9GTE

Crystal structure of TRIM21 PRY-SPRY domain bound to Suramin

• PDB DOI: https://doi.org/10.2210/pdb9GTE/pdb

• Classification: LIGASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-09-17 Released: 2024-10-30 
• Deposition Author(s): Kim, Y., Knapp, S., Kraemer, A., Structural Genomics Consortium (SGC)
• Funding Organization(s): Innovative Medicines Initiative

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.179 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 

Literature

Crystal structure of TRIM21 PRY-SPRY domain bound to Suramin

Kim, Y., Knapp, S., Kraemer, A., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 23.27 kDa 
• Atom Count: 1,796 
• Modelled Residue Count: 185 
• Deposited Residue Count: 188 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase TRIM21	A [auth B]	188	Mus musculus	Mutation(s): 0  Gene Names: Trim21, Ro52, Ssa1 EC: 2.3.2.27
UniProt
Find proteins for Q62191 (Mus musculus) Explore Q62191  Go to UniProtKB:  Q62191

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SVR (Subject of Investigation/LOI)	H [auth B]	8,8'-[CARBONYLBIS[IMINO-3,1-PHENYLENECARBONYLIMINO(4-METHYL-3,1-PHENYLENE)CARBONYLIMINO]]BIS-1,3,5-NAPHTHALENETRISULFON IC ACID C51 H40 N6 O23 S6 FIAFUQMPZJWCLV-UHFFFAOYSA-N
EDO	B, C [auth B], D [auth B], E [auth B], F [auth B], G [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 0.179 
• R-Value Work: 0.159 
• R-Value Observed: 0.160 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.591	α = 90
b = 56.014	β = 90
c = 69.008	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-30 
Deposition Author(s): Kim, Y., Knapp, S., Kraemer, A., Structural Genomics Consortium (SGC)

---

Funding Organization	Location	Grant Number
Innovative Medicines Initiative	Switzerland	875510

Revision History  

• Version 1.0: 2024-10-30
  Type: Initial release