1TQ4 | pdb_00001tq4

Crystal Structure of IIGP1: a paradigm for interferon inducible p47 resistance GTPases

• PDB DOI: https://doi.org/10.2210/pdb1TQ4/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2004-06-16 Released: 2004-09-21 
• Deposition Author(s): Ghosh, A., Uthaiah, R., Howard, J., Herrmann, C., Wolf, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 
  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Literature

Crystal Structure of IIGP1; A Paradigm for Interferon-Inducible p47 Resistance GTPases

Ghosh, A., Uthaiah, R., Howard, J., Herrmann, C., Wolf, E.

(2004) Mol Cell 15: 727-739

• PubMed: 15350217 
• DOI: https://doi.org/10.1016/j.molcel.2004.07.017
• Primary Citation Related Structures: 
  1TPZ, 1TQ2, 1TQ4, 1TQ6, 1TQD


• PubMed Abstract: 
  

  Interferon-inducible p47 GTPases are critical mediators of cell-autonomous resistance against several intracellular pathogens. Here we present the first crystal structure of a member of this novel GTPase family, IIGP1, in its nucleotide-free, GDP-, and GppNHp-bound form. The structure shows a Ras-like G domain between an N-terminal three-helix bundle and a complex system of C-terminal helices and loops. Sequence comparison and secondary structure prediction suggest the IIGP1 structure to be a valid model for the p47 GTPase family. The IIGP1 crystals contain a noncrystallographic dimer. We show that the dimer is required for cooperative GTP hydrolysis and GTP-dependent oligomerization of IIGP1. We also present the GDP- and GppNHp-bound monomeric structures of two dimer interface mutants. Our structures direct approaches to the analysis of the catalytic mechanism of IIGP1 and provide a coherent basis for structure-function studies aimed at elucidating the mechanistic basis of pathogen resistance caused by these enigmatic GTPases.

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Organizational Affiliation: 
• Department of Structural Biology, Max Planck Institute for Molecular Physiology, Otto-Hahn-Strasse 11, 44227 Dortmund, Germany.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 48.04 kDa 
• Atom Count: 3,676 
• Modeled Residue Count: 396 
• Deposited Residue Count: 413 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
interferon-inducible GTPase	A	413	Mus musculus	Mutation(s): 1  Gene Names: IIGP1 EC: 3.6.5
UniProt
Find proteins for Q9QZ85 (Mus musculus) Explore Q9QZ85  Go to UniProtKB:  Q9QZ85

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free:  0.230 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.193 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 68.7	α = 90
b = 71	β = 90
c = 87.9	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XDS	data reduction
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-09-21 
Deposition Author(s): Ghosh, A., Uthaiah, R., Howard, J., Herrmann, C., Wolf, E.

Revision History  

• Version 1.0: 2004-09-21
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2021-11-10
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-05-29
  Changes: Data collection