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- EMDB-22096: CryoEM map of Full-length Influenza Hemagglutinin (A/Vietnam/1203... -

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Basic information

Entry
Database: EMDB / ID: EMD-22096
TitleCryoEM map of Full-length Influenza Hemagglutinin (A/Vietnam/1203/2004) in complex with 1C4 Fab Fragment
Map data
Sample
  • Complex: Influenza hemagglutinin A/Vietnam/1203/2004 in complex with 1C4 Fab
    • Complex: Hemagglutinin
      • Protein or peptide: Influenza Hemagglutinin (A/Vietnam/1203/2004)
    • Complex: 1C4 Fab
      • Protein or peptide: Cyno antibody light chain
      • Protein or peptide: Cyno antibody heavy chain
Biological speciesInfluenza A virus / Macaca fascicularis (crab-eating macaque)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsQiu Y / Zhou Y
CitationJournal: Sci Transl Med / Year: 2021
Title: Broad neutralization of H1 and H3 viruses by adjuvanted influenza HA stem vaccines in nonhuman primates.
Authors: Nicole Darricarrère / Yu Qiu / Masaru Kanekiyo / Adrian Creanga / Rebecca A Gillespie / Syed M Moin / Jacqueline Saleh / Jose Sancho / Te-Hui Chou / Yanfeng Zhou / Ruijun Zhang / Shujia Dai ...Authors: Nicole Darricarrère / Yu Qiu / Masaru Kanekiyo / Adrian Creanga / Rebecca A Gillespie / Syed M Moin / Jacqueline Saleh / Jose Sancho / Te-Hui Chou / Yanfeng Zhou / Ruijun Zhang / Shujia Dai / Anthony Moody / Kevin O Saunders / Michelle C Crank / John R Mascola / Barney S Graham / Chih-Jen Wei / Gary J Nabel /
Abstract: Seasonal influenza vaccines confer protection against specific viral strains but have restricted breadth that limits their protective efficacy. The H1 and H3 subtypes of influenza A virus cause most ...Seasonal influenza vaccines confer protection against specific viral strains but have restricted breadth that limits their protective efficacy. The H1 and H3 subtypes of influenza A virus cause most of the seasonal epidemics observed in humans and are the major drivers of influenza A virus-associated mortality. The consequences of pandemic spread of COVID-19 underscore the public health importance of prospective vaccine development. Here, we show that headless hemagglutinin (HA) stabilized-stem immunogens presented on ferritin nanoparticles elicit broadly neutralizing antibody (bnAb) responses to diverse H1 and H3 viruses in nonhuman primates (NHPs) when delivered with a squalene-based oil-in-water emulsion adjuvant, AF03. The neutralization potency and breadth of antibodies isolated from NHPs were comparable to human bnAbs and extended to mismatched heterosubtypic influenza viruses. Although NHPs lack the immunoglobulin germline VH1-69 residues associated with the most prevalent human stem-directed bnAbs, other gene families compensated to generate bnAbs. Isolation and structural analyses of vaccine-induced bnAbs revealed extensive interaction with the fusion peptide on the HA stem, which is essential for viral entry. Antibodies elicited by these headless HA stabilized-stem vaccines neutralized diverse H1 and H3 influenza viruses and shared a mode of recognition analogous to human bnAbs, suggesting that these vaccines have the potential to confer broadly protective immunity against diverse viruses responsible for seasonal and pandemic influenza infections in humans.
History
DepositionJun 2, 2020-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateMar 17, 2021-
Current statusMar 17, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22096.png

Downloads & links

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Map

FileDownload / File: emd_22096.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.)
0.75 Å/pix.
x 400 pix.
= 300. Å		0.75 Å/pix.
x 400 pix.
= 300. Å		0.75 Å/pix.
x 400 pix.
= 300. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.75 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.015556862 - 0.058399234
Average (Standard dev.)0.00026739755 (±0.0021124354)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 300.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.750.750.75
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z300.000300.000300.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0160.0580.000

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Supplemental data

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Sample components

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Entire : Influenza hemagglutinin A/Vietnam/1203/2004 in complex with 1C4 Fab

EntireName: Influenza hemagglutinin A/Vietnam/1203/2004 in complex with 1C4 Fab
Components
  • Complex: Influenza hemagglutinin A/Vietnam/1203/2004 in complex with 1C4 Fab
    • Complex: Hemagglutinin
      • Protein or peptide: Influenza Hemagglutinin (A/Vietnam/1203/2004)
    • Complex: 1C4 Fab
      • Protein or peptide: Cyno antibody light chain
      • Protein or peptide: Cyno antibody heavy chain

