9IUN | pdb_00009iun

Crystal structure of Trim25 Pspry

• PDB DOI: https://doi.org/10.2210/pdb9IUN/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-22 Released: 2025-07-30 
• Deposition Author(s): Li, Y.L., Lin, T.W.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.265 (Depositor), 0.262 (DCC) 
• R-Value Work: 
  0.212 (Depositor), 0.214 (DCC) 

Starting Model: experimental

Literature

The structural basis of TRIM25-mediated regulation of RIG-I.

Li, Y., Wu, S., Tian, X., Kong, C., Hong, W., Xiao, T., Wang, S., Wei, Z., Su, Z., Ren, H., Song, Y., Hu, L., Lin, D., Yao, H., Han, J., Chen, X., Lin, T.

(2025) J Biol Chem 301: 108367-108367

• PubMed: 40024477 
• DOI: https://doi.org/10.1016/j.jbc.2025.108367
• Primary Citation Related Structures: 
  9IUN


• PubMed Abstract: 
  

  TRIM25, an E3 ligase, is an important regulator to modulate the functions of retinoic acid inducible gene-I (RIG-I) and other factors in innate immunity. Herein the structural interaction between the 2CARD domain of RIG-I and the PRYSPRY domain of TRIM25 was investigated by NMR, X-ray crystallography, computer-assisted modeling, and cell-based assays to elucidate the complex structure of PRYSPRY/2CARD. The interacting model indicated that docking of 2CARD onto PRYSPRY brought two RIG-I molecules into a close proximity to form a dimer. The attachment of a short ubiquitin chain covalently by the TRIM25's E3 ligase activity was favorable for tethering a neighboring RIG-I dimer to form the tetrameric RIG-I by noncovalent interactions. The data supported the notion that the TRIM25-RIG-I interaction was important to activate the RIG-I pathway to suppress the replication of RNA viruses, such as vesicular stomatitis virus. This work provides a structural rationale to delineate the underlying mechanism of TRIM25 regulation of RIG-I.

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Organizational Affiliation: 
• State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life Sciences, Xiamen University, Xiamen, Fujian, China; Cancer Research Center of Xiamen University, Xiamen, Fujian, China.
State Key Laboratory of Membrane Biology, Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, China.
College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, Fujian Province, China.
Institute of Molecular Enzymology, Soochow University, Soochow, Jiangsu, China.
Xiamen Key Laboratory of Clinical Efficacy and Evidence Studies of Traditional Chinese Medicine, The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China. Electronic address: [e-mail].
State Key Laboratory of Cellular Stress Biology, Innovation Center for Cell Signaling Network, State-province Joint Engineering Laboratory of Targeted Drugs from Natural Products, School of Life Sciences, Xiamen University, Xiamen, Fujian, China; Cancer Research Center of Xiamen University, Xiamen, Fujian, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 6-mer - A6 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 6-mer - A6 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 282.9 kDa 
• Atom Count: 19,317 
• Modeled Residue Count: 2,350 
• Deposited Residue Count: 2,460 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin/ISG15 ligase TRIM25	A, B, C, D, E, F, G, H, I, J, K, L	205	Homo sapiens	Mutation(s): 0  Gene Names: TRIM25, EFP, RNF147, ZNF147 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q14258 (Homo sapiens) Explore Q14258  Go to UniProtKB:  Q14258
PHAROS:  Q14258 GTEx:  ENSG00000121060

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.265 (Depositor), 0.262 (DCC) 
• R-Value Work:  0.212 (Depositor), 0.214 (DCC) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.015	α = 90
b = 182.015	β = 90
c = 221.32	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-07-30 
Deposition Author(s): Li, Y.L., Lin, T.W.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2025-07-30
  Type: Initial release
  
• Version 1.1: 2026-08-12
  Changes: Database references