (UniProt)
Find proteins for P62837 (Homo sapiens)
Explore P62837 
Go to UniProtKB:  P62837
NIH Common Fund Data Resources
PHAROS:  P62837
GTEx:  ENSG00000131508
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RING finger protein 165 C, F, I, L92Homo sapiensMutation(s): 0 
Gene Names: RNF165
EC: 2.3.2.27
Find proteins for Q6ZSG1 (Homo sapiens)
Explore Q6ZSG1 
Go to UniProtKB:  Q6ZSG1
NIH Common Fund Data Resources
PHAROS:  Q6ZSG1
GTEx:  ENSG00000141622
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Polyubiquitin-B B, E, H, K76Homo 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
Expand
  • 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

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • 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