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- PDB-9mkn: Structure of the Respiratory Syncytial Virus Fusion Protein Bound... -

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Basic information

Entry
Database: PDB / ID: 9mkn
TitleStructure of the Respiratory Syncytial Virus Fusion Protein Bound to Human Antibodies RSV_2245 and RSV_3301
Components
  • (Fusion glycoprotein ...) x 2
  • 2245 Fab Heavy Chain
  • 2245 Fab Light Chain
  • 3301 Fab Heavy Chain
  • 3301 Fab Light Chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / fusion protein / trimer / antibody / complex / ANTIVIRAL PROTEIN / VIRAL 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
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsJohnson, N.V. / McLellan, J.S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Generation of antigen-specific paired heavy-light chain antibody sequences using large language models
Authors: Wasdin, P.T. / Johnson, N.V. / Janke, A.K. / Held, S. / Marinov, T.M. / Jordaan, G. / Vandenabeele, L. / Pantouli, F. / Gillespie, R.A. / Vukovich, M.J. / Holt, C.M. / Kim, J.R. / Hansman, G. ...Authors: Wasdin, P.T. / Johnson, N.V. / Janke, A.K. / Held, S. / Marinov, T.M. / Jordaan, G. / Vandenabeele, L. / Pantouli, F. / Gillespie, R.A. / Vukovich, M.J. / Holt, C.M. / Kim, J.R. / Hansman, G. / Logue, J. / Chu, H.Y. / Andrews, S.F. / Kanekiyo, M. / Sautto, G. / Ross, T. / Sheward, D.J. / McLellan, J.S. / Abu-Shmais, A.A. / Georgiev, I.S.
History
DepositionDec 17, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 29, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fusion glycoprotein F2
B: Fusion glycoprotein F1
C: Fusion glycoprotein F2
D: Fusion glycoprotein F1
E: Fusion glycoprotein F2
F: Fusion glycoprotein F1
H: 2245 Fab Heavy Chain
I: 2245 Fab Heavy Chain
J: 2245 Fab Heavy Chain
L: 2245 Fab Light Chain
M: 2245 Fab Light Chain
N: 2245 Fab Light Chain
O: 3301 Fab Heavy Chain
P: 3301 Fab Light Chain
Q: 3301 Fab Heavy Chain
R: 3301 Fab Light Chain
S: 3301 Fab Heavy Chain
T: 3301 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)434,85018
Polymers434,85018
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Fusion glycoprotein ... , 2 types, 6 molecules ACEBDF

#1: Protein Fusion glycoprotein F2 / F2


Mass: 7913.058 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Respiratory syncytial virus / Production host: Homo sapiens (human) / References: UniProt: P03420
#2: Protein Fusion glycoprotein F1 / F1


Mass: 40693.469 Da / Num. of mol.: 3 / Mutation: I379V, M447V variant
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Respiratory syncytial virus / Production host: Homo sapiens (human) / References: UniProt: P03420

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Antibody , 4 types, 12 molecules HIJLMNOQSPRT

#3: Antibody 2245 Fab Heavy Chain


Mass: 23915.721 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody 2245 Fab Light Chain


Mass: 24065.750 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody 3301 Fab Heavy Chain


Mass: 24900.920 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#6: Antibody 3301 Fab Light Chain


Mass: 23460.980 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Details

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: Complex of trimeric fusion protein bound 1:1 to 2245 Fab VH/VL and 3301 Fab VH/VL
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: TFS GLACIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 49 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 140634 / Symmetry type: POINT

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