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- PDB-6l31: L1 protein of human papillomavirus 6 -

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Basic information

Entry
Database: PDB / ID: 6l31
TitleL1 protein of human papillomavirus 6
ComponentsMajor capsid protein L1
KeywordsVIRUS LIKE PARTICLE / Human papillomavirus / PsV / major protein / VIRAL PROTEIN / VIRUS
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / host cell nucleus / virion attachment to host cell / structural molecule activity
Similarity search - Function
Major capsid L1 (late) protein, Papillomavirus / Major capsid L1 (late) superfamily, Papillomavirus / L1 (late) protein / Double-stranded DNA virus, group I, capsid
Similarity search - Domain/homology
Major capsid protein L1 / Major capsid protein L1
Similarity search - Component
Biological speciesHuman papillomavirus type 6
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.18 Å
AuthorsLi, S.W. / Liu, X.L. / Gu, Y.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670935 China
National Natural Science Foundation of China31730029 China
CitationJournal: Emerg Microbes Infect / Year: 2019
Title: Neutralization sites of human papillomavirus-6 relate to virus attachment and entry phase in viral infection.
Authors: Xinlin Liu / Jie Chen / Zhiping Wang / Daning Wang / Maozhou He / Ciying Qian / Shuo Song / Xin Chi / Zhibo Kong / Qingbing Zheng / Yingbin Wang / Hai Yu / Qinjian Zhao / Jun Zhang / Shaowei ...Authors: Xinlin Liu / Jie Chen / Zhiping Wang / Daning Wang / Maozhou He / Ciying Qian / Shuo Song / Xin Chi / Zhibo Kong / Qingbing Zheng / Yingbin Wang / Hai Yu / Qinjian Zhao / Jun Zhang / Shaowei Li / Ying Gu / Ningshao Xia /
Abstract: Human papillomavirus type 6 (HPV6) is the major etiologic agent of genital warts and recurrent respiratory papillomatosis. Although the commercial HPV vaccines cover HPV6, the neutralization sites ...Human papillomavirus type 6 (HPV6) is the major etiologic agent of genital warts and recurrent respiratory papillomatosis. Although the commercial HPV vaccines cover HPV6, the neutralization sites and mode for HPV6 are poorly understood. Here, we identify the HPV6 neutralization sites and discriminate the inhibition of virus attachment and entry by three potent neutralizing antibodies (nAbs), 5D3, 17D5, and 15F7. Mutagenesis assays showed that these nAbs predominantly target surface loops BC, DE, and FG of HPV6 L1. Cryo-EM structures of the HPV6 pseudovirus (PsV) and its immune complexes revealed three distinct binding modalities - full-occupation-bound to capsid, top-center-bound-, and top-rim-bound to pentamers - and illustrated a structural atlas for three classes of antibody-bound footprints that are located at center-distal ring, center, and center-proximal ring of pentamer surface for 5D3, 17D5, and 15F7, respectively. Two modes of neutralization were identified: mAb 5D3 and 17D5 block HPV PsV from attaching to the extracellular matrix (ECM) and the cell surface, whereas 15F7 allows PsV attachment but prohibits PsV from entering the cell. These findings highlight three neutralization sites of HPV6 L1 and outline two antibody-mediated neutralization mechanisms against HPV6, which will be relevant for HPV virology and antiviral inhibitor design. HighlightsMajor neutralization sites of HPV6 were mapped on the pseudovirus cryo-EM structuremAb 15F7 binds HPV6 capsid with a novel top-rim binding modality and confers a post-attachment neutralizationmAb 17D5 binds capsid in top-centre manner but unexpectedly prevents virus from attachment to cell surface.
History
DepositionOct 7, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 25, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update

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Assembly

Deposited unit
A: Major capsid protein L1
B: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1
F: Major capsid protein L1


Theoretical massNumber of molelcules
Total (without water)298,5296
Polymers298,5296
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area35030 Å2
ΔGint-179 kcal/mol
Surface area136380 Å2

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Components

#1: Protein
Major capsid protein L1


Mass: 49754.789 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 6 / Gene: L1 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A140GKY2, UniProt: P69898*PLUS
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: Human papillomavirus type 6 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Human papillomavirus type 6
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: YES / Enveloped: NO / Isolate: SUBSPECIES / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 30 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 4.18 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 173490 / Symmetry type: POINT

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