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- PDB-9lm6: Cryo-EM structure of prefusion-stabilized RSV F (DS-Cav1 strain: ... -

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Basic information

Entry
Database: PDB / ID: 9lm6
TitleCryo-EM structure of prefusion-stabilized RSV F (DS-Cav1 strain: A2) in complex with nanobody 1D8
Components
  • Fusion glycoprotein F0
  • nanobody 1D8
KeywordsANTIVIRAL PROTEIN/IMMUNE SYSTEM / respiratory syncytial virus / fusion protein / complex / nanobody / 1D8 / 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 speciesRespiratory syncytial virus A2
Camelus bactrianus (Bactrian camel)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.26 Å
AuthorsWang, Q.Q. / Ke, X.L. / Li, E.T. / Hong, D.X. / Li, H.X. / Cheng, Z.K. / Zhang, J.C. / Jin, T.C. / Shu, B. / Chiu, S.
Funding support China, 1items
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, Q.Q. / Ke, X.L.
History
DepositionJan 18, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Jan 21, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fusion glycoprotein F0
D: nanobody 1D8
B: Fusion glycoprotein F0
E: nanobody 1D8
C: Fusion glycoprotein F0
F: nanobody 1D8


Theoretical massNumber of molelcules
Total (without water)235,7476
Polymers235,7476
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Fusion glycoprotein F0


Mass: 63260.383 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Respiratory syncytial virus A2 / Production host: Homo sapiens (human) / References: UniProt: P03420
#2: Antibody nanobody 1D8


Mass: 15321.834 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus bactrianus (Bactrian camel) / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 1 prefusion-stabilized RSV F (DS-Cav1 strain: A2) trimer complexed with 3 1D8 nanobodies
Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)Organism: Camelus bactrianus (Bactrian camel)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
120 mMN-2-hydroxyethylpiperazine-N-2-ethane sulfonic acidHEPES1
2150 mMsodium chlorideNaCl1
SpecimenConc.: 0.25 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy imaging

MicroscopyModel: JEOL CRYO ARM 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
4cryoSPARCCTF correction
10cryoSPARCinitial Euler assignment
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.26 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 280787 / Algorithm: FOURIER SPACE / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00613485
ELECTRON MICROSCOPYf_angle_d0.63118267
ELECTRON MICROSCOPYf_dihedral_angle_d20.2894905
ELECTRON MICROSCOPYf_chiral_restr0.0442139
ELECTRON MICROSCOPYf_plane_restr0.0042325

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