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- EMDB-9139: H7 HA0 in complex with Fab from H7.5 IgG -

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Basic information

Entry
Database: EMDB / ID: EMD-9139
TitleH7 HA0 in complex with Fab from H7.5 IgG
Map dataH7 HA0 in complex with Fv from H7.5 IgG
Sample
  • Complex: H7 HA0 in complex with H7.5 Fab
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain
    • Protein or peptide: Heavy chain Fv of H7.5 Fab
    • Protein or peptide: Light chain Fv of H7.5 Fab
  • 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
Biological speciesInfluenza A virus (A/New York/107/2003(H7N2)) / Influenza A virus / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsPallesen J / Turner HL / Ward AB
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)U19 AI117905 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201400024C United States
CitationJournal: PLoS Biol / Year: 2019
Title: Potent anti-influenza H7 human monoclonal antibody induces separation of hemagglutinin receptor-binding head domains.
Authors: Hannah L Turner / Jesper Pallesen / Shanshan Lang / Sandhya Bangaru / Sarah Urata / Sheng Li / Christopher A Cottrell / Charles A Bowman / James E Crowe / Ian A Wilson / Andrew B Ward /
Abstract: Seasonal influenza virus infections can cause significant morbidity and mortality, but the threat from the emergence of a new pandemic influenza strain might have potentially even more devastating ...Seasonal influenza virus infections can cause significant morbidity and mortality, but the threat from the emergence of a new pandemic influenza strain might have potentially even more devastating consequences. As such, there is intense interest in isolating and characterizing potent neutralizing antibodies that target the hemagglutinin (HA) viral surface glycoprotein. Here, we use cryo-electron microscopy (cryoEM) to decipher the mechanism of action of a potent HA head-directed monoclonal antibody (mAb) bound to an influenza H7 HA. The epitope of the antibody is not solvent accessible in the compact, prefusion conformation that typifies all HA structures to date. Instead, the antibody binds between HA head protomers to an epitope that must be partly or transiently exposed in the prefusion conformation. The "breathing" of the HA protomers is implied by the exposure of this epitope, which is consistent with metastability of class I fusion proteins. This structure likely therefore represents an early structural intermediate in the viral fusion process. Understanding the extent of transient exposure of conserved neutralizing epitopes also may lead to new opportunities to combat influenza that have not been appreciated previously.
History
DepositionSep 27, 2018-
Header (metadata) releaseOct 24, 2018-
Map releaseFeb 20, 2019-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.058
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.058
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6mlm
  • Surface level: 0.058
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9139.png

Downloads & links

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Map

FileDownload / File: emd_9139.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationH7 HA0 in complex with Fv from H7.5 IgG
Voxel sizeX=Y=Z: 1.02 Å
Density
Contour LevelBy AUTHOR: 0.058 / Movie #1: 0.058
Minimum - Maximum-0.12226801 - 0.21910833
Average (Standard dev.)0.00014316238 (±0.008092738)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 261.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.021.021.02
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z261.120261.120261.120
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.1220.2190.000

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Supplemental data

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Additional map: H7 HA0 in complex with Fv from H7.5 IgG

Fileemd_9139_additional.map
AnnotationH7 HA0 in complex with Fv from H7.5 IgG
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: H7 HA0 in complex with Fv from H7.5 IgG

Fileemd_9139_half_map_1.map
AnnotationH7 HA0 in complex with Fv from H7.5 IgG
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: H7 HA0 in complex with Fv from H7.5 IgG

Fileemd_9139_half_map_2.map
AnnotationH7 HA0 in complex with Fv from H7.5 IgG
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : H7 HA0 in complex with H7.5 Fab

EntireName: H7 HA0 in complex with H7.5 Fab
Components
  • Complex: H7 HA0 in complex with H7.5 Fab
    • Protein or peptide: Hemagglutinin HA1 chain
    • Protein or peptide: Hemagglutinin HA2 chain
    • Protein or peptide: Heavy chain Fv of H7.5 Fab
    • Protein or peptide: Light chain Fv of H7.5 Fab
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: H7 HA0 in complex with H7.5 Fab

SupramoleculeName: H7 HA0 in complex with H7.5 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
Source (natural)Organism: Influenza A virus (A/New York/107/2003(H7N2))
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: 293F
Molecular weightTheoretical: 230 KDa

