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- EMDB-16813: Tomogram of GBP1 coatomers assembled on brain polar lipid-derived... -

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Basic information

Entry
Database: EMDB / ID: EMD-16813
TitleTomogram of GBP1 coatomers assembled on brain polar lipid-derived small unilamellar vesicles.
Map dataElectron cryotomogram of GBP1 coatomers on BPLE SUVs.
Sample
  • Organelle or cellular component: Membrane-assembled coatomer formed by GDP-AlF3-stabilised GBP1 dimers on brain polar lipid-derived SUVs.
KeywordsGBP1 / cryo-ET / liposome / coatomer / IMMUNE SYSTEM
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsKuhm TI / Jakobi AJ
Funding supportEuropean Union, Netherlands, 2 items
OrganizationGrant numberCountry
European Research Council (ERC)852880European Union
Netherlands Organisation for Scientific Research (NWO)NWO.STU.018-2.007 Netherlands
CitationJournal: Nat Struct Mol Biol / Year: 2025
Title: Structural basis of antimicrobial membrane coat assembly by human GBP1.
Authors: Tanja Kuhm / Clémence Taisne / Cecilia de Agrela Pinto / Luca Gross / Evdokia A Giannopoulou / Stefan T Huber / Els Pardon / Jan Steyaert / Sander J Tans / Arjen J Jakobi /
Abstract: Guanylate-binding proteins (GBPs) are interferon-inducible guanosine triphosphate hydrolases (GTPases) mediating host defense against intracellular pathogens. Their antimicrobial activity hinges on ...Guanylate-binding proteins (GBPs) are interferon-inducible guanosine triphosphate hydrolases (GTPases) mediating host defense against intracellular pathogens. Their antimicrobial activity hinges on their ability to self-associate and coat pathogen-associated compartments or cytosolic bacteria. Coat formation depends on GTPase activity but how nucleotide binding and hydrolysis prime coat formation remains unclear. Here, we report the cryo-electron microscopy structure of the full-length human GBP1 dimer in its guanine nucleotide-bound state and describe the molecular ultrastructure of the GBP1 coat on liposomes and bacterial lipopolysaccharide membranes. Conformational changes of the middle and GTPase effector domains expose the isoprenylated C terminus for membrane association. The α-helical middle domains form a parallel, crossover arrangement essential for coat formation and position the extended effector domain for intercalation into the lipopolysaccharide layer of gram-negative membranes. Nucleotide binding and hydrolysis create oligomeric scaffolds with contractile abilities that promote membrane extrusion and fragmentation. Our data offer a structural and mechanistic framework for understanding GBP1 effector functions in intracellular immunity.
History
DepositionMar 9, 2023-
Header (metadata) releaseMar 27, 2024-
Map releaseMar 27, 2024-
UpdateFeb 5, 2025-
Current statusFeb 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16813.png

Downloads & links

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Map

FileDownload / File: emd_16813.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationElectron cryotomogram of GBP1 coatomers on BPLE SUVs.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.15 Å/pix.
x 248 pix.
= 1525.2 Å		6.15 Å/pix.
x 1538 pix.
= 9458.7 Å		6.15 Å/pix.
x 942 pix.
= 5793.3 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 6.15 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-112.515590000000003 - 81.794129999999996
Average (Standard dev.)1.2886975 (±4.291028)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions1538942248
Spacing9421538248
CellA: 5793.3003 Å / B: 9458.7 Å / C: 1525.2001 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_16813_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Mask #2

Fileemd_16813_msk_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unbinned electron cryotomogram of GBP1 coatomers on BPLE SUVs.

Fileemd_16813_additional_1.map
AnnotationUnbinned electron cryotomogram of GBP1 coatomers on BPLE SUVs.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Membrane-assembled coatomer formed by GDP-AlF3-stabilised GBP1 di...

EntireName: Membrane-assembled coatomer formed by GDP-AlF3-stabilised GBP1 dimers on brain polar lipid-derived SUVs.
Components
  • Organelle or cellular component: Membrane-assembled coatomer formed by GDP-AlF3-stabilised GBP1 dimers on brain polar lipid-derived SUVs.

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Supramolecule #1: Membrane-assembled coatomer formed by GDP-AlF3-stabilised GBP1 di...

SupramoleculeName: Membrane-assembled coatomer formed by GDP-AlF3-stabilised GBP1 dimers on brain polar lipid-derived SUVs.
type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 98 % / Chamber temperature: 20 K / Instrument: LEICA EM GP / Details: Blotted for 4 seconds from the carbon side..
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: CMC Utrecht / Diameter: 10 nm

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Electron microscopy

MicroscopeJEOL 3200FSC
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-10 / Number grids imaged: 1 / Number real images: 61 / Average exposure time: 2.0 sec. / Average electron dose: 1.54 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 12000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 5.0 µm
Sample stageSpecimen holder model: JEOL 3200FSC CRYOHOLDER / Cooling holder cryogen: NITROGEN

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Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Resolution method: OTHER / Software - Name: IMOD / Number images used: 61

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