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- EMDB-27808: RSV F trimer bound to RSV-199 Fab -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-27808
TitleRSV F trimer bound to RSV-199 Fab
Map data
Sample
  • Complex: RSV fusion protein complex with RSV-199 Fab
    • Protein or peptide: RSV fusion protein
    • Protein or peptide: RSV-199 Light chain protein
    • Protein or peptide: RSV-199 Heavy chain protein
Keywordshuman antibodies / RSV and MPV Fusion protein / complex Cryo-EM structure / viral protein and antiviral protein / STRUCTURAL PROTEIN
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / host cell plasma membrane / virion membrane / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesHuman respiratory syncytial virus A2 / Homo sapiens (human)
Methodsingle particle reconstruction / Resolution: 2.46 Å
AuthorsWen X / Jardetzky TS
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)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 8, 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_27808.png

Downloads & links

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Map

FileDownload / File: emd_27808.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 320 pix.
= 355.2 Å		1.11 Å/pix.
x 320 pix.
= 355.2 Å		1.11 Å/pix.
x 320 pix.
= 355.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.11 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.414
Minimum - Maximum-4.0556607 - 6.454188
Average (Standard dev.)0.002796603 (±0.11132955)
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_27808_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_27808_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : RSV fusion protein complex with RSV-199 Fab

EntireName: RSV fusion protein complex with RSV-199 Fab
Components
  • Complex: RSV fusion protein complex with RSV-199 Fab
    • Protein or peptide: RSV fusion protein
    • Protein or peptide: RSV-199 Light chain protein
    • Protein or peptide: RSV-199 Heavy chain protein

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

SupramoleculeName: RSV fusion protein complex with RSV-199 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human respiratory syncytial virus A2

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Macromolecule #1: RSV fusion protein

MacromoleculeName: RSV fusion protein / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Human respiratory syncytial virus A2
Molecular weightTheoretical: 53.92973 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QNITEEFYQS TCSAVSKGYL SALRTGWYTS VITIELSNIK ENKCNGTDAK VKLIKQELDK YKNAVTELQL LMQSTPAANN RARRELPRF MNYTLNNAKK TNVTLSKKRK RRFLGFLLGV GSAIASGVAV CKVLHLEGEV NKIKSALLST NKAVVSLSNG V SVLTFKVL ...String:
QNITEEFYQS TCSAVSKGYL SALRTGWYTS VITIELSNIK ENKCNGTDAK VKLIKQELDK YKNAVTELQL LMQSTPAANN RARRELPRF MNYTLNNAKK TNVTLSKKRK RRFLGFLLGV GSAIASGVAV CKVLHLEGEV NKIKSALLST NKAVVSLSNG V SVLTFKVL DLKNYIDKQL LPIVNKQSCS ISNIETVIEF QQKNNRLLEI TREFSVNAGV TTPVSTYMLT NSELLSLIND MP ITNDQKK LMSNNVQIVR QQSYSIMCII KEEVLAYVVQ LPLYGVIDTP CWKLHTSPLC TTNTKEGSNI CLTRTDRGWY CDN AGSVSF FPQAETCKVQ SNRVFCDTMN SLTLPSEVNL CNVDIFNPKY DCKIMTSKTD VSSSVITSLG AIVSCYGKTK CTAS NKNRG IIKTFSNGCD YVSNKGVDTV SVGNTLYYVN KQEGKSLYVK GEPIINFYDP LVFPSDEFDA SISQVNEKIN QSLAF IRKS

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: RSV-199 Light chain protein

MacromoleculeName: RSV-199 Light chain protein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / 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 protein

MacromoleculeName: RSV-199 Heavy chain protein / type: protein_or_peptide / ID: 3 / Number of copies: 3 / 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

Concentration1.5 mg/mL
BufferpH: 7.5
GridModel: Quantifoil R2/1 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / 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 / Nominal defocus max: 40.0 µm / Nominal defocus min: 4.508 µm / Nominal magnification: 81000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4178389
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5u68

Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.46 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: Coot / Number images used: 476914
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC
Final angle assignmentType: OTHER / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 100 / Software - Name: cryoSPARC

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Atomic model buiding 1

Initial modelPDB ID:

5u68


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-8dzw:
RSV F trimer bound to RSV-199 Fab

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