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- EMDB-22302: Cryo-EM Structure of Vaccine-Elicited Rhesus Antibody 789-203-3C1... -

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Basic information

Entry
Database: EMDB / ID: EMD-22302
TitleCryo-EM Structure of Vaccine-Elicited Rhesus Antibody 789-203-3C12 in Complex with Stabilized SI06 (A/Solomon Islands/3/06) Influenza Hemagglutinin Trimer
Map dataCryo-EM structure of vaccine-elicited Rhesus VH6-1 antibody 789-203-3C12
Sample
  • Organelle or cellular component: Influenza Hemagglutinin SI06 Trimer in complex with 789-203-3C12 Fab
    • Organelle or cellular component: 789-203-3C12 Fab Heavy and Light Chains
      • Protein or peptide: 789-203-3C12 Fab Light Chain
      • Protein or peptide: 789-203-3C12 Fab Heavy Chain
    • Organelle or cellular component: Influenza HemagglutininHemagglutinin (influenza)
      • Protein or peptide: Hemagglutinin HA1 chain
      • Protein or peptide: Hemagglutinin HA2 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 / 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
Biological speciesMacaca mulatta (Rhesus monkey) / Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Methodsingle particle reconstruction / cryo EM / Resolution: 3.85 Å
AuthorsCerutti G / Gorman J / Kwong PD / Shapiro L
Funding support United States, 2 items
OrganizationGrant numberCountry
Bill & Melinda Gates Foundation United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Immunity / Year: 2022
Title: Co-immunization with hemagglutinin stem immunogens elicits cross-group neutralizing antibodies and broad protection against influenza A viruses.
Authors: Syed M Moin / Jeffrey C Boyington / Seyhan Boyoglu-Barnum / Rebecca A Gillespie / Gabriele Cerutti / Crystal Sao-Fong Cheung / Alberto Cagigi / John R Gallagher / Joshua Brand / Madhu ...Authors: Syed M Moin / Jeffrey C Boyington / Seyhan Boyoglu-Barnum / Rebecca A Gillespie / Gabriele Cerutti / Crystal Sao-Fong Cheung / Alberto Cagigi / John R Gallagher / Joshua Brand / Madhu Prabhakaran / Yaroslav Tsybovsky / Tyler Stephens / Brian E Fisher / Adrian Creanga / Sila Ataca / Reda Rawi / Kizzmekia S Corbett / Michelle C Crank / Gunilla B Karlsson Hedestam / Jason Gorman / Adrian B McDermott / Audray K Harris / Tongqing Zhou / Peter D Kwong / Lawrence Shapiro / John R Mascola / Barney S Graham / Masaru Kanekiyo /
Abstract: Current influenza vaccines predominantly induce immunity to the hypervariable hemagglutinin (HA) head, requiring frequent vaccine reformulation. Conversely, the immunosubdominant yet conserved HA ...Current influenza vaccines predominantly induce immunity to the hypervariable hemagglutinin (HA) head, requiring frequent vaccine reformulation. Conversely, the immunosubdominant yet conserved HA stem harbors a supersite that is targeted by broadly neutralizing antibodies (bnAbs), representing a prime target for universal vaccines. Here, we showed that the co-immunization of two HA stem immunogens derived from group 1 and 2 influenza A viruses elicits cross-group protective immunity and neutralizing antibody responses in mice, ferrets, and nonhuman primates (NHPs). Immunized mice were protected from multiple group 1 and 2 viruses, and all animal models showed broad serum-neutralizing activity. A bnAb isolated from an immunized NHP broadly neutralized and protected against diverse viruses, including H5N1 and H7N9. Genetic and structural analyses revealed strong homology between macaque and human bnAbs, illustrating common biophysical constraints for acquiring cross-group specificity. Vaccine elicitation of stem-directed cross-group-protective immunity represents a step toward the development of broadly protective influenza vaccines.
History
DepositionJul 15, 2020-
Header (metadata) releaseJul 21, 2021-
Map releaseJul 21, 2021-
UpdateFeb 1, 2023-
Current statusFeb 1, 2023Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xsk
  • Surface level: 0.18
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6xsk
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22302.png

Downloads & links

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Map

FileDownload / File: emd_22302.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of vaccine-elicited Rhesus VH6-1 antibody 789-203-3C12
Voxel sizeX=Y=Z: 1.07 Å
Density
Contour LevelBy AUTHOR: 0.18 / Movie #1: 0.18
Minimum - Maximum-0.41797325 - 0.9147035
Average (Standard dev.)0.0003822083 (±0.020683471)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 385.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z385.200385.200385.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.4180.9150.000

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Supplemental data

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Additional map: Unsharpened map

Fileemd_22302_additional_1.map
AnnotationUnsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-volume 1

Fileemd_22302_half_map_1.map
Annotationhalf-volume 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half-volume 2

Fileemd_22302_half_map_2.map
Annotationhalf-volume 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Influenza Hemagglutinin SI06 Trimer in complex with 789-203-3C12 Fab

EntireName: Influenza Hemagglutinin SI06 Trimer in complex with 789-203-3C12 Fab
Components
  • Organelle or cellular component: Influenza Hemagglutinin SI06 Trimer in complex with 789-203-3C12 Fab
    • Organelle or cellular component: 789-203-3C12 Fab Heavy and Light Chains
      • Protein or peptide: 789-203-3C12 Fab Light Chain
      • Protein or peptide: 789-203-3C12 Fab Heavy Chain
    • Organelle or cellular component: Influenza HemagglutininHemagglutinin (influenza)
      • Protein or peptide: Hemagglutinin HA1 chain
      • Protein or peptide: Hemagglutinin HA2 chain
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Influenza Hemagglutinin SI06 Trimer in complex with 789-203-3C12 Fab

