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- EMDB-27846: HMPV F monomer bound to RSV-199 Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-27846
TitleHMPV F monomer bound to RSV-199 Fab
Map data
Sample
  • Complex: MPV fusion protein complex with RSV-199 Fab
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: RSV-199 light chain
    • Protein or peptide: RSV-199 heavy chain
Keywordshuman antibodies / RSV and MPV Fusion protein / complex Cryo-EM structure / viral protein and antiviral protein / BIOSYNTHETIC PROTEIN
Biological speciesHuman metapneumovirus / Human metapneumovirus A / Homo sapiens (human)
Methodsingle particle reconstruction / Resolution: 3.48 Å
AuthorsWen X / Jardetzky TS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)R01AI137523 United States
CitationJournal: Cell Host Microbe / Year: 2023
Title: Potent cross-neutralization of respiratory syncytial virus and human metapneumovirus through a structurally conserved antibody recognition mode.
Authors: Xiaolin Wen / Naveenchandra Suryadevara / Nurgun Kose / Jing Liu / Xiaoyan Zhan / Laura S Handal / Lauren E Williamson / Andrew Trivette / Robert H Carnahan / Theodore S Jardetzky / James E Crowe /
Abstract: Respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) infections pose a significant health burden. Using pre-fusion conformation fusion (F) proteins, we isolated a panel of anti-F ...Respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) infections pose a significant health burden. Using pre-fusion conformation fusion (F) proteins, we isolated a panel of anti-F antibodies from a human donor. One antibody (RSV-199) potently cross-neutralized 8 RSV and hMPV strains by recognizing antigenic site III, which is partially conserved in RSV and hMPV F. Next, we determined the cryoelectron microscopy (cryo-EM) structures of RSV-199 bound to RSV F trimers, hMPV F monomers, and an unexpected dimeric form of hMPV F. These structures revealed how RSV-199 engages both RSV and hMPV F proteins through conserved interactions of the antibody heavy-chain variable region and how variability within heavy-chain complementarity-determining region 3 (HCDR3) can be accommodated at the F protein interface in site-III-directed antibodies. Furthermore, RSV-199 offered enhanced protection against RSV A and B strains and hMPV in cotton rats. These findings highlight the mechanisms of broad neutralization and therapeutic potential of RSV-199.
History
DepositionAug 16, 2022-
Header (metadata) releaseAug 16, 2023-
Map releaseAug 16, 2023-
UpdateAug 23, 2023-
Current statusAug 23, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_27846.png

Downloads & links

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Map

FileDownload / File: emd_27846.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.11 Å
Density
Contour LevelBy AUTHOR: 0.45
Minimum - Maximum-5.279264 - 7.8786955
Average (Standard dev.)0.0008528882 (±0.08866402)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 355.2 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_27846_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_27846_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : MPV fusion protein complex with RSV-199 Fab

EntireName: MPV fusion protein complex with RSV-199 Fab
Components
  • Complex: MPV fusion protein complex with RSV-199 Fab
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: RSV-199 light chain
    • Protein or peptide: RSV-199 heavy chain

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Supramolecule #1: MPV fusion protein complex with RSV-199 Fab

SupramoleculeName: MPV fusion protein complex with RSV-199 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human metapneumovirus

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Macromolecule #1: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Human metapneumovirus A
Molecular weightTheoretical: 47.960742 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GLKESYLEES CSTITEGYLS VLRTGWYTNV FTLEVGDVEN LTCADGPSLI KTELDLTKSA LRELRTVSAD QLAREEQIEN PRRRRFVLG AIALGVCTAA AVTAGVAIAK TIRLESEVTA IKNALKKTNE AVSTLGNGVR VLATAVRELK DFVSKNLTRA I NKNKCDIP ...String:
GLKESYLEES CSTITEGYLS VLRTGWYTNV FTLEVGDVEN LTCADGPSLI KTELDLTKSA LRELRTVSAD QLAREEQIEN PRRRRFVLG AIALGVCTAA AVTAGVAIAK TIRLESEVTA IKNALKKTNE AVSTLGNGVR VLATAVRELK DFVSKNLTRA I NKNKCDIP DLKMAVSFSQ FNRRFLNVVR QFSDNAGITP AISLDLMTDA ELARAVSNMP TSAGQIKLML ENRAMVRRKG FG ILIGVYG SSVIYMVQLP IFGVIDTPCW IVKAAPSCSE KKGNYACLLR EDQGWYCQNA GSTVYYPNEK DCETRGDHVF CDT ACGINV AEQSKECNIN ISTTNYPCKV STGRHPISMV ALSPLGALVA CYKGVSCSIG SNRVGIIKQL NKGCSYITNQ DADT VTIDN TVYQLSKVEG EQHVIKGRPV SSSFDPVKFP EDQF

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Macromolecule #2: RSV-199 light chain

MacromoleculeName: RSV-199 light chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.819264 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QAVVTQPPSV SGAPGQRVII SCTGSGSNLG ADYGVHWYQQ LPGTAPKLLI YGDRNRPSGV PDRFSGSKSG TSASLAITGL QAEDEADYY CQSYDRSLNW VFGGGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV N AGVETTKP ...String:
QAVVTQPPSV SGAPGQRVII SCTGSGSNLG ADYGVHWYQQ LPGTAPKLLI YGDRNRPSGV PDRFSGSKSG TSASLAITGL QAEDEADYY CQSYDRSLNW VFGGGTKLTV LGQPKAAPSV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV N AGVETTKP SKQSNNKYAA SSYLSLTPEQ WKSHKSYSCQ VTHEGSTVEK TVAPAECS

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Macromolecule #3: RSV-199 heavy chain

MacromoleculeName: RSV-199 heavy chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 24.022906 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVESGGG VVKPGGSLRV SCVVSGFTFS SYRMHWVRQA PGKGLEWVSS ITASSSYINY AESVKGRFTI SRDNAKNSLY LQMNSLRAE DTAVYYCARD ENTGISHYWF DPWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL ...String:
QVQLVESGGG VVKPGGSLRV SCVVSGFTFS SYRMHWVRQA PGKGLEWVSS ITASSSYINY AESVKGRFTI SRDNAKNSLY LQMNSLRAE DTAVYYCARD ENTGISHYWF DPWGQGTLVT VSSASTKGPS VFPLAPSSKS TSGGTAALGC LVKDYFPEPV T VSWNSGAL TSGVHTFPAV LQSSGLYSLS SVVTVPSSSL GTQTYICNVN HKPSNTKVDK KVEPKSC

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Experimental details

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Structure determination

Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.8 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec.

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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 / Nominal defocus max: 40.0 µm / Nominal defocus min: 3.451 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2774162
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4dag

Initial angle assignmentType: OTHER
Final 3D classificationNumber classes: 100 / Software - Name: cryoSPARC
Final angle assignmentType: OTHER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.48 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number images used: 165267

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