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- EMDB-27562: Postfusion Nipah virus fusion protein in complex with Fab 1H1, lo... -

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Basic information

Entry
Database: EMDB / ID: EMD-27562
TitlePostfusion Nipah virus fusion protein in complex with Fab 1H1, low resolution reconstruction including the six helix bundle
Map dataPostfusion Nipah virus fusion protein in complex with Fab 1H1, low resolution reconstruction including the six helix bundle
Sample
  • Complex: Postfusion Nipah virus fusion protein in complex with Fab 1H1
KeywordsNipah / Nipah virus / NiV / fusion / F / antibody / neutralizing / conserved epitope / neutralizing antibody / six helix bundle / VIRAL PROTEIN
Biological speciesNipah henipavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsByrne PO / Blade EG / McLellan JS
Funding support United States, 1 items
OrganizationGrant numberCountry
Welch FoundationF-0003-19620604 United States
CitationJournal: To Be Published
Title: Postfusion Nipah virus fusion protein in complex with Fab 1H1
Authors: Byrne PO / Blade EG / McLellan JS
History
DepositionJul 11, 2022-
Header (metadata) releaseJul 19, 2023-
Map releaseJul 19, 2023-
UpdateJul 19, 2023-
Current statusJul 19, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27562.png

Downloads & links

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Map

FileDownload / File: emd_27562.map.gz / Format: CCP4 / Size: 729 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostfusion Nipah virus fusion protein in complex with Fab 1H1, low resolution reconstruction including the six helix bundle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 576 pix.
= 466.56 Å		0.81 Å/pix.
x 576 pix.
= 466.56 Å		0.81 Å/pix.
x 576 pix.
= 466.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.29262653 - 0.5429534
Average (Standard dev.)0.00002900322 (±0.008474832)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions576576576
Spacing576576576
CellA=B=C: 466.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_27562_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Additional Map

Fileemd_27562_additional_1.map
AnnotationAdditional Map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 1

Fileemd_27562_half_map_1.map
AnnotationHalf Map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map 2

Fileemd_27562_half_map_2.map
AnnotationHalf Map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Postfusion Nipah virus fusion protein in complex with Fab 1H1

EntireName: Postfusion Nipah virus fusion protein in complex with Fab 1H1
Components
  • Complex: Postfusion Nipah virus fusion protein in complex with Fab 1H1

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Supramolecule #1: Postfusion Nipah virus fusion protein in complex with Fab 1H1

SupramoleculeName: Postfusion Nipah virus fusion protein in complex with Fab 1H1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Nipah henipavirus

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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

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 13527
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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