SupramoleculeName: Influenza Hemagglutinin SI06 Trimer in complex with 789-203-3C12 Fab
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1-#4

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Supramolecule #2: 789-203-3C12 Fab Heavy and Light Chains

SupramoleculeName: 789-203-3C12 Fab Heavy and Light Chains / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Macaca mulatta (Rhesus monkey)

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Supramolecule #3: Influenza Hemagglutinin

SupramoleculeName: Influenza Hemagglutinin / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Source (natural)Organism: Influenza A virus (A/Solomon Islands/3/2006(H1N1))

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Macromolecule #1: 789-203-3C12 Fab Light Chain

MacromoleculeName: 789-203-3C12 Fab Light Chain / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 23.209664 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIQMTQSPSS LSASVGDTVT ITCRASQSIS SWLAWYQQKP GKAPNLLIYR ASTLQSGVPS RFSGSGSGTD FTLTISSLQS EDFATYFCQ QSTSSPFTFG PGTKLDIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
DIQMTQSPSS LSASVGDTVT ITCRASQSIS SWLAWYQQKP GKAPNLLIYR ASTLQSGVPS RFSGSGSGTD FTLTISSLQS EDFATYFCQ QSTSSPFTFG PGTKLDIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGEC

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Macromolecule #2: 789-203-3C12 Fab Heavy Chain

MacromoleculeName: 789-203-3C12 Fab Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Macaca mulatta (Rhesus monkey)
Molecular weightTheoretical: 49.298629 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQESGPG LVKPSEILSL TCAVSGGSFS SYCWGWIRQP PGKGLEWIGS ICGSGGSNYL NPSLKSRVTL SVDTSKNQFS LILNSVTAA DTAVYYCARE GITIFGVVIP RVLDSWGQGA VVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS ...String:
QVQLQESGPG LVKPSEILSL TCAVSGGSFS SYCWGWIRQP PGKGLEWIGS ICGSGGSNYL NPSLKSRVTL SVDTSKNQFS LILNSVTAA DTAVYYCARE GITIFGVVIP RVLDSWGQGA VVTVSSASTK GPSVFPLAPS SKSTSGGTAA LGCLVKDYFP E PVTVSWNS GALTSGVHTF PAVLQSSGLY SLSSVVTVPS SSLGTQTYIC NVNHKPSNTK VDKKVEPKSC DKTHTCPPCP AP ELLGGPS VFLFPPKPKD TLMISRTPEV TCVVVDVSHE DPEVKFNWYV DGVEVHNAKT KPREEQYNST YRVVSVLTVL HQD WLNGKE YKCKVSNKAL PAPIEKTISK AKGQPREPQV YTLPPSRDEL TKNQVSLTCL VKGFYPSDIA VEWESNGQPE NNYK TTPPV LDSDGSFFLY SKLTVDKSRW QQGNVFSCSV MHEALHNHYT QKSLSLSPGK

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Macromolecule #3: Hemagglutinin HA1 chain

MacromoleculeName: Hemagglutinin HA1 chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Strain: A/Solomon Islands/3/2006(H1N1)
Molecular weightTheoretical: 38.269184 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKVKLLVLLC TFTATYADTI CIGYHANNST DTVDTVCEKN VTVTHSVNLL EDSHNGKLCL LKGIAPLQLG NCSVAGWILG NPECELLIS RESWSYIVEK PNPENGTCYP GHFADYEELR EQLSSVSSFE RFEIFPKESS WPNHTTTGVS ASCSHNGESS F YKNLLWLT ...String:
MKVKLLVLLC TFTATYADTI CIGYHANNST DTVDTVCEKN VTVTHSVNLL EDSHNGKLCL LKGIAPLQLG NCSVAGWILG NPECELLIS RESWSYIVEK PNPENGTCYP GHFADYEELR EQLSSVSSFE RFEIFPKESS WPNHTTTGVS ASCSHNGESS F YKNLLWLT GKNGLYPNLS KSYANNKEKE VLVLWGVHHP PNIGDQRALY HKENAYVSVV SSHYSRKFTP EIAKRPKVRD QE GRINYYW TLLEPGDTII FEANGNLIAP RYAFALSRGF GSGIINSNAP MDECDAKCQT PQGAINSSLP FQNVHPVTIG ECP KYVRSA KLRMVTGLRN IPSIQSR

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Macromolecule #4: Hemagglutinin HA2 chain

MacromoleculeName: Hemagglutinin HA2 chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Influenza A virus (A/Solomon Islands/3/2006(H1N1))
Strain: A/Solomon Islands/3/2006(H1N1)
Molecular weightTheoretical: 25.26409 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADQKS TQNAINCITN KVNSVIEKMN TQFTAVGKEF NKLERRMENL NKKVDDGFI DIWTYNAELL VLLENERTLD FHDSNVKNLY EKVKSQLKNN AKEIGNGCFE FYHKCNDECM ESVKNGTYDY P KYSEESKL ...String:
GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADQKS TQNAINCITN KVNSVIEKMN TQFTAVGKEF NKLERRMENL NKKVDDGFI DIWTYNAELL VLLENERTLD FHDSNVKNLY EKVKSQLKNN AKEIGNGCFE FYHKCNDECM ESVKNGTYDY P KYSEESKL NREKIDGVSG RLVPRGSPGS GYIPEAPRDG QAYVRKDGEW VLLSTFLGHH HHHH

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 15 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

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

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 116041

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Atomic model buiding 1

Initial modelPDB ID:

6fyt

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-6xsk:
Cryo-EM Structure of Vaccine-Elicited Rhesus Antibody 789-203-3C12 in Complex with Stabilized SI06 (A/Solomon Islands/3/06) Influenza Hemagglutinin Trimer

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