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- EMDB-25637: Negative stain map of polyclonal Fab 236.7 binding the RBS epitop... -

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Basic information

Entry
Database: EMDB / ID: EMD-25637
TitleNegative stain map of polyclonal Fab 236.7 binding the RBS epitope of H1 HA
Map dataNegative stain map of polyclonal Fab 236.7 binding the RBS epitope of H1 HA
Sample
  • Complex: Polyclonal Fab 236.7 binding the RBS epitope of H1 HA
    • Complex: Polyclonal Fab
    • Complex: Hemagglutinin
Keywordsanchor / antibodies / influenza A virus / hemagglutinin / IMMUNE SYSTEM
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane
Similarity search - Function
Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsHan J / Richey ST / 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: Nature / Year: 2022
Title: Broadly neutralizing antibodies target a haemagglutinin anchor epitope.
Authors: Jenna J Guthmiller / Julianna Han / Henry A Utset / Lei Li / Linda Yu-Ling Lan / Carole Henry / Christopher T Stamper / Meagan McMahon / George O'Dell / Monica L Fernández-Quintero / Alec W ...Authors: Jenna J Guthmiller / Julianna Han / Henry A Utset / Lei Li / Linda Yu-Ling Lan / Carole Henry / Christopher T Stamper / Meagan McMahon / George O'Dell / Monica L Fernández-Quintero / Alec W Freyn / Fatima Amanat / Olivia Stovicek / Lauren Gentles / Sara T Richey / Alba Torrents de la Peña / Victoria Rosado / Haley L Dugan / Nai-Ying Zheng / Micah E Tepora / Dalia J Bitar / Siriruk Changrob / Shirin Strohmeier / Min Huang / Adolfo García-Sastre / Klaus R Liedl / Jesse D Bloom / Raffael Nachbagauer / Peter Palese / Florian Krammer / Lynda Coughlan / Andrew B Ward / Patrick C Wilson /
Abstract: Broadly neutralizing antibodies that target epitopes of haemagglutinin on the influenza virus have the potential to provide near universal protection against influenza virus infection. However, viral ...Broadly neutralizing antibodies that target epitopes of haemagglutinin on the influenza virus have the potential to provide near universal protection against influenza virus infection. However, viral mutants that escape broadly neutralizing antibodies have been reported. The identification of broadly neutralizing antibody classes that can neutralize viral escape mutants is critical for universal influenza virus vaccine design. Here we report a distinct class of broadly neutralizing antibodies that target a discrete membrane-proximal anchor epitope of the haemagglutinin stalk domain. Anchor epitope-targeting antibodies are broadly neutralizing across H1 viruses and can cross-react with H2 and H5 viruses that are a pandemic threat. Antibodies that target this anchor epitope utilize a highly restricted repertoire, which encodes two public binding motifs that make extensive contacts with conserved residues in the fusion peptide. Moreover, anchor epitope-targeting B cells are common in the human memory B cell repertoire and were recalled in humans by an oil-in-water adjuvanted chimeric haemagglutinin vaccine, which is a potential universal influenza virus vaccine. To maximize protection against seasonal and pandemic influenza viruses, vaccines should aim to boost this previously untapped source of broadly neutralizing antibodies that are widespread in the human memory B cell pool.
History
DepositionDec 6, 2021-
Header (metadata) releaseJan 12, 2022-
Map releaseJan 12, 2022-
UpdateJan 17, 2024-
Current statusJan 17, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0207
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0207
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25637.png

Downloads & links

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Map

FileDownload / File: emd_25637.map.gz / Format: CCP4 / Size: 15.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain map of polyclonal Fab 236.7 binding the RBS epitope of H1 HA
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: 0.0207 / Movie #1: 0.0207
Minimum - Maximum-0.04116609 - 0.06341436
Average (Standard dev.)0.0004807606 (±0.0049619535)
SymmetrySpace group: 1
Details

EMDB XML:

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

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.771.771.77
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z283.200283.200283.200
α/β/γ90.00090.00090.000
start NX/NY/NZ535354
NX/NY/NZ132140135
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS160160160
D min/max/mean-0.0410.0630.000

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Supplemental data

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Sample components

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Entire : Polyclonal Fab 236.7 binding the RBS epitope of H1 HA

EntireName: Polyclonal Fab 236.7 binding the RBS epitope of H1 HA
Components
  • Complex: Polyclonal Fab 236.7 binding the RBS epitope of H1 HA
    • Complex: Polyclonal Fab
    • Complex: Hemagglutinin

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Supramolecule #1: Polyclonal Fab 236.7 binding the RBS epitope of H1 HA

SupramoleculeName: Polyclonal Fab 236.7 binding the RBS epitope of H1 HA / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Strain: A/Michigan/45/2015 H1N1

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Supramolecule #2: Polyclonal Fab

SupramoleculeName: Polyclonal Fab / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Hemagglutinin

SupramoleculeName: Hemagglutinin / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Homo sapiens (human) / Strain: A/Michigan/45/2015 H1N1

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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 / Details: Tris-buffered saline
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
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:

4m4y

Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 2215
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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