7VEX

Crystal Structure of GTP-bound Irgb6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 

Starting Models: experimental
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This is version 1.2 of the entry. See complete history


Literature

Structural basis of membrane recognition of Toxoplasma gondii vacuole by Irgb6.

Saijo-Hamano, Y.Sherif, A.A.Pradipta, A.Sasai, M.Sakai, N.Sakihama, Y.Yamamoto, M.Standley, D.M.Nitta, R.

(2022) Life Sci Alliance 5

  • DOI: https://doi.org/10.26508/lsa.202101149
  • Primary Citation of Related Structures:  
    7VES, 7VEX

  • PubMed Abstract: 

    The p47 immunity-related GTPase (IRG) Irgb6 plays a pioneering role in host defense against Toxoplasma gondii infection. Irgb6 is recruited to the parasitophorous vacuole membrane (PVM) formed by T. gondii and disrupts it. Despite the importance of this process, the molecular mechanisms accounting for PVM recognition by Irgb6 remain elusive because of lack of structural information on Irgb6. Here we report the crystal structures of mouse Irgb6 in the GTP-bound and nucleotide-free forms. Irgb6 exhibits a similar overall architecture to other IRGs in which GTP binding induces conformational changes in both the dimerization interface and the membrane-binding interface. The membrane-binding interface of Irgb6 assumes a unique conformation, composed of N- and C-terminal helical regions forming a phospholipid binding site. In silico docking of phospholipids further revealed membrane-binding residues that were validated through mutagenesis and cell-based assays. Collectively, these data demonstrate a novel structural basis for Irgb6 to recognize T. gondii PVM in a manner distinct from other IRGs.


  • Organizational Affiliation

    Division of Structural Medicine and Anatomy, Department of Physiology and Cell Biology, Kobe University Graduate School of Medicine, Kobe, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
T-cell-specific guanine nucleotide triphosphate-binding protein 2417Mus musculusMutation(s): 0 
Gene Names: Tgtp2Ifggb6Irgb6Mg21Tgtp
EC: 3.6.5
UniProt
Find proteins for Q3T9E4 (Mus musculus)
Explore Q3T9E4 
Go to UniProtKB:  Q3T9E4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3T9E4
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
B [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.51 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.148 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.618α = 90
b = 75.743β = 90
c = 80.62γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Agency for Medical Research and Development (AMED)JapanJP20fk0108137
Japan Agency for Medical Research and Development (AMED)JapanJP20wm0325010
Japan Agency for Medical Research and Development (AMED)JapanJP20jm0210067
Japan Agency for Medical Research and Development (AMED)JapanJP20am0101108
Japan Agency for Medical Research and Development (AMED)JapanJP20gm0810013
Japan Society for the Promotion of Science (JSPS)Japan21K06988
Japan Society for the Promotion of Science (JSPS)Japan20B304
Japan Society for the Promotion of Science (JSPS)Japan19H04809
Japan Society for the Promotion of Science (JSPS)Japan19H00970
Japan Society for the Promotion of Science (JSPS)Japan19H03396
Japan Agency for Medical Research and Development (AMED)JapanJP19am0101070
Japan Society for the Promotion of Science (JSPS)JapanJPMJMS2024

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-03
    Type: Initial release
  • Version 1.1: 2022-02-16
    Changes: Database references
  • Version 1.2: 2023-11-29
    Changes: Data collection, Refinement description