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- EMDB-63931: Respiratory Syncytial Virus pre-F trimer bound by neutralizing an... -

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Basic information

Entry
Database: EMDB / ID: EMD-63931
TitleRespiratory Syncytial Virus pre-F trimer bound by neutralizing antibody PR306007
Map data
Sample
  • Complex: The complex of PR306007 and the RSV A2 pre-F protein
    • Protein or peptide: Fusion glycoprotein F2
    • Protein or peptide: Fusion glycoprotein F1
    • Protein or peptide: PR306007 Light chain protein
    • Protein or peptide: PR306007 Hight chain protein
KeywordsRSV / pre-F / neutralizing antibody / IMMUNE SYSTEM (includes antibodies / antigens) / STRUCTURAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope ...symbiont-mediated induction of syncytium formation / Translation of respiratory syncytial virus mRNAs / RSV-host interactions / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / Respiratory syncytial virus (RSV) attachment and entry / host cell Golgi membrane / entry receptor-mediated virion attachment to host cell / fusion of virus membrane with host plasma membrane / viral envelope / symbiont entry into host cell / host cell plasma membrane / virion membrane / identical protein binding / plasma membrane
Similarity search - Function
Precursor fusion glycoprotein F0, Paramyxoviridae / Fusion glycoprotein F0
Similarity search - Domain/homology
Fusion glycoprotein F0
Similarity search - Component
Biological speciesRespiratory syncytial virus / Respiratory syncytial virus A2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.08 Å
AuthorsZheng Z / Zixian S / Rui F / Yu G
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271256 China
National Natural Science Foundation of China (NSFC)32300146 China
CitationJournal: Plos Pathog. / Year: 2025
Title: Discovery and molecular mechanism of potent neutralizing antibody from humanized mice with respiratory syncytial virus
Authors: Zheng Z / Zixian S / Rui F / Yu G
History
DepositionMar 24, 2025-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63931.png

Downloads & links

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Map

FileDownload / File: emd_63931.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å		1.07 Å/pix.
x 256 pix.
= 273.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.27
Minimum - Maximum-0.7802147 - 1.6922393
Average (Standard dev.)0.0014537182 (±0.055573627)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 273.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63931_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_63931_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 : The complex of PR306007 and the RSV A2 pre-F protein

EntireName: The complex of PR306007 and the RSV A2 pre-F protein
Components
  • Complex: The complex of PR306007 and the RSV A2 pre-F protein
    • Protein or peptide: Fusion glycoprotein F2
    • Protein or peptide: Fusion glycoprotein F1
    • Protein or peptide: PR306007 Light chain protein
    • Protein or peptide: PR306007 Hight chain protein

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Supramolecule #1: The complex of PR306007 and the RSV A2 pre-F protein

SupramoleculeName: The complex of PR306007 and the RSV A2 pre-F protein / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Respiratory syncytial virus

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Macromolecule #1: Fusion glycoprotein F2

MacromoleculeName: Fusion glycoprotein F2 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Respiratory syncytial virus A2
Molecular weightTheoretical: 8.758934 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QNITEEFYQS TCSAVSKGYL SALRTGWYTS VITIELSNIK ENKCNGTDAK VKLIKQELDK YKNAVTELQL LMQSTPAT

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: Fusion glycoprotein F1

MacromoleculeName: Fusion glycoprotein F1 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Respiratory syncytial virus A2
Molecular weightTheoretical: 45.028449 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: FLGFLLGVGS AIASGVAVCK VLHLEGEVNK IKSALLSTNK AVVSLSNGVS VLTFKVLDLK NYIDKQLLPI LNKQSCSISN IETVIEFQQ KNNRLLEITR EFSVNAGVTT PVSTYMLTNS ELLSLINDMP ITNDQKKLMS NNVQIVRQQS YSIMCIIKEE V LAYVVQLP ...String:
FLGFLLGVGS AIASGVAVCK VLHLEGEVNK IKSALLSTNK AVVSLSNGVS VLTFKVLDLK NYIDKQLLPI LNKQSCSISN IETVIEFQQ KNNRLLEITR EFSVNAGVTT PVSTYMLTNS ELLSLINDMP ITNDQKKLMS NNVQIVRQQS YSIMCIIKEE V LAYVVQLP LYGVIDTPCW KLHTSPLCTT NTKEGSNICL TRTDRGWYCD NAGSVSFFPQ AETCKVQSNR VFCDTMNSLT LP SEVNLCN VDIFNPKYDC KIMTSKTDVS SSVITSLGAI VSCYGKTKCT ASNKNRGIIK TFSNGCDYVS NKGVDTVSVG NTL YYVNKQ EGKSLYVKGE PIINFYDPLV FPSDEFDASI SQVNEKINQS LAFIRKSDEL LSAIGGYIPE APRDGQAYVR KDGE WVLLS TFL

UniProtKB: Fusion glycoprotein F0

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Macromolecule #3: PR306007 Light chain protein

MacromoleculeName: PR306007 Light chain protein / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.448681 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
IQLTQSPSTL SASVNDRVTL TCRASQSISS WLAWYQQKPG KAPKLLIYQA SSLQSGVPSR FTGSGSGTEF TLTISSLQPD DFATYYCQQ FNSYWTFGQG TKVEI

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Macromolecule #4: PR306007 Hight chain protein

MacromoleculeName: PR306007 Hight chain protein / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.044427 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VQLVQSGAEV KKPGASVKVS CKASGYTFTS YDINWVRQAT GQGLEWMGWM NPNSGNTGYA QKFQGRVTMT RQTSRSTAYM ELSSLRSED TAVYYCARED WGSAAFDSWG QGTMVTVSSA

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation state3D array

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4mmv

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.08 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 27206
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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