8H4O | pdb_00008h4o

Crystal Structure of nucleotide-free Irgb6_T95D mutant

• PDB DOI: https://doi.org/10.2210/pdb8H4O/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-10-11 Released: 2023-10-18 
• Deposition Author(s): Saijo-Hamano, Y., Okuma, H., Sakai, N., Kato, T., Imasaki, T., Nitta, R.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS), Japan Science and Technology

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.283 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Literature

Structural basis of Irgb6 inactivation by Toxoplasma gondii through the phosphorylation of switch I.

Okuma, H., Saijo-Hamano, Y., Yamada, H., Sherif, A.A., Hashizaki, E., Sakai, N., Kato, T., Imasaki, T., Kikkawa, S., Nitta, E., Sasai, M., Abe, T., Sugihara, F., Maniwa, Y., Kosako, H., Takei, K., Standley, D.M., Yamamoto, M., Nitta, R.

(2024) Genes Cells 29: 17-38

• PubMed: 37984375 
• DOI: https://doi.org/10.1111/gtc.13080
• Primary Citation of Related Structures:  
  8H4O


• PubMed Abstract: 
  

  Irgb6 is a priming immune-related GTPase (IRG) that counteracts Toxoplasma gondii. It is known to be recruited to the low virulent type II T. gondii parasitophorous vacuole (PV), initiating cell-autonomous immunity. However, the molecular mechanism by which immunity-related GTPases become inactivated after the parasite infection remains obscure. Here, we found that Thr95 of Irgb6 is prominently phosphorylated in response to low virulent type II T. gondii infection. We observed that a phosphomimetic T95D mutation in Irgb6 impaired its localization to the PV and exhibited reduced GTPase activity in vitro. Structural analysis unveiled an atypical conformation of nucleotide-free Irgb6-T95D, resulting from a conformational change in the G-domain that allosterically modified the PV membrane-binding interface. In silico docking corroborated the disruption of the physiological membrane binding site. These findings provide novel insights into a T. gondii-induced allosteric inactivation mechanism of Irgb6.

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Organizational Affiliation: 
• Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Japan.
Department of Neuroscience, Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, Okayama University, Okayama, Japan.
Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka, Japan.
Laboratory of Systems Immunology, WPI Immunology Frontier Research Center, Osaka University, Osaka, Japan.
Laboratory of Immunoparasitology, Osaka University, Osaka, Japan.
Department of Immunoparasitology, Research Institute for Microbial Diseases, Osaka, Japan.
RIKEN SPring-8 Center, Sayo-gun, Japan.
Core Instrumentation Facility, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.
Division of Thoracic Surgery, Kobe University Graduate School of Medicine, Kobe, Japan.
Division of Cell Signaling, Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, Japan.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 94.69 kDa 
• Atom Count: 6,489 
• Modeled Residue Count: 793 
• Deposited Residue Count: 834 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
T-cell-specific guanine nucleotide triphosphate-binding protein 2	A, B	417	Mus musculus	Mutation(s): 1  Gene Names: Tgtp2, Ifggb6, Irgb6, Mg21, Tgtp EC: 3.6.5
UniProt
Find proteins for Q3T9E4 (Mus musculus) Explore Q3T9E4  Go to UniProtKB:  Q3T9E4

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.283 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.532	α = 90
b = 80.613	β = 90
c = 147.649	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-18 
Deposition Author(s): Saijo-Hamano, Y., Okuma, H., Sakai, N., Kato, T., Imasaki, T., Nitta, R.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	JP21gm0810013
Japan Society for the Promotion of Science (JSPS)	Japan	21K06988
Japan Society for the Promotion of Science (JSPS)	Japan	21H05254
Japan Society for the Promotion of Science (JSPS)	Japan	21K19352
Japan Society for the Promotion of Science (JSPS)	Japan	22H02795
Japan Science and Technology	Japan	JPMJMS2024

Revision History  

• Version 1.0: 2023-10-18
  Type: Initial release
  
• Version 1.1: 2024-07-03
  Changes: Database references