Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 70.79 kDa 
• Atom Count: 5018 
• Modelled Residue Count: 612 
• Deposited Residue Count: 628 
• Unique protein chains: 3

5EYA

TRIM25 RING domain in complex with Ubc13-Ub conjugate

• PDB DOI: 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)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.228 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 

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: 10.1016/j.celrep.2016.06.070
• Primary Citation of 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.

---

Organizational Affiliation: 

Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA 22908, USA. Electronic address: [e-mail].

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

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  Gene Names: TRIM25, EFP, RNF147, ZNF147 EC: 6.3.2 (UniProt), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14258 (Homo sapiens) Explore Q14258  Go to UniProtKB:  Q14258
PHAROS:  Q14258

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

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 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 
• 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

• Deposited Date: 2015-11-24 
• Released Date: 2016-08-17 
Deposition Author(s): Pornillos, O., Sanchez, J.G.

---

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