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- EMDB-21973: CryoEM structure of influenza hemagglutinin A/Victoria/361/2011 i... -

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Basic information

Entry
Database: EMDB / ID: EMD-21973
TitleCryoEM structure of influenza hemagglutinin A/Victoria/361/2011 in complex with cyno antibody 3B10
Map data
Sample
  • Complex: Influenza hemagglutinin A/Victoria/361/2011 in complex with 3B10 Fab
    • Complex: Hemagglutinin
      • Protein or peptide: Hemagglutinin
    • Complex: Cyno antibody
      • Protein or peptide: Cyno antibody heavy chain
      • Protein or peptide: Cyno antibody light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Keywordsinfluenza / hemagglutinin / antibody / vaccine / broadly neutralizing antibody / ANTIVIRAL PROTEIN
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / 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 / 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 speciesInfluenza A virus / Macaca fascicularis (crab-eating macaque)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.7 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
DepositionMay 14, 2020-
Header (metadata) releaseMar 10, 2021-
Map releaseMar 10, 2021-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6wzt
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21973.png

Downloads & links

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Map

FileDownload / File: emd_21973.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 250 pix.
= 265. Å		1.06 Å/pix.
x 250 pix.
= 265. Å		1.06 Å/pix.
x 250 pix.
= 265. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.029460026 - 0.05463551
Average (Standard dev.)0.00026456016 (±0.0021362924)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 265.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z250250250
origin x/y/z0.0000.0000.000
length x/y/z265.000265.000265.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-170-170-170
NX/NY/NZ340340340
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS250250250
D min/max/mean-0.0290.0550.000

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Supplemental data

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Sample components

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Entire : Influenza hemagglutinin A/Victoria/361/2011 in complex with 3B10 Fab

EntireName: Influenza hemagglutinin A/Victoria/361/2011 in complex with 3B10 Fab
Components
  • Complex: Influenza hemagglutinin A/Victoria/361/2011 in complex with 3B10 Fab
    • Complex: Hemagglutinin
      • Protein or peptide: Hemagglutinin
    • Complex: Cyno antibody
      • Protein or peptide: Cyno antibody heavy chain
      • Protein or peptide: Cyno antibody light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Influenza hemagglutinin A/Victoria/361/2011 in complex with 3B10 Fab

SupramoleculeName: Influenza hemagglutinin A/Victoria/361/2011 in complex with 3B10 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Influenza A virus
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: Macaca fascicularis (crab-eating macaque)

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Supramolecule #3: Cyno antibody

SupramoleculeName: Cyno antibody / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2-#3

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Macromolecule #1: Hemagglutinin

MacromoleculeName: Hemagglutinin / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus
Strain: A/reassortant/NYMC X-217(A/Puerto Rico/8/1934 x A/Victoria/361/2011)(H3N2)
Molecular weightTheoretical: 56.721504 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QKLPGNDNST ATLCLGHHAV PNGTIVKTIT NDQIEVTNAT ELVQNSSIGE ICDSPHQILD GENCTLIDAL LGDPQCDGFQ NKKWDLFVE RSKAYSNCFP YDVPDYASLR SLVASSGTLE FNNESFNWTG VTQNGTSSAC IRRSNNSFFS RLNWLTQLNF K YPALNVTM ...String:
QKLPGNDNST ATLCLGHHAV PNGTIVKTIT NDQIEVTNAT ELVQNSSIGE ICDSPHQILD GENCTLIDAL LGDPQCDGFQ NKKWDLFVE RSKAYSNCFP YDVPDYASLR SLVASSGTLE FNNESFNWTG VTQNGTSSAC IRRSNNSFFS RLNWLTQLNF K YPALNVTM PNNEQFDKLY IWGVHHPVTD KDQIFLYAQS SGRITVSTKR SQQAVIPNIG YRPRIRNIPS RISIYWTIVK PG DILLINS TGNLIAPRGY FKIRSGKSSI MRSDAPIGKC NSECITPNGS IPNDKPFQNV NRITYGACPR YVKQSTLKLA TGM RNVPEK QTRGIFGAIA GFIENGWEGM VDGWYGFRHQ NSEGRGQAAD LKSTQAAIDQ INGKLNRLIG KTNEKFHQIE KEFS EVEGR IQDLEKYVED TKIDLWSYNA ELLVALENQH TIDLTDSEMN KLFEKTKKQL RENAEDMGNG CFKIYHKCDN ACIGS IRNG TYDHDVYRDE ALNNRFQIK

UniProtKB: Hemagglutinin

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Macromolecule #2: Cyno antibody heavy chain

MacromoleculeName: Cyno antibody heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)
Molecular weightTheoretical: 24.700625 KDa
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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Macromolecule #3: Cyno antibody light chain

MacromoleculeName: Cyno antibody light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)
Molecular weightTheoretical: 23.095521 KDa
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 #6: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 6 / Number of copies: 3 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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

Concentration0.13 mg/mL
BufferpH: 8.5
GridModel: C-flat-2/2 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 42.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 114332
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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