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- EMDB-42536: CryoEM map of A/Shanghai/1/2013 H7 HA -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-42536
TitleCryoEM map of A/Shanghai/1/2013 H7 HA
Map dataShanghai13H7_sharp
Sample
  • Complex: A/Shanghai/1/2013 H7 HA
    • Protein or peptide: A/Shanghai/1/2013 H7 HA
KeywordscryoEMPEM / Flu Hemagglutinin / Central stem epitope / VIRAL PROTEIN
Biological speciesInfluenza A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHuang J / Han J / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
Bill & Melinda Gates FoundationINV-004923 United States
CitationJournal: Immunity / Year: 2024
Title: Eliciting a single amino acid change by vaccination generates antibody protection against group 1 and group 2 influenza A viruses.
Authors: Rashmi Ray / Faez Amokrane Nait Mohamed / Daniel P Maurer / Jiachen Huang / Berk A Alpay / Larance Ronsard / Zhenfei Xie / Julianna Han / Monica Fernandez-Quintero / Quynh Anh Phan / Rebecca ...Authors: Rashmi Ray / Faez Amokrane Nait Mohamed / Daniel P Maurer / Jiachen Huang / Berk A Alpay / Larance Ronsard / Zhenfei Xie / Julianna Han / Monica Fernandez-Quintero / Quynh Anh Phan / Rebecca L Ursin / Mya Vu / Kathrin H Kirsch / Thavaleak Prum / Victoria C Rosado / Thalia Bracamonte-Moreno / Vintus Okonkwo / Julia Bals / Caitlin McCarthy / Usha Nair / Masaru Kanekiyo / Andrew B Ward / Aaron G Schmidt / Facundo D Batista / Daniel Lingwood /
Abstract: Broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin (HA) stem of influenza A viruses (IAVs) tend to be effective against either group 1 or group 2 viral diversity. In rarer cases, ...Broadly neutralizing antibodies (bnAbs) targeting the hemagglutinin (HA) stem of influenza A viruses (IAVs) tend to be effective against either group 1 or group 2 viral diversity. In rarer cases, intergroup protective bnAbs can be generated by human antibody paratopes that accommodate the conserved glycan differences between the group 1 and group 2 stems. We applied germline-engaging nanoparticle immunogens to elicit a class of cross-group bnAbs from physiological precursor frequency within a humanized mouse model. Cross-group protection depended on the presence of the human bnAb precursors within the B cell repertoire, and the vaccine-expanded antibodies enriched for an N55T substitution in the CDRH2 loop, a hallmark of the bnAb class. Structurally, this single mutation introduced a flexible fulcrum to accommodate glycosylation differences and could alone enable cross-group protection. Thus, broad IAV immunity can be expanded from the germline repertoire via minimal antigenic input and an exceptionally simple antibody development pathway.
History
DepositionOct 30, 2023-
Header (metadata) releaseMay 8, 2024-
Map releaseMay 8, 2024-
UpdateMay 29, 2024-
Current statusMay 29, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42536.png

Downloads & links

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Map

FileDownload / File: emd_42536.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationShanghai13H7_sharp
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 384 pix.
= 278.4 Å		0.73 Å/pix.
x 384 pix.
= 278.4 Å		0.73 Å/pix.
x 384 pix.
= 278.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.725 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.18
Minimum - Maximum-0.47606695 - 0.6874581
Average (Standard dev.)-0.00018623944 (±0.019261641)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 278.40002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Shanghai13H7 halfA

Fileemd_42536_half_map_1.map
AnnotationShanghai13H7_halfA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Shanghai13H7 halfB

Fileemd_42536_half_map_2.map
AnnotationShanghai13H7_halfB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A/Shanghai/1/2013 H7 HA

EntireName: A/Shanghai/1/2013 H7 HA
Components
  • Complex: A/Shanghai/1/2013 H7 HA
    • Protein or peptide: A/Shanghai/1/2013 H7 HA

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Supramolecule #1: A/Shanghai/1/2013 H7 HA

SupramoleculeName: A/Shanghai/1/2013 H7 HA / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Influenza A virus

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Macromolecule #1: A/Shanghai/1/2013 H7 HA

MacromoleculeName: A/Shanghai/1/2013 H7 HA / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DKICLGHHAV SNGTKVNTLT ERGVEVVNAT ETVERTNIPR ICSKGKRTVD LGQCGLLGTI TGPPQCDQFL EFSADLIIER REGSDVCFPG KFVNEEALRQ ILRESGGIDK EAMGFTYSGI RTNGATSSCR RSGSSFYAEM KWLLSNTDNA AFPQMTKSYK NTRKNPALIV ...String:
DKICLGHHAV SNGTKVNTLT ERGVEVVNAT ETVERTNIPR ICSKGKRTVD LGQCGLLGTI TGPPQCDQFL EFSADLIIER REGSDVCFPG KFVNEEALRQ ILRESGGIDK EAMGFTYSGI RTNGATSSCR RSGSSFYAEM KWLLSNTDNA AFPQMTKSYK NTRKNPALIV WGIHHSGSTA EQTKLYGSGN KLVTVGSSNY QQSFVPSPGA RTQVNGQSGR IDFHWLMLNP NDTVTFSFNG AFIAPDRASF LRGKSMGIQS GVQVDADCEG DCYYSGGTII SNLPFQNIDS RAVGKCPRYV KQRSLLLATG MKNVPEI PK GRGLFGAIAG FIENGWEGLI DGWYGFRHQN AQGEGTAADY KSTQSAIDQI TGKLNRLIEK TNQQFELIDN EFTEVEKQIG NVINWTRDSI TEVWSYNAEL LVAMENQHTI DLADSEMDKL YERVKRQLRE NAEEDGTGCF EIFHKCDDDC MASIRNNTYD HSKYREEAMQ NRIQID GSG YIPEAPRDGQ AYVRKDGEWV LLSTFLGSGL NDIFEAQKIE WHEGHHHHHH

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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

Concentration0.7 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormula
50.0 nMTris
100.0 nMNaClSodium chloride
0.1 %Octyl-beta-Glucoside
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.7000000000000001 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2

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Image processing

Startup modelType of model: INSILICO MODEL / Details: CryoSPARC Ab-initio
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.0) / Number images used: 231246
FSC plot (resolution estimation)

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