5VZW

TRIM23 RING domain in complex with UbcH5-Ub


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.278 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure and catalytic activation of the TRIM23 RING E3 ubiquitin ligase.

Dawidziak, D.M.Sanchez, J.G.Wagner, J.M.Ganser-Pornillos, B.K.Pornillos, O.

(2017) Proteins 85: 1957-1961

  • DOI: 10.1002/prot.25348
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tripartite motif (TRIM) proteins comprise a large family of RING-type ubiquitin E3 ligases that regulate important biological processes. An emerging general model is that TRIMs form elongated antiparallel coiled-coil dimers that prevent interaction o ...

    Tripartite motif (TRIM) proteins comprise a large family of RING-type ubiquitin E3 ligases that regulate important biological processes. An emerging general model is that TRIMs form elongated antiparallel coiled-coil dimers that prevent interaction of the two attendant RING domains. The RING domains themselves bind E2 conjugating enzymes as dimers, implying that an active TRIM ligase requires higher-order oligomerization of the basal coiled-coil dimers. Here, we report crystal structures of the TRIM23 RING domain in isolation and in complex with an E2-ubiquitin conjugate. Our results indicate that TRIM23 enzymatic activity requires RING dimerization, consistent with the general model of TRIM activation.


    Organizational Affiliation

    Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, Virginia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 D2
A, B
147Homo sapiensMutation(s): 2 
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
Ubiquitin
C, D
79Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase TRIM23
F, G
123Homo sapiensMutation(s): 0 
Gene Names: TRIM23 (ARD1, ARFD1, RNF46)
EC: 2.3.2.27
Find proteins for P36406 (Homo sapiens)
Go to Gene View: TRIM23
Go to UniProtKB:  P36406
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
F, G
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.278 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 52.830α = 90.00
b = 109.355β = 90.00
c = 122.963γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01-GM112508

Revision History 

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Database references