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- EMDB-43153: hGBP1 conformer on the bacterial outer membrane -

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Basic information

Entry
Database: EMDB / ID: EMD-43153
TitlehGBP1 conformer on the bacterial outer membrane
Map datahGBP1 monomer
Sample
  • Cell: human GBP1 coats with Salmonella minicell
    • Other: Human guanylate-binding protein 1
Keywordsdynamin superfamily / GTPase / ANTIMICROBIAL PROTEIN
Biological speciesSalmonella enterica subsp. enterica serovar Typhimurium (bacteria) / Homo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 9.7 Å
AuthorsZhu S / MacMicking J
Funding support United States, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI068041-14 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI108834-07 United States
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2024
Title: Native architecture of a human GBP1 defense complex for cell-autonomous immunity to infection.
Authors: Shiwei Zhu / Clinton J Bradfield / Agnieszka Maminska / Eui-Soon Park / Bae-Hoon Kim / Pradeep Kumar / Shuai Huang / Minjeong Kim / Yongdeng Zhang / Joerg Bewersdorf / John D MacMicking /
Abstract: All living organisms deploy cell-autonomous defenses to combat infection. In plants and animals, large supramolecular complexes often activate immune proteins for protection. In this work, we ...All living organisms deploy cell-autonomous defenses to combat infection. In plants and animals, large supramolecular complexes often activate immune proteins for protection. In this work, we resolved the native structure of a massive host-defense complex that polymerizes 30,000 guanylate-binding proteins (GBPs) over the surface of gram-negative bacteria inside human cells. Construction of this giant nanomachine took several minutes and remained stable for hours, required guanosine triphosphate hydrolysis, and recruited four GBPs plus caspase-4 and Gasdermin D as a cytokine and cell death immune signaling platform. Cryo-electron tomography suggests that GBP1 can adopt an extended conformation for bacterial membrane insertion to establish this platform, triggering lipopolysaccharide release that activated coassembled caspase-4. Our "open conformer" model provides a dynamic view into how the human GBP1 defense complex mobilizes innate immunity to infection.
History
DepositionDec 16, 2023-
Header (metadata) releaseMar 20, 2024-
Map releaseMar 20, 2024-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_43153.png

Downloads & links

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Map

FileDownload / File: emd_43153.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationhGBP1 monomer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.69 Å/pix.
x 256 pix.
= 689.408 Å		2.69 Å/pix.
x 256 pix.
= 689.408 Å		2.69 Å/pix.
x 256 pix.
= 689.408 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.693 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0877
Minimum - Maximum-0.31626612 - 0.55788696
Average (Standard dev.)0.00011426235 (±0.011144574)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 689.408 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_43153_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_43153_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_43153_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : human GBP1 coats with Salmonella minicell

EntireName: human GBP1 coats with Salmonella minicell
Components
  • Cell: human GBP1 coats with Salmonella minicell
    • Other: Human guanylate-binding protein 1

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Supramolecule #1: human GBP1 coats with Salmonella minicell

SupramoleculeName: human GBP1 coats with Salmonella minicell / type: cell / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Salmonella enterica subsp. enterica serovar Typhimurium (bacteria)

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Macromolecule #1: Human guanylate-binding protein 1

MacromoleculeName: Human guanylate-binding protein 1 / type: other / ID: 1 / Classification: other
Source (natural)Organism: Homo sapiens (human)
SequenceString: MASEIHMTGP MCLIENTNGR LMANPEALKI LSAITQPMVV VAIVGLYRTG KSYLMNKLAG KKKGFSLGST VQSHTKGIWM WCVPHPKKPG HILVLLDTEG LGDVEKGDNQ NDSWIFALAV LLSSTFVYNS IGTINQQAMD QLYYVTELTH RIRSKSSPDE NENEVEDSAD ...String:
MASEIHMTGP MCLIENTNGR LMANPEALKI LSAITQPMVV VAIVGLYRTG KSYLMNKLAG KKKGFSLGST VQSHTKGIWM WCVPHPKKPG HILVLLDTEG LGDVEKGDNQ NDSWIFALAV LLSSTFVYNS IGTINQQAMD QLYYVTELTH RIRSKSSPDE NENEVEDSAD FVSFFPDFVW TLRDFSLDLE ADGQPLTPDE YLTYSLKLKK GTSQKDETFN LPRLCIRKFF PKKKCFVFDR PVHRRKLAQL EKLQDEELDP EFVQQVADFC SYIFSNSKTK TLSGGIQVNG PRLESLVLTY VNAISSGDLP CMENAVLALA QIENSAAVQK AIAHYEQQMG QKVQLPTESL QELLDLHRDS EREAIEVFIR SSFKDVDHLF QKELAAQLEK KRDDFCKQNQ EASSDRCSGL LQVIFSPLEE EVKAGIYSKP GGYRLFVQKL QDLKKKYYEE PRKGIQAEEI LQTYLKSKES MTDAILQTDQ TLTEKEKEIE VERVKAESAQ ASAKMLQEMQ RKNEQMMEQK ERSYQEHLKQ LTEKMENDRV QLLKEQERTL ALKLQEQEQL LKEGFQKESR IMKNEIQDLQ TKMRRRKACT IS
Recombinant expressionOrganism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 2.86 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number subtomograms used: 12858
ExtractionNumber tomograms: 8 / Number images used: 30057
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementOverall B value: 400

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