5EYA

TRIM25 RING domain in complex with Ubc13-Ub conjugate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Mechanism of TRIM25 Catalytic Activation in the Antiviral RIG-I Pathway.

Sanchez, J.G.Chiang, J.J.Sparrer, K.M.Alam, S.L.Chi, M.Roganowicz, M.D.Sankaran, B.Gack, M.U.Pornillos, O.

(2016) Cell Rep 16: 1315-1325

  • DOI: 10.1016/j.celrep.2016.06.070

  • PubMed Abstract: 
  • Antiviral response pathways induce interferon by higher-order assembly of signaling complexes called signalosomes. Assembly of the RIG-I signalosome is regulated by K63-linked polyubiquitin chains, which are synthesized by the E3 ubiquitin ligase, TR ...

    Antiviral response pathways induce interferon by higher-order assembly of signaling complexes called signalosomes. Assembly of the RIG-I signalosome is regulated by K63-linked polyubiquitin chains, which are synthesized by the E3 ubiquitin ligase, TRIM25. We have previously shown that the TRIM25 coiled-coil domain is a stable, antiparallel dimer that positions two catalytic RING domains on opposite ends of an elongated rod. We now show that the RING domain is a separate self-association motif that engages ubiquitin-conjugated E2 enzymes as a dimer. RING dimerization is required for catalysis, TRIM25-mediated RIG-I ubiquitination, interferon induction, and antiviral activity. We also provide evidence that RING dimerization and E3 ligase activity are promoted by binding of the TRIM25 SPRY domain to the RIG-I effector domain. These results indicate that TRIM25 actively participates in higher-order assembly of the RIG-I signalosome and helps to fine-tune the efficiency of the RIG-I-mediated antiviral response.


    Organizational Affiliation

    Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.,Department of Microbiology, University of Chicago, Chicago, IL 60637, USA.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA. Electronic address: opornillos@virginia.edu.,Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA.,Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA.,Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA; Department of Microbiology, University of Chicago, Chicago, IL 60637, USA. Electronic address: mgack@uchicago.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-conjugating enzyme E2 N
A, B
152Homo sapiensMutation(s): 1 
Gene Names: UBE2N (BLU)
EC: 2.3.2.23
Find proteins for P61088 (Homo sapiens)
Go to Gene View: UBE2N
Go to UniProtKB:  P61088
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tripartite motif-containing 25 variant
F, G
86Homo sapiensMutation(s): 0 
Gene Names: TRIM25 (EFP, RNF147, ZNF147)
EC: 6.3.2.n3
Find proteins for Q14258 (Homo sapiens)
Go to Gene View: TRIM25
Go to UniProtKB:  Q14258
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
C, D
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 
F, G
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 53.047α = 90.00
b = 75.779β = 90.00
c = 169.101γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling

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: 2016-08-17
    Type: Initial release
  • Version 1.1: 2017-09-27
    Type: Author supporting evidence, Derived calculations