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- EMDB-22180: CryoEM structure of influenza hemagglutinin A/Michigan/45/2015 in... -

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Basic information

Entry
Database: EMDB / ID: EMD-22180
TitleCryoEM structure of influenza hemagglutinin A/Michigan/45/2015 in complex with cyno antibody 1C4
Map data
Sample
  • Complex: A/Michigan/45/2015(H1N1) hemagglutinin in complex with 1C4 Fab
    • Complex: Hemagglutinin
      • Protein or peptide: Hemagglutinin HA1 chain
      • Protein or peptide: Hemagglutinin HA2 chain
    • Complex: 1C4 Fab
      • Protein or peptide: 1C4 Fab heavy chain
      • Protein or peptide: 1C4 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / membrane => GO:0016020 / 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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus (A/Michigan/45/2015(H1N1)) / Macaca fascicularis (crab-eating macaque)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 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 17, 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: 0.02
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xgc
  • Surface level: 0.02
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22180.png

Downloads & links

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Map

FileDownload / File: emd_22180.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.059 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.06848428 - 0.11415439
Average (Standard dev.)0.00019993474 (±0.002521548)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 317.7 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0591.0591.059
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z317.700317.700317.700
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/NS300300300
D min/max/mean-0.0680.1140.000

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Supplemental data

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Sample components

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Entire : A/Michigan/45/2015(H1N1) hemagglutinin in complex with 1C4 Fab

EntireName: A/Michigan/45/2015(H1N1) hemagglutinin in complex with 1C4 Fab
Components
  • Complex: A/Michigan/45/2015(H1N1) hemagglutinin in complex with 1C4 Fab
    • Complex: Hemagglutinin
      • Protein or peptide: Hemagglutinin HA1 chain
      • Protein or peptide: Hemagglutinin HA2 chain
    • Complex: 1C4 Fab
      • Protein or peptide: 1C4 Fab heavy chain
      • Protein or peptide: 1C4 Fab light chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: A/Michigan/45/2015(H1N1) hemagglutinin in complex with 1C4 Fab

SupramoleculeName: A/Michigan/45/2015(H1N1) hemagglutinin in complex with 1C4 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Molecular weightTheoretical: 320 kDa/nm

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Supramolecule #2: Hemagglutinin

SupramoleculeName: Hemagglutinin / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Influenza A virus (A/Michigan/45/2015(H1N1))
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: 1C4 Fab

SupramoleculeName: 1C4 Fab / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)
Recombinant expressionOrganism: Homo sapiens (human)

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Macromolecule #1: Hemagglutinin HA1 chain

MacromoleculeName: Hemagglutinin HA1 chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Michigan/45/2015(H1N1)) / Strain: A/Michigan/45/2015(H1N1)
Molecular weightTheoretical: 36.432949 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DTLCIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDKHNGK LCKLRGVAPL HLGKCNIAGW ILGNPECESL STASSWSYIV ETSNSDNGT CYPGDFINYE ELREQLSSVS SFERFEIFPK TSSWPNHDSN KGVTAACPHA GAKSFYKNLI WLVKKGNSYP K LNQSYIND ...String:
DTLCIGYHAN NSTDTVDTVL EKNVTVTHSV NLLEDKHNGK LCKLRGVAPL HLGKCNIAGW ILGNPECESL STASSWSYIV ETSNSDNGT CYPGDFINYE ELREQLSSVS SFERFEIFPK TSSWPNHDSN KGVTAACPHA GAKSFYKNLI WLVKKGNSYP K LNQSYIND KGKEVLVLWG IHHPSTTADQ QSLYQNADAY VFVGTSRYSK KFKPEIATRP KVRDQEGRMN YYWTLVEPGD KI TFEATGN LVVPRYAFTM ERNAGSGIII SDTPVHDCNT TCQTPEGAIN TSLPFQNIHP ITIGKCPKYV KSTKLRLATG LRN VPSIQS R

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Macromolecule #2: Hemagglutinin HA2 chain

MacromoleculeName: Hemagglutinin HA2 chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Michigan/45/2015(H1N1)) / Strain: A/Michigan/45/2015(H1N1)
Molecular weightTheoretical: 25.109902 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADLKS TQNAIDKITN KVNSVIEKMN TQFTAVGKEF NHLEKRIENL NKKVDDGFL DIWTYNAELL VLLENERTLD YHDSNVKNLY EKVRNQLKNN AKEIGNGCFE FYHKCDNTCM ESVKNGTYDY P KYSEEAKL ...String:
GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADLKS TQNAIDKITN KVNSVIEKMN TQFTAVGKEF NHLEKRIENL NKKVDDGFL DIWTYNAELL VLLENERTLD YHDSNVKNLY EKVRNQLKNN AKEIGNGCFE FYHKCDNTCM ESVKNGTYDY P KYSEEAKL NREKIDSGRL VPRGSPGSGY IPEAPRDGQA YVRKDGEWVL LSTFLGHHHH HH

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Macromolecule #3: 1C4 Fab heavy chain

MacromoleculeName: 1C4 Fab heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)
Molecular weightTheoretical: 25.605572 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EVQLVESGGG LAKPGGSLRL SCAASGFTFS TYAMHWVRQA PGKGLEWISG INSGGGSTWY TASVKGRFTI SRDNSKSTLS LQMNSLRTE DTAVYYCAKD GGNAIFGLVI TNYGLDSWGQ GAVVTVSSAS TKGPSVFPLA PSSRSTSEST AALGCLVKDY F PEPVTVSW ...String:
EVQLVESGGG LAKPGGSLRL SCAASGFTFS TYAMHWVRQA PGKGLEWISG INSGGGSTWY TASVKGRFTI SRDNSKSTLS LQMNSLRTE DTAVYYCAKD GGNAIFGLVI TNYGLDSWGQ GAVVTVSSAS TKGPSVFPLA PSSRSTSEST AALGCLVKDY F PEPVTVSW NSGSLTSGVH TFPAVLQSSG LYSLSSVVTV PSSSLGTQTY VCNVNHKPSN TKVDKRVEIK TCGGGSKPPT HH HHHH

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Macromolecule #4: 1C4 Fab light chain

MacromoleculeName: 1C4 Fab light chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca fascicularis (crab-eating macaque)
Molecular weightTheoretical: 22.837086 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSVLTQPPSA SGAPGQSVTI SCSGSSSNFG SNHVYWYQQL SGKAPKLLIY NNNRRPSGVP DRFSGSKSGT SASLAISGLQ SEDEADYYC SVWDSSLNNV LFGGGTRLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGVVK VAWKADGNSV N TGVETTTP ...String:
QSVLTQPPSA SGAPGQSVTI SCSGSSSNFG SNHVYWYQQL SGKAPKLLIY NNNRRPSGVP DRFSGSKSGT SASLAISGLQ SEDEADYYC SVWDSSLNNV LFGGGTRLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGVVK VAWKADGNSV N TGVETTTP SKQSNNKYAA SSYLSLTSDQ WKSHKSYSCQ VTHEGSTVEK TVAPAECS

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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: 15 / 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

BufferpH: 8.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 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

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 449762
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: MAXIMUM LIKELIHOOD

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