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Supramolecule #1: Influenza hemagglutinin A/Vietnam/1203/2004 in complex with 1C4 Fab

SupramoleculeName: Influenza hemagglutinin A/Vietnam/1203/2004 in complex with 1C4 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 336 KDa

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Supramolecule #2: Hemagglutinin

SupramoleculeName: Hemagglutinin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Influenza A virus
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: 1C4 Fab

SupramoleculeName: 1C4 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Influenza Hemagglutinin (A/Vietnam/1203/2004)

MacromoleculeName: Influenza Hemagglutinin (A/Vietnam/1203/2004) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEKIVLLFAI VSLVKSDQIC IGYHANNSTE QVDTIMEKNV TVTHAQDILE KKHNGKLCDL DGVKPLILRD CSVAGWLLGN PMCDEFINVP EWSYIVEKAN PVNDLCYPGD FNDYEELKHL LSRINHFEKI QIIPKSSWSS HEASLGVSSA CPYQGKSSFF RNVVWLIKKN ...String:
MEKIVLLFAI VSLVKSDQIC IGYHANNSTE QVDTIMEKNV TVTHAQDILE KKHNGKLCDL DGVKPLILRD CSVAGWLLGN PMCDEFINVP EWSYIVEKAN PVNDLCYPGD FNDYEELKHL LSRINHFEKI QIIPKSSWSS HEASLGVSSA CPYQGKSSFF RNVVWLIKKN STYPTIKRSY NNTNQEDLLV LWGIHHPNDA AEQTKLYQNP TTYISVGTST LNQRLVPRIA TRSKVNGQSG RMEFFWTILK PNDAINFESN GNFIAPEYAY KIVKKGDSTI MKSELEYGNC NTKCQTPMGA INSSMPFHNI HPLTIGECPK YVKSNRLVLA TGLRNSPQRE RRRKKRGLFG AIAGFIEGGW QGMVDGWYGY HHSNEQGSGY AADKESTQKA IDGVTNKVNS IIDKMNTQFE AVGREFNNLE RRIENLNKKM EDGFLDVWTY NAELLVLMEN ERTLDFHDSN VKNLYDKVRL QLRDNAKELG NGCFEFYHKC DNECMESVRN GTYDYPQYSE EARLKREEIS GVKLESIGIY QILSIYSTVA SSLALAIMVA GLSLWMCSNG SLQCRICI

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Macromolecule #2: Cyno antibody light chain

MacromoleculeName: Cyno antibody light chain / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDTVT ITCRASQSIS SWLAWYQQKP GKAPKLLIYK ASSLQGGVPS RFSGSGSGSD FTLTISSLQS EDFATYYCQ QYSGRPPTFG QGTKVEIKRA VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDTVT ITCRASQSIS SWLAWYQQKP GKAPKLLIYK ASSLQGGVPS RFSGSGSGSD FTLTISSLQS EDFATYYCQ QYSGRPPTFG QGTKVEIKRA VAAPSVFIFP PSEDQVKSGT VSVVCLLNNF YPREASVKWK VDGALKTGNS Q ESVTEQDS KDNTYSLSST LTLSSTDYQS HNVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #3: Cyno antibody heavy chain

MacromoleculeName: Cyno antibody heavy chain / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVKPSETLSL TCAVSGGTFS AYYWGWIRQP PGKGLEWIGS ISGGSGSTDY SPSLKSRATI SRDTSKNQFS LKLTSVTAA DTAVYYCVRK YWGDYYANWF DVWGPGVLVT VSSASTKGPS VFPLAPCSRS TSESTAALGC LVKDYFPEPV T VSWNSGSL ...String:
QVQLQESGPG LVKPSETLSL TCAVSGGTFS AYYWGWIRQP PGKGLEWIGS ISGGSGSTDY SPSLKSRATI SRDTSKNQFS LKLTSVTAA DTAVYYCVRK YWGDYYANWF DVWGPGVLVT VSSASTKGPS VFPLAPCSRS TSESTAALGC LVKDYFPEPV T VSWNSGSL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYVCNVN HKPSNTKVDK RVEIKTCGGG SKPPT

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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

Concentration0.2 mg/mL
BufferpH: 7
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 45.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 506644
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING

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