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- EMDB-49057: Dimeric structure of GM4951 -

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Basic information

Entry
Database: EMDB / ID: EMD-49057
TitleDimeric structure of GM4951
Map data
Sample
  • Complex: GM4951
    • Protein or peptide: Interferon inducible GTPase 1C
KeywordsLipid droplet associated protein. / LIPID BINDING PROTEIN
Function / homology
Function and homology information


autophagosome assembly / cellular response to interferon-beta / innate immune response / GTPase activity / endoplasmic reticulum membrane / GTP binding
Similarity search - Function
Immunity-related GTPases-like / : / Interferon-inducible GTPase (IIGP) / IRG-type guanine nucleotide-binding (G) domain / IRG-type guanine nucleotide-binding (G) domain profile. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Interferon inducible GTPase 1C
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 Å
AuthorsRaj R / Beutler B
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01 AI125581 United States
CitationJournal: Nat Commun / Year: 2025
Title: Structural insights into GM4951 as a lipid droplet GTPase regulating hepatic lipid metabolism.
Authors: Rishi Raj / Yiao Jiang / Rahul Kumar Jha / Eva Marie Y Moresco / Himanshu Joshi / Zhao Zhang / Bruce Beutler /
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 ...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.
History
DepositionFeb 5, 2025-
Header (metadata) releaseJan 14, 2026-
Map releaseJan 14, 2026-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49057.png

Downloads & links

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Map

FileDownload / File: emd_49057.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.66 Å/pix.
x 480 pix.
= 318.72 Å		0.66 Å/pix.
x 480 pix.
= 318.72 Å		0.66 Å/pix.
x 480 pix.
= 318.72 Å

Surface

Projections

Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.664 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.045
Minimum - Maximum-0.10969421 - 0.2935138
Average (Standard dev.)0.00006430503 (±0.00461751)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions480480480
Spacing480480480
CellA=B=C: 318.72 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_49057_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_49057_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GM4951

EntireName: GM4951
Components
  • Complex: GM4951
    • Protein or peptide: Interferon inducible GTPase 1C

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Supramolecule #1: GM4951

SupramoleculeName: GM4951 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Interferon inducible GTPase 1C

MacromoleculeName: Interferon inducible GTPase 1C / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 48.562184 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: HHHHHHSQDP MGQLFSSRRS EDQDLSSSFI EYLKECEKGI NIIPHEIITS IEINMKKGNI QEVNSTVRDM LREIDNTPLN VALTGETGS GKSSFINTLR GIGHEEGGAA HTGVTDKTKE RHPYEHPKMP NVVFWDLPGT GSEDFQPKTY LEKMKFYEYD F FIIISATR ...String:
HHHHHHSQDP MGQLFSSRRS EDQDLSSSFI EYLKECEKGI NIIPHEIITS IEINMKKGNI QEVNSTVRDM LREIDNTPLN VALTGETGS GKSSFINTLR GIGHEEGGAA HTGVTDKTKE RHPYEHPKMP NVVFWDLPGT GSEDFQPKTY LEKMKFYEYD F FIIISATR FKKNDIDLAK AIGIMKKEFY FVRTQVDSDL RNEEDFKPQT FDREKVLQDI RLNCVNTFRE NGIAEPPIFL IS NKNVCHY DFPVLMDKLI SDLPVFKRQN FMFSLPNITD SVIEKKRNFL RWKTWLEGFA DGLLSFFLES DLETLEKSMK FYR TVFGVD DASLQRLARA WEIDQVDQVR AMIKSPAVFT PTDEETIQER LSRYNQEFCL ANGYLLPKNH CREILYLKLY FLDM VTEDA KTLLKEICLR N

UniProtKB: Interferon inducible GTPase 1C

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 367948
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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