5FER

Complex of TRIM25 RING with UbcH5-Ub


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity.

Koliopoulos, M.G.Esposito, D.Christodoulou, E.Taylor, I.A.Rittinger, K.

(2016) Embo J. 35: 1204-1218

  • DOI: 10.15252/embj.201593741
  • Primary Citation of Related Structures:  5FEY

  • PubMed Abstract: 
  • TRIM E3 ubiquitin ligases regulate a wide variety of cellular processes and are particularly important during innate immune signalling events. They are characterized by a conserved tripartite motif in their N-terminal portion which comprises a canoni ...

    TRIM E3 ubiquitin ligases regulate a wide variety of cellular processes and are particularly important during innate immune signalling events. They are characterized by a conserved tripartite motif in their N-terminal portion which comprises a canonical RING domain, one or two B-box domains and a coiled-coil region that mediates ligase dimerization. Self-association via the coiled-coil has been suggested to be crucial for catalytic activity of TRIMs; however, the precise molecular mechanism underlying this observation remains elusive. Here, we provide a detailed characterization of the TRIM ligases TRIM25 and TRIM32 and show how their oligomeric state is linked to catalytic activity. The crystal structure of a complex between the TRIM25 RING domain and an ubiquitin-loaded E2 identifies the structural and mechanistic features that promote a closed E2~Ub conformation to activate the thioester for ubiquitin transfer allowing us to propose a model for the regulation of activity in the full-length protein. Our data reveal an unexpected diversity in the self-association mechanism of TRIMs that might be crucial for their biological function.


    Organizational Affiliation

    Mill Hill Laboratory, Molecular Structure of Cell Signalling Laboratory, The Francis Crick Institute, London, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin/ISG15 ligase TRIM25
A, D
85Homo sapiensGene Names: TRIM25 (EFP, RNF147, ZNF147)
EC: 2.3.2.27, 6.3.2.n3
Find proteins for Q14258 (Homo sapiens)
Go to Gene View: TRIM25
Go to UniProtKB:  Q14258
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 D1
B, E
150Homo sapiensGene Names: UBE2D1 (SFT, UBC5A, UBCH5, UBCH5A)
EC: 2.3.2.23, 2.3.2.24
Find proteins for P51668 (Homo sapiens)
Go to Gene View: UBE2D1
Go to UniProtKB:  P51668
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S27a
C, F
76Bos taurusGene Names: RPS27A (UBA80, UBCEP1)
Find proteins for P62992 (Bos taurus)
Go to Gene View: RPS27A
Go to UniProtKB:  P62992
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.227 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 60.480α = 90.00
b = 71.700β = 90.00
c = 160.430γ = 90.00
Software Package:
Software NamePurpose
xia2data scaling
AutoSolphasing
PHENIXrefinement
xia2data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Medical Research Council (United Kingdom)United KingdomU117565398
The Francis Crick InstituteUnited KingdomFCI01

Revision History 

  • Version 1.0: 2016-05-18
    Type: Initial release
  • Version 1.1: 2016-06-15
    Type: Database references
  • Version 1.2: 2017-09-13
    Type: Author supporting evidence