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- EMDB-47489: Cryo EM structure of pertussis toxin in complex with neutralizing... -

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Basic information

Entry
Database: EMDB / ID: EMD-47489
TitleCryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-221
Map datastructure of pertussis toxin in complex with neutralizing Fab PERT-221
Sample
  • Complex: pertussis toxin in complex with neutralizing Fab PERT-221
KeywordsPTx / mAb / Complex / Whooping / TOXIN
Biological speciesBordetella pertussis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsBinshtein E / Crowe JE
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo EM structure of pertussis toxin in complex with neutralizing Fab PERT-221
Authors: Binshtein E / Crowe JE
History
DepositionOct 23, 2024-
Header (metadata) releaseOct 29, 2025-
Map releaseOct 29, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47489.png

Downloads & links

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Map

FileDownload / File: emd_47489.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationstructure of pertussis toxin in complex with neutralizing Fab PERT-221
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 460 pix.
= 297.62 Å		0.65 Å/pix.
x 460 pix.
= 297.62 Å		0.65 Å/pix.
x 460 pix.
= 297.62 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.647 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.0017567389 - 2.0403335
Average (Standard dev.)0.0008306024 (±0.019587135)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions460460460
Spacing460460460
CellA=B=C: 297.62 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_47489_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_47489_half_map_2.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : pertussis toxin in complex with neutralizing Fab PERT-221

EntireName: pertussis toxin in complex with neutralizing Fab PERT-221
Components
  • Complex: pertussis toxin in complex with neutralizing Fab PERT-221

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Supramolecule #1: pertussis toxin in complex with neutralizing Fab PERT-221

SupramoleculeName: pertussis toxin in complex with neutralizing Fab PERT-221
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Bordetella pertussis (bacteria)

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 17846 / Average electron dose: 59.54 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 241902
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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