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 

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:  

  • 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 mo ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 D2
A, D, G, J
152Homo sapiensMutation(s): 4 
Gene Names: UBE2D2 (PUBC1, UBC4, UBC5B, UBCH4, UBCH5B)
EC: 2.3.2.23
Find proteins for P62837 (Homo sapiens)
Go to Gene View: UBE2D2
Go to UniProtKB:  P62837
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RING finger protein 165
C, F, I, L
92Homo sapiensMutation(s): 0 
Gene Names: RNF165
EC: 2.3.2.27
Find proteins for Q6ZSG1 (Homo sapiens)
Go to Gene View: RNF165
Go to UniProtKB:  Q6ZSG1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
B, E, H, K
76Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
C, F, I, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.65 Å
  • R-Value Free: 0.238 
  • R-Value Work: 0.192 
  • Space Group: P 3
Unit Cell:
Length (Å)Angle (°)
a = 113.046α = 90.00
b = 113.046β = 90.00
c = 135.667γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
SCALAdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-12-09
    Type: Initial release
  • Version 1.1: 2015-12-16
    Type: Derived calculations
  • Version 1.2: 2015-12-30
    Type: Database references
  • Version 1.3: 2016-01-20
    Type: Database references