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 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 ...

    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
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 D2A,
C [auth D],
E [auth G],
G [auth J]		152Homo 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)
UniProt & NIH Common Fund Data Resources
Find proteins for P62837 (Homo sapiens)
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PHAROS:  P62837
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UniProt GroupP62837
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence 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)
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PHAROS:  Q6ZSG1
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UniProt GroupQ6ZSG1
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Entity ID: 3
MoleculeChainsSequence 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)
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PHAROS:  P0CG47
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UniProt GroupP0CG47
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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