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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/New York/107/2003(H7N2)) / Strain: A/New York/107/2003(H7N2)
Molecular weightTheoretical: 36.01882 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MNTQILAFIA CVLTGVKGDK ICLGHHAVAN GTKVNTLTER GIEVVNATET VETTNIKKIC TQGKRPTDLG QCGLLGTLIG PPQCDQFLE FSSDLIIERR EGTDICYPGR FTNEESLRQI LRRSGGIGKE SMGFTYSGIR TNGATSACTR SGSSFYAEMK W LLSNSDNA ...String:
MNTQILAFIA CVLTGVKGDK ICLGHHAVAN GTKVNTLTER GIEVVNATET VETTNIKKIC TQGKRPTDLG QCGLLGTLIG PPQCDQFLE FSSDLIIERR EGTDICYPGR FTNEESLRQI LRRSGGIGKE SMGFTYSGIR TNGATSACTR SGSSFYAEMK W LLSNSDNA AFPQMTKAYR NPRNKPALII WGVHHSESVS EQTKLYGSGN KLITVRSSKY QQSFTPNPGA RRIDFHWLLL DP NDTVTFT FNGAFIAPDR TSFFRGESLG VQSDAPLDSS CRGDCFHSGG TIVSSLPFQN INSRTVGKCP RYVKQKSLLL ATG MRNVPE KP

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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 / Strain: A/New York/107/2003(H7N2)
Molecular weightTheoretical: 25.583803 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: KPRGLFGAIA GFIENGWEGL INGWYGFRHQ NAQGEGTAAD YKSTQSAIDQ ITGKLNRLIG KTNQQFELID NEFNEIEQQI GNVINWTRD AMTEIWSYNA ELLVAMENQH TIDLADSEMS KLYERVKKQL RENAEEDGTG CFEIFHKCDD QCMESIRNNT Y DHTQYRTE ...String:
KPRGLFGAIA GFIENGWEGL INGWYGFRHQ NAQGEGTAAD YKSTQSAIDQ ITGKLNRLIG KTNQQFELID NEFNEIEQQI GNVINWTRD AMTEIWSYNA ELLVAMENQH TIDLADSEMS KLYERVKKQL RENAEEDGTG CFEIFHKCDD QCMESIRNNT Y DHTQYRTE SLQNRIQIDP VKLSSGYKDI ILWFSFGASC FLLLAIAMGL VFICIKNGNM QCTICI

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Macromolecule #3: Heavy chain Fv of H7.5 Fab

MacromoleculeName: Heavy chain Fv of H7.5 Fab / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.441402 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: VQLVQSGAEV KKPGASVKVS CKASGYTLTR YYFHWVRQAP GQGFEWMGII NPNGGGTSYA QKFGDRVIMT SDMSTSTIYM ELSSLRSED TAVYYCARDM PYYHDSGGPL FDLWGQGTLV TVSSASTKGP SVFPLAPSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV ...String:
VQLVQSGAEV KKPGASVKVS CKASGYTLTR YYFHWVRQAP GQGFEWMGII NPNGGGTSYA QKFGDRVIMT SDMSTSTIYM ELSSLRSED TAVYYCARDM PYYHDSGGPL FDLWGQGTLV TVSSASTKGP SVFPLAPSGG TAALGCLVKD YFPEPVTVSW N SGALTSGV HTFPAVLQSS GLYSLSSVVT VPSSSLGTQT YICNVNHKPS NTKVDKKVEP K

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Macromolecule #4: Light chain Fv of H7.5 Fab

MacromoleculeName: Light chain Fv of H7.5 Fab / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.340836 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: EIVMTQSPSS LSASVGDRVT ITCRPSQSIS TFLNWYEQKP GKAPKLLIYD ASSLQSGVPS RFSGSGSGTE FTLTISSLQP EDFATYYCQ QSFSTPYTFG QGTRLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS ...String:
EIVMTQSPSS LSASVGDRVT ITCRPSQSIS TFLNWYEQKP GKAPKLLIYD ASSLQSGVPS RFSGSGSGTE FTLTISSLQP EDFATYYCQ QSFSTPYTFG QGTRLEIKRT VAAPSVFIFP PSDEQLKSGT ASVVCLLNNF YPREAKVQWK VDNALQSGNS Q ESVTEQDS KDSTYSLSST LTLSKADYEK HKVYACEVTH QGLSSPVTKS FNRGE

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 9 / 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
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average exposure time: 7.0 sec. / Average electron dose: 67.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5f45
PDB Unreleased entry


Details: molmap simulated map lowpass filtered to 40A.
Initial angle assignmentType: OTHER / Software - Name: RELION (ver. 1.4)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 1.4)
Final angle assignmentType: OTHER / Software - Name: RELION (ver. 1.4)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 30032
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5f45
PDB Unreleased entry

RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6mlm:
H7 HA0 in complex with Fv from H7.5 IgG

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