5FPH

The GTPase domains of the immunity-related Irga6 dimerize in a parallel head-to-head fashion

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.297 
  • R-Value Observed: 0.298 

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This is version 2.1 of the entry. See complete history. 


Literature

The Immunity-Related Gtpase Irga6 Dimerizes in a Parallel Head-to-Head Fashion.

Schulte, K., Pawlowski, N., Faelber, K., Froehlich, C., Howard, J., Daumke, O.

(2016) BMC Biol 14: 14

  • DOI: https://doi.org/10.1186/s12915-016-0236-7
  • Primary Citation of Related Structures:  
    5FPH

  • PubMed Abstract: 

    The immunity-related GTPases (IRGs) constitute a powerful cell-autonomous resistance system against several intracellular pathogens. Irga6 is a dynamin-like protein that oligomerizes at the parasitophorous vacuolar membrane (PVM) of Toxoplasma gondii leading to its vesiculation. Based on a previous biochemical analysis, it has been proposed that the GTPase domains of Irga6 dimerize in an antiparallel fashion during oligomerization.

    • Organizational Affiliation: 

    Max-Delbrueck-Centrum for Molecular Medicine, Crystallography, Robert-Rössle-Strasse 10, 13125, Berlin, Germany.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
INTERFERON-INDUCIBLE GTPASE 1
A, B, C, D, E
A, B, C, D, E, F, G
423Mus musculusMutation(s): 4 
EC: 3.6.5
UniProt
Find proteins for Q9QZ85 (Mus musculus)
Explore Q9QZ85 
Go to UniProtKB:  Q9QZ85
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9QZ85
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP
Download Ideal Coordinates CCD File 
H [auth A]
K [auth B]
N [auth C]
S [auth E]
W [auth F]
H [auth A],
K [auth B],
N [auth C],
S [auth E],
W [auth F],
Z [auth G]
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
TRS
Query on TRS
Download Ideal Coordinates CCD File 
Q [auth C],
V [auth E]		2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
MG
Query on MG
Download Ideal Coordinates CCD File 
AA [auth G]
BA [auth G]
I [auth A]
J [auth A]
L [auth B]
AA [auth G],
BA [auth G],
I [auth A],
J [auth A],
L [auth B],
M [auth B],
O [auth C],
P [auth C],
R [auth D],
T [auth E],
U [auth E],
X [auth F],
Y [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D, E
A, B, C, D, E, F, G
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.317 
  • R-Value Work: 0.297 
  • R-Value Observed: 0.298 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.51α = 90
b = 98.51β = 90
c = 1289.4γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-10
    Type: Initial release
  • Version 1.1: 2016-03-16
    Changes: Database references
  • Version 1.2: 2017-07-12
    Changes: Derived calculations
  • Version 2.0: 2021-08-11
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Other
  • Version 2.1: 2024-01-10
    Changes: Data collection, Refinement description