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- EMDB-48715: Cryo-EM map of vaccine elicited antibody 22F5 bound to post-fusio... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-48715
TitleCryo-EM map of vaccine elicited antibody 22F5 bound to post-fusion conformation of Langya virus F protein
Map dataSharpened map
Sample
  • Complex: Vaccine elicted antibody 22F5 bound to post-fusion conformation of Langya virus F protein
    • Complex: Langya virus F protein
    • Complex: 22F5 Fab
KeywordsHenipavirus / Langya virus / vaccine-elicited antibody / DII domain / shrew-origin / ANTIVIRAL PROTEIN
Biological speciesLangya virus / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.31 Å
AuthorsKumar U / Acharya P
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Structural and Antigenic Characterization of Novel and Diverse Henipavirus Glycoproteins
Authors: May AJ / Lella M / Lindenberger J / Berkman A / Kumar U / Haynes BF / Acharya P
History
DepositionJan 19, 2025-
Header (metadata) releaseJun 3, 2026-
Map releaseJun 3, 2026-
UpdateJun 3, 2026-
Current statusJun 3, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48715.png

Downloads & links

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Map

FileDownload / File: emd_48715.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å		1.1 Å/pix.
x 320 pix.
= 352. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.186
Minimum - Maximum-1.8013783 - 2.3585498
Average (Standard dev.)-0.0006292171 (±0.04031596)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 352.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_48715_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_48715_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 : Vaccine elicted antibody 22F5 bound to post-fusion conformation o...

EntireName: Vaccine elicted antibody 22F5 bound to post-fusion conformation of Langya virus F protein
Components
  • Complex: Vaccine elicted antibody 22F5 bound to post-fusion conformation of Langya virus F protein
    • Complex: Langya virus F protein
    • Complex: 22F5 Fab

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Supramolecule #1: Vaccine elicted antibody 22F5 bound to post-fusion conformation o...

SupramoleculeName: Vaccine elicted antibody 22F5 bound to post-fusion conformation of Langya virus F protein
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: Langya virus F protein

SupramoleculeName: Langya virus F protein / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Langya virus

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Supramolecule #3: 22F5 Fab

SupramoleculeName: 22F5 Fab / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Mus musculus (house mouse)

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Instrument: LEICA EM GP

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 59.6 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.31 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 271130
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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