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

Structural basis of TRIM25 regulation of RIG-I

Li, Y.L., Lin, T.W.

To be published.

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