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- EMDB-25655: CryoEM map of anchor 222-1C06 Fab and lateral patch 2B05 Fab bind... -

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Basic information

Entry
Database: EMDB / ID: EMD-25655
TitleCryoEM map of anchor 222-1C06 Fab and lateral patch 2B05 Fab binding H1 HA
Map dataCryoEM map of anchor 222-1C06 Fab and lateral patch 2B05 Fab binding H1 HA
Sample
  • Complex: CryoEM map of anchor 222-1C06 Fab and lateral patch 2B05 Fab binding H1 HA
    • Complex: Monoclonal antibodies 222-1C06 and 2B05
      • Protein or peptide: 2B05 mAb light chain
      • Protein or peptide: 2B05 mAb heavy chain
      • Protein or peptide: 222-1C06 mAb heavy chain
      • Protein or peptide: 222-1C06 mAb light chain
    • Complex: Hemagglutinin
      • 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 speciesHomo sapiens (human) / Influenza A virus (A/California/04/2009(H1N1))
Methodsingle particle reconstruction / cryo EM / Resolution: 3.38 Å
AuthorsHan J / Ward AB
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)75N93019C00051 United States
CitationJournal: Nature / Year: 2022
Title: Broadly neutralizing antibodies target a haemagglutinin anchor epitope.
Authors: Jenna J Guthmiller / Julianna Han / Henry A Utset / Lei Li / Linda Yu-Ling Lan / Carole Henry / Christopher T Stamper / Meagan McMahon / George O'Dell / Monica L Fernández-Quintero / Alec W ...Authors: Jenna J Guthmiller / Julianna Han / Henry A Utset / Lei Li / Linda Yu-Ling Lan / Carole Henry / Christopher T Stamper / Meagan McMahon / George O'Dell / Monica L Fernández-Quintero / Alec W Freyn / Fatima Amanat / Olivia Stovicek / Lauren Gentles / Sara T Richey / Alba Torrents de la Peña / Victoria Rosado / Haley L Dugan / Nai-Ying Zheng / Micah E Tepora / Dalia J Bitar / Siriruk Changrob / Shirin Strohmeier / Min Huang / Adolfo García-Sastre / Klaus R Liedl / Jesse D Bloom / Raffael Nachbagauer / Peter Palese / Florian Krammer / Lynda Coughlan / Andrew B Ward / Patrick C Wilson /
Abstract: Broadly neutralizing antibodies that target epitopes of haemagglutinin on the influenza virus have the potential to provide near universal protection against influenza virus infection. However, viral ...Broadly neutralizing antibodies that target epitopes of haemagglutinin on the influenza virus have the potential to provide near universal protection against influenza virus infection. However, viral mutants that escape broadly neutralizing antibodies have been reported. The identification of broadly neutralizing antibody classes that can neutralize viral escape mutants is critical for universal influenza virus vaccine design. Here we report a distinct class of broadly neutralizing antibodies that target a discrete membrane-proximal anchor epitope of the haemagglutinin stalk domain. Anchor epitope-targeting antibodies are broadly neutralizing across H1 viruses and can cross-react with H2 and H5 viruses that are a pandemic threat. Antibodies that target this anchor epitope utilize a highly restricted repertoire, which encodes two public binding motifs that make extensive contacts with conserved residues in the fusion peptide. Moreover, anchor epitope-targeting B cells are common in the human memory B cell repertoire and were recalled in humans by an oil-in-water adjuvanted chimeric haemagglutinin vaccine, which is a potential universal influenza virus vaccine. To maximize protection against seasonal and pandemic influenza viruses, vaccines should aim to boost this previously untapped source of broadly neutralizing antibodies that are widespread in the human memory B cell pool.
History
DepositionDec 7, 2021-
Header (metadata) releaseJan 12, 2022-
Map releaseJan 12, 2022-
UpdateMar 30, 2022-
Current statusMar 30, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.24
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.24
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7t3d
  • Surface level: 0.24
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7t3d
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_25655.png

Downloads & links

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Map

FileDownload / File: emd_25655.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryoEM map of anchor 222-1C06 Fab and lateral patch 2B05 Fab binding H1 HA
Voxel sizeX=Y=Z: 1.15 Å
Density
Contour LevelBy AUTHOR: 0.24 / Movie #1: 0.24
Minimum - Maximum-0.69306785 - 1.5040632
Average (Standard dev.)-0.0009095331 (±0.042256244)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 368.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.151.151.15
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z368.000368.000368.000
α/β/γ90.00090.00090.000
start NX/NY/NZ253841
NX/NY/NZ999350
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.6931.504-0.001

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Supplemental data

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Mask #1

Fileemd_25655_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM half map of anchor 222-1C06 Fab and...

Fileemd_25655_half_map_1.map
AnnotationCryoEM half map of anchor 222-1C06 Fab and lateral patch 2B05 Fab binding H1 HA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CryoEM half map of anchor 222-1C06 Fab and...

Fileemd_25655_half_map_2.map
AnnotationCryoEM half map of anchor 222-1C06 Fab and lateral patch 2B05 Fab binding H1 HA
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CryoEM map of anchor 222-1C06 Fab and lateral patch 2B05 Fab bind...

