7C3K

Crystal Structure of mIRGB10

• PDB DOI: https://doi.org/10.2210/pdb7C3K/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus molossinus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-05-12 Released: 2021-04-21 
• Deposition Author(s): Ha, H.J., Jeong, J.H., Kim, Y.G., Park, H.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.272 
• R-Value Work: 0.213 

Literature

Molecular basis of IRGB10 oligomerization and membrane association for pathogen membrane disruption.

Ha, H.J., Chun, H.L., Lee, S.Y., Jeong, J.H., Kim, Y.G., Park, H.H.

(2021) Commun Biol 4: 92-92

• PubMed: 33469160 
• DOI: https://doi.org/10.1038/s42003-020-01640-7
• Primary Citation of Related Structures:  
  7C3K


• PubMed Abstract: 
  

  Immunity-related GTPase B10 (IRGB10) belongs to the interferon (IFN)-inducible GTPases, a family of proteins critical to host defense. It is induced by IFNs after pathogen infection, and plays a role in liberating pathogenic ligands for the activation of the inflammasome by directly disrupting the pathogen membrane. Although IRGB10 has been intensively studied owing to its functional importance in the cell-autonomous immune response, the molecular mechanism of IRGB10-mediated microbial membrane disruption is still unclear. In this study, we report the structure of mouse IRGB10. Our structural study showed that IRGB10 bound to GDP forms an inactive head-to-head dimer. Further structural analysis and comparisons indicated that IRGB10 might change its conformation to activate its membrane-binding and disruptive functions. Based on this observation, we propose a model of the working mechanism of IRGB10 during pathogen membrane disruption.

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Organizational Affiliation: 

College of Pharmacy, Chung-Ang University, Seoul, 06974, Republic of Korea.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 94.3 kDa 
• Atom Count: 6,343 
• Modelled Residue Count: 772 
• Deposited Residue Count: 822 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Immunity-related GTPase family member b10	A, B	411	Mus musculus molossinus	Mutation(s): 0  Gene Names: Irgb10
UniProt
Find proteins for Q0GUM3 (Mus musculus) Explore Q0GUM3  Go to UniProtKB:  Q0GUM3

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	C [auth A], D [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 0.272 
• R-Value Work: 0.213 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.51	α = 90
b = 63.19	β = 98.7
c = 117.92	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-04-21 
Deposition Author(s): Ha, H.J., Jeong, J.H., Kim, Y.G., Park, H.H.

Revision History  

• Version 1.0: 2021-04-21
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Refinement description