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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 / 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 / Maturation of hRSV A proteins / Assembly and release of respiratory syncytial virus (RSV) virions / 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
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: Cell / Year: 2025
Title: Generation of antigen-specific paired-chain antibodies using large language models.
Authors: Perry T Wasdin / Nicole V Johnson / Alexis K Janke / Sofia Held / Toma M Marinov / Gwen Jordaan / Rebecca A Gillespie / Léna Vandenabeele / Fani Pantouli / Olivia C Powers / Matthew J ...Authors: Perry T Wasdin / Nicole V Johnson / Alexis K Janke / Sofia Held / Toma M Marinov / Gwen Jordaan / Rebecca A Gillespie / Léna Vandenabeele / Fani Pantouli / Olivia C Powers / Matthew J Vukovich / Clinton M Holt / Jeongryeol Kim / Grant Hansman / Jennifer Logue / Helen Y Chu / Sarah F Andrews / Masaru Kanekiyo / Giuseppe A Sautto / Ted M Ross / Daniel J Sheward / Jason S McLellan / Alexandra A Abu-Shmais / Ivelin S Georgiev /
Abstract: The traditional process of antibody discovery is limited by inefficiency, high costs, and low success rates. Recent approaches employing artificial intelligence (AI) have been developed to optimize ...The traditional process of antibody discovery is limited by inefficiency, high costs, and low success rates. Recent approaches employing artificial intelligence (AI) have been developed to optimize existing antibodies and generate antibody sequences in a target-agnostic manner. In this work, we present MAGE (monoclonal antibody generator), a sequence-based protein language model (PLM) fine-tuned for the task of generating paired human variable heavy- and light-chain antibody sequences against targets of interest. We show that MAGE can generate novel and diverse antibody sequences with experimentally validated binding specificity against SARS-CoV-2, an emerging avian influenza H5N1, and respiratory syncytial virus A (RSV-A). MAGE represents a first-in-class model capable of designing human antibodies against multiple targets with no starting template.
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
Revision 1.1Nov 19, 2025Group: Data collection / Database references / Category: citation / citation_author / em_admin
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _em_admin.last_update
Revision 1.2Dec 24, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update
Revision 1.1Dec 24, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin / Data content type: EM metadata / EM metadata / EM metadata
Item: _citation.journal_volume / _citation.page_first / _em_admin.last_update

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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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