EntireName: CryoEM map of anchor 222-1C06 Fab and lateral patch 2B05 Fab binding H1 HA
Components
  • Complex: CryoEM map of anchor 222-1C06 Fab and lateral patch 2B05 Fab binding H1 HA
    • Complex: Monoclonal antibodies 222-1C06 and 2B05
      • Protein or peptide: 2B05 mAb light chain
      • Protein or peptide: 2B05 mAb heavy chain
      • Protein or peptide: 222-1C06 mAb heavy chain
      • Protein or peptide: 222-1C06 mAb light chain
    • Complex: Hemagglutinin
      • 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: CryoEM map of anchor 222-1C06 Fab and lateral patch 2B05 Fab bind...

SupramoleculeName: CryoEM map of anchor 222-1C06 Fab and lateral patch 2B05 Fab binding H1 HA
type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: #1-#6
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293F

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Supramolecule #2: Monoclonal antibodies 222-1C06 and 2B05

SupramoleculeName: Monoclonal antibodies 222-1C06 and 2B05 / type: complex / Chimera: Yes / ID: 2 / Parent: 1 / Macromolecule list: #3-#6
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293F

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Supramolecule #3: Hemagglutinin

SupramoleculeName: Hemagglutinin / type: complex / Chimera: Yes / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Influenza A virus (A/California/04/2009(H1N1))
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293F

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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/California/04/2009(H1N1)) / Strain: swl A/California/04/2009 H1N1
Molecular weightTheoretical: 36.729402 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ADPGDTLCIG YHANNSTDTV DTVLEKNVTV THSVNLLEDK HNGKLCKLRG VAPLHLGKCN IAGWILGNPE CESLSTASSW SYIVETPSS DNGTCYPGDF IDYEELREQL SSVSSFERFE IFPKTSSWPN HDSNKGVTAA CPHAGAKSFY KNLIWLVKKG N SYPKLSKS ...String:
ADPGDTLCIG YHANNSTDTV DTVLEKNVTV THSVNLLEDK HNGKLCKLRG VAPLHLGKCN IAGWILGNPE CESLSTASSW SYIVETPSS DNGTCYPGDF IDYEELREQL SSVSSFERFE IFPKTSSWPN HDSNKGVTAA CPHAGAKSFY KNLIWLVKKG N SYPKLSKS YINDKGKEVL VLWGIHHPST SADQQSLYQN ADTYVFVGSS RYSKKFKPEI AIRPKVRDQE GRMNYYWTLV EP GDKITFE ATGNLVVPRY AFAMERNAGS GIIISDTPVH DCNTTCQTPK GAINTSLPFQ NIHPITIGKC PKYVKSTKLR LAT GLRNIP SIQSR

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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/California/04/2009(H1N1)) / Strain: swl A/California/04/2009 H1N1
Molecular weightTheoretical: 19.977125 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
GLFGAIAGFI EGGWTGMVDG WYGYHHQNEQ GSGYAADLKS TQNAIDKITN KVNSVIEKMN TQFTAVGKEF NHLEKRIENL NKKVDDGFL DIWTYNAELL VLLENERTLD YHDSNVKNLY EKVRSQLKNN AKEIGNGCFE FYHKCDNTCM ESVKNGTYDY P KYSEEAKL NREEID

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Macromolecule #3: 2B05 mAb light chain

MacromoleculeName: 2B05 mAb light chain / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.76912 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSAFVGDRVT IACQASQDIR IHLNWYQQKP GKAPKLLIYD ASNLEAGVPS RFSGSGSGTD FTFTISSLQP EDIATYYCQ HYHNLPRTFG GGTKVEIK

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Macromolecule #4: 2B05 mAb heavy chain

MacromoleculeName: 2B05 mAb heavy chain / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.805238 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VQLLESGGGL VQPGGSLSLS CAASGFTFSS FAMSWVRQAP VKGLEWVSMI SAGGGNTYYA DSVKGRFTIS RDNSKSTLYL QMSSLTAED TAVYYCAKSD SSGFQYGRRE FWGQGTLVTV S

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Macromolecule #5: 222-1C06 mAb heavy chain

MacromoleculeName: 222-1C06 mAb heavy chain / type: protein_or_peptide / ID: 5 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.528006 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGD LVQPGGSLRL SCVVSGFTFS TYSMNWVRQA PGKGLEWVSY ISSSSLSRYY ADSVKGRFTI SRDNAKNSLS LQLNSLRAE DTAVYYCVRG SITWPTEYYL DYWGQGTLVT VSS

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Macromolecule #6: 222-1C06 mAb light chain

MacromoleculeName: 222-1C06 mAb light chain / type: protein_or_peptide / ID: 6 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.657012 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EIVMTQSPAT LSVSPGERAT LSCRASQTIR SDLAWYQQKP GQPPRLIIYG ASTRATGIPA RFSGSGSGTE FTLTISSLQS EDSAVYFCQ QYNNWPPLTF GGGTKVEIK

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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / 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

Concentration0.5 mg/mL
BufferpH: 7.4 / Details: Tris-buffered saline
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Average electron dose: 49.9 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7mem

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2) / Number images used: 48846
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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