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- EMDB-27124: Acylation domain local refinement for integrin alphaM/beta2 ectod... -

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Basic information

Entry
Database: EMDB / ID: EMD-27124
TitleAcylation domain local refinement for integrin alphaM/beta2 ectodomain in complex with adenylate cyclase toxin RTX751 and M1F5 Fab
Map dataAcylation domain local refinement unsharpened map
Sample
  • Complex: Ternary complex of integrin alphaM/beta2 ectodomain with adenylate cyclase toxin RTX domain and M1F5 Fab
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsGoldsmith JA / McLellan JS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI155453 United States
CitationJournal: Cell Rep / Year: 2022
Title: Structural basis for non-canonical integrin engagement by Bordetella adenylate cyclase toxin.
Authors: Jory A Goldsmith / Andrea M DiVenere / Jennifer A Maynard / Jason S McLellan /
Abstract: Integrins are ubiquitous cell-surface heterodimers that are exploited by pathogens and toxins, including leukotoxins that target β integrins on phagocytes. The Bordetella adenylate cyclase toxin ...Integrins are ubiquitous cell-surface heterodimers that are exploited by pathogens and toxins, including leukotoxins that target β integrins on phagocytes. The Bordetella adenylate cyclase toxin (ACT) uses the αβ integrin as a receptor, but the structural basis for integrin binding and neutralization by antibodies is poorly understood. Here, we use cryoelectron microscopy to determine a 2.7 Å resolution structure of an ACT fragment bound to αβ. This structure reveals that ACT interacts with the headpiece and calf-2 of the α subunit in a non-canonical manner specific to bent, inactive αβ. Neutralizing antibody epitopes map to ACT residues involved in α binding, providing the basis for antibody-mediated attachment inhibition. Furthermore, binding to αβ positions the essential ACT acylation sites, which are conserved among toxins exported by type I secretion systems, at the cell membrane. These findings reveal a structural mechanism for integrin-mediated attachment and explain antibody-mediated neutralization of ACT intoxication.
History
DepositionMay 27, 2022-
Header (metadata) releaseAug 17, 2022-
Map releaseAug 17, 2022-
UpdateSep 14, 2022-
Current statusSep 14, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27124.png

Downloads & links

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Map

FileDownload / File: emd_27124.map.gz / Format: CCP4 / Size: 147.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAcylation domain local refinement unsharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 338 pix.
= 362.674 Å		1.07 Å/pix.
x 338 pix.
= 362.674 Å		1.07 Å/pix.
x 338 pix.
= 362.674 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.073 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.24
Minimum - Maximum-0.8235849 - 1.8674226
Average (Standard dev.)-0.00015987268 (±0.014769612)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions338338338
Spacing338338338
CellA=B=C: 362.67398 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Acylation domain local refinement sharpened map (DeepEMhancer)

Fileemd_27124_additional_1.map
AnnotationAcylation domain local refinement sharpened map (DeepEMhancer)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Acylation domain local refinement half-map B

Fileemd_27124_half_map_1.map
AnnotationAcylation domain local refinement half-map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Acylation domain local refinement half-map A

Fileemd_27124_half_map_2.map
AnnotationAcylation domain local refinement half-map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ternary complex of integrin alphaM/beta2 ectodomain with adenylat...

EntireName: Ternary complex of integrin alphaM/beta2 ectodomain with adenylate cyclase toxin RTX domain and M1F5 Fab
Components
  • Complex: Ternary complex of integrin alphaM/beta2 ectodomain with adenylate cyclase toxin RTX domain and M1F5 Fab

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Supramolecule #1: Ternary complex of integrin alphaM/beta2 ectodomain with adenylat...

SupramoleculeName: Ternary complex of integrin alphaM/beta2 ectodomain with adenylate cyclase toxin RTX domain and M1F5 Fab
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#5
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 80.0 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

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

3k6s

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 347508
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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