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- EMDB-71481: Negative stain map of H15 HA (A/wedge-tailed shearwater/Western A... -

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Basic information

Entry
Database: EMDB / ID: EMD-71481
TitleNegative stain map of H15 HA (A/wedge-tailed shearwater/Western Australia/2576/1979) in complex with monoclonal Fab 3G11
Map dataNegative stain map of H15 HA (A/wedge-tailed shearwater/Western Australia/2576/1979) in complex with monoclonal Fab 3G11
Sample
  • Complex: Negative stain map of H15 HA (A/wedge-tailed shearwater/Western Australia/2576/1979) in complex with monoclonal Fab 3G11
Keywordsinfluenza virus / hemagglutinin / avian influenza virus / antibody Fab complex / glycoprotein / VIRAL PROTEIN
Biological speciesInfluenza A virus (A/shearwater/West Australia/2576/79(H15N9))
Methodsingle particle reconstruction / negative staining / Resolution: 25.0 Å
AuthorsLeon AN / Bhavsar D / Han JH / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: To Be Published
Title: Characterization of the antigenicity of influenza A virus hemagglutinin subtype H15
Authors: Bhavsar D / Leon AN
History
DepositionJun 26, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_71481.png

Downloads & links

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Map

FileDownload / File: emd_71481.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain map of H15 HA (A/wedge-tailed shearwater/Western Australia/2576/1979) in complex with monoclonal Fab 3G11
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.67 Å/pix.
x 208 pix.
= 347.36 Å		1.67 Å/pix.
x 208 pix.
= 347.36 Å		1.67 Å/pix.
x 208 pix.
= 347.36 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.67 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0182
Minimum - Maximum-0.039431628 - 0.120415546
Average (Standard dev.)0.000033170243 (±0.005025566)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions208208208
Spacing208208208
CellA=B=C: 347.36 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Negative stain half map A of H15 HA...

Fileemd_71481_half_map_1.map
AnnotationNegative stain half map A of H15 HA (A/wedge-tailed shearwater/Western Australia/2576/1979) in complex with monoclonal Fab 3G11
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Negative stain half map B of H15 HA...

Fileemd_71481_half_map_2.map
AnnotationNegative stain half map B of H15 HA (A/wedge-tailed shearwater/Western Australia/2576/1979) in complex with monoclonal Fab 3G11
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Negative stain map of H15 HA (A/wedge-tailed shearwater/Western A...

EntireName: Negative stain map of H15 HA (A/wedge-tailed shearwater/Western Australia/2576/1979) in complex with monoclonal Fab 3G11
Components
  • Complex: Negative stain map of H15 HA (A/wedge-tailed shearwater/Western Australia/2576/1979) in complex with monoclonal Fab 3G11

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Supramolecule #1: Negative stain map of H15 HA (A/wedge-tailed shearwater/Western A...

SupramoleculeName: Negative stain map of H15 HA (A/wedge-tailed shearwater/Western Australia/2576/1979) in complex with monoclonal Fab 3G11
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Influenza A virus (A/shearwater/West Australia/2576/79(H15N9))

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.015 mg/mL
BufferpH: 7.4
StainingType: NEGATIVE / Material: 2% w/v uranyl formate
GridModel: Homemade / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 25.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 1.0 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: OTHER
Details: apo negative stain map of A/Hong Kong/4801/2014 H3 generated by depositing lab
Final reconstructionResolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: RELION / Number images used: 12700
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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