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
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9N2R

Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history

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 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.

Macromolecule Content 

  • Total Structure Weight: 296.22 kDa 
  • Atom Count: 19,459 
  • Modeled Residue Count: 2,350 
  • Deposited Residue Count: 2,496 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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

View Full Validation Report



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