5EYA | pdb_00005eya

TRIM25 RING domain in complex with Ubc13-Ub conjugate

• PDB DOI: https://doi.org/10.2210/pdb5EYA/pdb

• Classification: SIGNALING PROTEIN/Transferase
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-11-24 Released: 2016-08-17 
• Deposition Author(s): Pornillos, O., Sanchez, J.G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.192 (Depositor) 

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

• PubMed: 27425606 
• DOI: https://doi.org/10.1016/j.celrep.2016.06.070
• Primary Citation Related Structures: 
  5EYA


• 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, 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.

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Organizational Affiliation: 
• 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.
Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA.
Molecular Biophysics and Integrated Bioimaging, Berkeley Center for Structural Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, 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: [e-mail].
Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 70.79 kDa 
• Atom Count: 5,018 
• Modeled Residue Count: 612 
• Deposited Residue Count: 628 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 N	A, D [auth B]	152	Homo sapiens	Mutation(s): 1  Gene Names: UBE2N, BLU EC: 2.3.2.23
UniProt & NIH Common Fund Data Resources
Find proteins for P61088 (Homo sapiens) Explore P61088  Go to UniProtKB:  P61088
PHAROS:  P61088 GTEx:  ENSG00000177889

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tripartite motif-containing 25 variant	B [auth F], C [auth G]	86	Homo sapiens	Mutation(s): 0  EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q14258 (Homo sapiens) Explore Q14258  Go to UniProtKB:  Q14258
PHAROS:  Q14258 GTEx:  ENSG00000121060

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Polyubiquitin-B	E [auth C], F [auth D]	76	Homo sapiens	Mutation(s): 0  Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens) Explore P0CG47  Go to UniProtKB:  P0CG47
PHAROS:  P0CG47 GTEx:  ENSG00000170315

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth F], H [auth F], I [auth G], J [auth G]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.192 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.047	α = 90
b = 75.779	β = 90
c = 169.101	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-08-17 
Deposition Author(s): Pornillos, O., Sanchez, J.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM112508

Revision History  

• Version 1.0: 2016-08-17
  Type: Initial release
  
• Version 1.1: 2017-09-27
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2019-12-25
  Changes: Author supporting evidence
• Version 1.3: 2024-10-09
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary