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- EMDB-22939: H5 hemagglutinin ectodomain bound to 2 polyclonal Fab fragments e... -

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Basic information

Entry
Database: EMDB / ID: EMD-22939
TitleH5 hemagglutinin ectodomain bound to 2 polyclonal Fab fragments elicited by the qsMosaic-I53_dn5 immunogen
Map data
Sample
  • Complex: H5 hemagglutinin ectodomain bound to 2 polyclonal Fab fragments elicited by the qsMosaic-I53_dn5 immunogen
    • Complex: H5 hemagglutinin ectodomain
    • Complex: Polyclonal Fab fragments elicited by the qsMosaic-I53_dn5 immunogen
Biological speciesunidentified influenza virus / Macaca mulatta (Rhesus monkey)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsPark YJ / Veesler D
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM120553 United States
CitationJournal: Nature / Year: 2021
Title: Quadrivalent influenza nanoparticle vaccines induce broad protection.
Authors: Seyhan Boyoglu-Barnum / Daniel Ellis / Rebecca A Gillespie / Geoffrey B Hutchinson / Young-Jun Park / Syed M Moin / Oliver J Acton / Rashmi Ravichandran / Mike Murphy / Deleah Pettie / Nick ...Authors: Seyhan Boyoglu-Barnum / Daniel Ellis / Rebecca A Gillespie / Geoffrey B Hutchinson / Young-Jun Park / Syed M Moin / Oliver J Acton / Rashmi Ravichandran / Mike Murphy / Deleah Pettie / Nick Matheson / Lauren Carter / Adrian Creanga / Michael J Watson / Sally Kephart / Sila Ataca / John R Vaile / George Ueda / Michelle C Crank / Lance Stewart / Kelly K Lee / Miklos Guttman / David Baker / John R Mascola / David Veesler / Barney S Graham / Neil P King / Masaru Kanekiyo /
Abstract: Influenza vaccines that confer broad and durable protection against diverse viral strains would have a major effect on global health, as they would lessen the need for annual vaccine reformulation ...Influenza vaccines that confer broad and durable protection against diverse viral strains would have a major effect on global health, as they would lessen the need for annual vaccine reformulation and immunization. Here we show that computationally designed, two-component nanoparticle immunogens induce potently neutralizing and broadly protective antibody responses against a wide variety of influenza viruses. The nanoparticle immunogens contain 20 haemagglutinin glycoprotein trimers in an ordered array, and their assembly in vitro enables the precisely controlled co-display of multiple distinct haemagglutinin proteins in defined ratios. Nanoparticle immunogens that co-display the four haemagglutinins of licensed quadrivalent influenza vaccines elicited antibody responses in several animal models against vaccine-matched strains that were equivalent to or better than commercial quadrivalent influenza vaccines, and simultaneously induced broadly protective antibody responses to heterologous viruses by targeting the subdominant yet conserved haemagglutinin stem. The combination of potent receptor-blocking and cross-reactive stem-directed antibodies induced by the nanoparticle immunogens makes them attractive candidates for a supraseasonal influenza vaccine candidate with the potential to replace conventional seasonal vaccines.
History
DepositionNov 4, 2020-
Header (metadata) releaseApr 7, 2021-
Map releaseApr 7, 2021-
UpdateMay 5, 2021-
Current statusMay 5, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.25
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22939.png

Downloads & links

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Map

FileDownload / File: emd_22939.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 400 pix.
= 420. Å		1.05 Å/pix.
x 400 pix.
= 420. Å		1.05 Å/pix.
x 400 pix.
= 420. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25 / Movie #1: 0.25
Minimum - Maximum-0.17899597 - 1.1096318
Average (Standard dev.)0.0010900032 (±0.03312074)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 419.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z420.000420.000420.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1791.1100.001

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Supplemental data

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Additional map: #1

Fileemd_22939_additional_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_22939_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_22939_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : H5 hemagglutinin ectodomain bound to 2 polyclonal Fab fragments e...

EntireName: H5 hemagglutinin ectodomain bound to 2 polyclonal Fab fragments elicited by the qsMosaic-I53_dn5 immunogen
Components
  • Complex: H5 hemagglutinin ectodomain bound to 2 polyclonal Fab fragments elicited by the qsMosaic-I53_dn5 immunogen
    • Complex: H5 hemagglutinin ectodomain
    • Complex: Polyclonal Fab fragments elicited by the qsMosaic-I53_dn5 immunogen

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Supramolecule #1: H5 hemagglutinin ectodomain bound to 2 polyclonal Fab fragments e...

SupramoleculeName: H5 hemagglutinin ectodomain bound to 2 polyclonal Fab fragments elicited by the qsMosaic-I53_dn5 immunogen
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: H5 hemagglutinin ectodomain

SupramoleculeName: H5 hemagglutinin ectodomain / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: unidentified influenza virus
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: Polyclonal Fab fragments elicited by the qsMosaic-I53_dn5 immunogen

SupramoleculeName: Polyclonal Fab fragments elicited by the qsMosaic-I53_dn5 immunogen
type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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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

Concentration1 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: cryoSPARC ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 19849
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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