8H4O

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 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 

Literature

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

Okuma, H., Saijo-Hamano, Y., Sherif, A.A., Hashizaki, E., Sakai, N., Kato, K., Imasaki, T., Nitta, E., Sasai, M., Kosako, H., Standley, D.M., Yamamoto, M., Nitta, R.

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

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 
• Modelled 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 
• R-Value Work: 0.226 
• R-Value Observed: 0.228 
• 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