9N2R | pdb_00009n2r

Structure of GTP-bound GM4951


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 
    0.247 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.211 (Depositor) 

Starting Model: in silico
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Ligand Structure Quality Assessment 


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Literature

Structural insights into GM4951 as a lipid droplet GTPase regulating hepatic lipid metabolism.

Raj, R.Jiang, Y.Jha, R.K.Moresco, E.M.Y.Joshi, H.Zhang, Z.Beutler, B.

(2025) Nat Commun 16: 11458-11458

  • DOI: https://doi.org/10.1038/s41467-025-66253-2
  • Primary Citation of Related Structures:  
    9N2Q, 9N2R, 9N2S, 9N2T, 9N6D

  • PubMed Abstract: 

    GM4951 is an immunity-related GTPase (IRG) that counteracts hepatic lipid accumulation in mice fed a high-fat diet. We determine full-length protein structures of GTPγS- and GDP-bound GM4951, and two missense mutants (N86K or D125G) associated with metabolic dysfunction-associated steatotic liver disease (MASLD) in mice. All four structures reveal a conserved GTPase domain fold and a helix bundle composed of the N- and C-terminal regions. Each mutation alters the dynamics of the switch-I and switch-II loops important for catalytic function and lipid droplet (LD) localization. GM4951 predominantly forms dimers in vitro. Cryo-electron microscopy reveals a dimer interface formed by the helical domains of two protomers (tail to tail), distinct from other IRGs. The N-terminal helices are necessary for LD localization, while a disulfide bond between helices in the GTPase domain and C-terminus is necessary for interaction with MASLD-associated HSD17B13. Distinct N- and C-terminal conformations set GM4951 apart from other IRGs structurally and functionally.


  • Organizational Affiliation
    • Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, USA. Rishi.Raj@UTSouthwestern.edu.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interferon inducible GTPase 1C416Mus musculusMutation(s): 0 
Gene Names: Iigp1cEG240327Gm4951Ifgga2
UniProt & NIH Common Fund Data Resources
Find proteins for Q3UED7 (Mus musculus)
Explore Q3UED7 
Go to UniProtKB:  Q3UED7
IMPC:  MGI:3644953
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ3UED7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GSP (Subject of Investigation/LOI)
Query on GSP

Download Ideal Coordinates CCD File 
AA [auth E]
EA [auth F]
I [auth B]
M [auth A]
Q [auth C]
AA [auth E],
EA [auth F],
I [auth B],
M [auth A],
Q [auth C],
X [auth D]
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
C10 H16 N5 O13 P3 S
XOFLBQFBSOEHOG-UUOKFMHZSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
BA [auth F]
CA [auth F]
DA [auth F]
G [auth B]
H [auth B]
BA [auth F],
CA [auth F],
DA [auth F],
G [auth B],
H [auth B],
J [auth A],
K [auth A],
L [auth A],
N [auth C],
O [auth C],
P [auth C],
S [auth D],
T [auth D],
U [auth D],
V [auth D],
W [auth D],
Z [auth E]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
R [auth C],
Y [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free:  0.247 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.759α = 92.31
b = 100.245β = 101.24
c = 152.347γ = 89.86
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01 AI125581

Revision History  (Full details and data files)

  • Version 1.0: 2026-01-14
    Type: Initial release