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- EMDB-26929: Negative stain half map of cH4/3 state 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-26929
TitleNegative stain half map of cH4/3 state 1
Map dataNegative stain map of cH4/3 state 1
Sample
  • Organelle or cellular component: Negative stain map of cH4/3 state 1
KeywordsHemagglutinin / chimeric HA / broadly neutralizing stem antibody / CR9114 / IMMUNE SYSTEM
Biological speciesInfluenza A virus
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsHan J / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93109C00051 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Influenza chimeric hemagglutinin structures in complex with broadly protective antibodies to the stem and trimer interface.
Authors: Xueyong Zhu / Julianna Han / Weina Sun / Eduard Puente-Massaguer / Wenli Yu / Peter Palese / Florian Krammer / Andrew B Ward / Ian A Wilson /
Abstract: Influenza virus hemagglutinin (HA) has been the primary target for influenza vaccine development. Broadly protective antibodies targeting conserved regions of the HA unlock the possibility of ...Influenza virus hemagglutinin (HA) has been the primary target for influenza vaccine development. Broadly protective antibodies targeting conserved regions of the HA unlock the possibility of generating universal influenza immunity. Two group 2 influenza A chimeric HAs, cH4/3 and cH15/3, were previously designed to elicit antibodies to the conserved HA stem. Here, we show by X-ray crystallography and negative-stain electron microscopy that a broadly protective antistem antibody can stably bind to cH4/3 and cH15/3 HAs, thereby validating their potential as universal vaccine immunogens. Furthermore, flexibility was observed in the head domain of the chimeric HA structures, suggesting that antibodies could also potentially interact with the head interface epitope. Our structural and binding studies demonstrated that a broadly protective antihead trimeric interface antibody could indeed target the more open head domain of the cH15/3 HA trimer. Thus, in addition to inducing broadly protective antibodies against the conserved HA stem, chimeric HAs may also be able to elicit antibodies against the conserved trimer interface in the HA head domain, thereby increasing the vaccine efficacy.
History
DepositionMay 9, 2022-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26929.png

Downloads & links

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Map

FileDownload / File: emd_26929.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain map of cH4/3 state 1
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.77 Å/pix.
x 160 pix.
= 283.2 Å		1.77 Å/pix.
x 160 pix.
= 283.2 Å		1.77 Å/pix.
x 160 pix.
= 283.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.77 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018
Minimum - Maximum-0.03935259 - 0.1015321
Average (Standard dev.)0.00034279126 (±0.005336667)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions160160160
Spacing160160160
CellA=B=C: 283.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Negative stain half map of cH4/3 state 1

Fileemd_26929_half_map_1.map
AnnotationNegative stain half map of cH4/3 state 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Negative stain half map of cH4/3 state 1

Fileemd_26929_half_map_2.map
AnnotationNegative stain half map of cH4/3 state 1
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 cH4/3 state 1

EntireName: Negative stain map of cH4/3 state 1
Components
  • Organelle or cellular component: Negative stain map of cH4/3 state 1

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Supramolecule #1: Negative stain map of cH4/3 state 1

SupramoleculeName: Negative stain map of cH4/3 state 1 / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Source (natural)Organism: Influenza A virus

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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

BufferpH: 7.4
StainingType: NEGATIVE / Material: uranyl formate

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: -2.0 µm / Nominal defocus min: -1.0 µm
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

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

3m5g

Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 1538
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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