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- EMDB-63217: Cryo-EM structure of prefusion-stabilized RSV F (DS-Cav1 strain: ... -

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Basic information

Entry
Database: EMDB / ID: EMD-63217
TitleCryo-EM structure of prefusion-stabilized RSV F (DS-Cav1 strain: A2) in complex with nanobody 1D8
Map data
Sample
  • Complex: 1 prefusion-stabilized RSV F (DS-Cav1 strain: A2) trimer complexed with 3 1D8 nanobodies
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: nanobody 1D8
Keywordsrespiratory syncytial virus / fusion protein / complex / nanobody / 1D8 / ANTIVIRAL PROTEIN/IMMUNE SYSTEM / ANTIVIRAL 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 / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / 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 / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / host cell Golgi membrane / Respiratory syncytial virus (RSV) attachment and entry / 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 speciesCamelus bactrianus (Bactrian camel) / Respiratory syncytial virus A2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsWang QQ / Ke XL / Li ET / Hong DX / Li HX / Cheng ZK / Zhang JC / Jin TC / Shu B / Chiu S
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Cryo-EM structure of prefusion-stabilized RSV F (DS-Cav1 strain: A2) in complex with nanobody 1D8
Authors: Wang QQ / Ke XL
History
DepositionJan 18, 2025-
Header (metadata) releaseJan 21, 2026-
Map releaseJan 21, 2026-
UpdateJan 21, 2026-
Current statusJan 21, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63217.png

Downloads & links

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Map

FileDownload / File: emd_63217.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.95 Å/pix.
x 240 pix.
= 228. Å		0.95 Å/pix.
x 240 pix.
= 228. Å		0.95 Å/pix.
x 240 pix.
= 228. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.95 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04
Minimum - Maximum-0.15001944 - 0.42374375
Average (Standard dev.)0.0013813326 (±0.017233375)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 228.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_63217_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_63217_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 : 1 prefusion-stabilized RSV F (DS-Cav1 strain: A2) trimer complexe...

EntireName: 1 prefusion-stabilized RSV F (DS-Cav1 strain: A2) trimer complexed with 3 1D8 nanobodies
Components
  • Complex: 1 prefusion-stabilized RSV F (DS-Cav1 strain: A2) trimer complexed with 3 1D8 nanobodies
    • Protein or peptide: Fusion glycoprotein F0
    • Protein or peptide: nanobody 1D8

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Supramolecule #1: 1 prefusion-stabilized RSV F (DS-Cav1 strain: A2) trimer complexe...

SupramoleculeName: 1 prefusion-stabilized RSV F (DS-Cav1 strain: A2) trimer complexed with 3 1D8 nanobodies
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Camelus bactrianus (Bactrian camel)

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Macromolecule #1: Fusion glycoprotein F0

MacromoleculeName: Fusion glycoprotein F0 / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Respiratory syncytial virus A2
Molecular weightTheoretical: 63.260383 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MELLILKANA ITTILTAVTF CFASGQNITE EFYQSTCSAV SKGYLSALRT GWYTSVITIE LSNIKENKCN GTDAKVKLIK QELDKYKNA VTELQLLMQS TPATNNRARR ELPRFMNYTL NNAKKTNVTL SKKRKRRFLG FLLGVGSAIA SGVAVCKVLH L EGEVNKIK ...String:
MELLILKANA ITTILTAVTF CFASGQNITE EFYQSTCSAV SKGYLSALRT GWYTSVITIE LSNIKENKCN GTDAKVKLIK QELDKYKNA VTELQLLMQS TPATNNRARR ELPRFMNYTL NNAKKTNVTL SKKRKRRFLG FLLGVGSAIA SGVAVCKVLH L EGEVNKIK SALLSTNKAV VSLSNGVSVL TFKVLDLKNY IDKQLLPILN KQSCSISNIE TVIEFQQKNN RLLEITREFS VN AGVTTPV STYMLTNSEL LSLINDMPIT NDQKKLMSNN VQIVRQQSYS IMCIIKEEVL AYVVQLPLYG VIDTPCWKLH TSP LCTTNT KEGSNICLTR TDRGWYCDNA GSVSFFPQAE TCKVQSNRVF CDTMNSLTLP SEVNLCNVDI FNPKYDCKIM TSKT DVSSS VITSLGAIVS CYGKTKCTAS NKNRGIIKTF SNGCDYVSNK GVDTVSVGNT LYYVNKQEGK SLYVKGEPII NFYDP LVFP SDEFDASISQ VNEKINQSLA FIRKSDELLS AIGGYIPEAP RDGQAYVRKD GEWVLLSTFL EAAAKEAAAK EAAAKH HHH HHHHHH

UniProtKB: Fusion glycoprotein F0

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Macromolecule #2: nanobody 1D8

MacromoleculeName: nanobody 1D8 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Camelus bactrianus (Bactrian camel)
Molecular weightTheoretical: 15.321834 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
MQLQLVESGG GLVQAGGSLR LSCAASEHTY CFYDMSWYRQ APGKEREFVS GIDIDGSARY ADSVKGRFTI SQDNAANTVY LQMNSLKPE DTAMYYCKTR LCGEADTYCS GGDCRDSGYW GQGTQVTVSS SRGSHHHHHH

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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

Concentration0.25 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
20.0 mMHEPESN-2-hydroxyethylpiperazine-N-2-ethane sulfonic acid
150.0 mMNaClsodium chloride
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeJEOL CRYO ARM 300
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8dzw

Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 280787
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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