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- PDB-7dnk: 2-fold subparticles refinement of human papillomavirus type 58 ps... -

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Basic information

Entry
Database: PDB / ID: 7dnk
Title2-fold subparticles refinement of human papillomavirus type 58 pseudovirus in complexed with the Fab fragment of 5G9
Components
  • Major capsid protein L1
  • The heavy chain of 5G9 Fab fragment
  • The light chain of 5G9 Fab fragment
KeywordsIMMUNE SYSTEM/VIRAL PROTEIN / Immune complex / VIRAL PROTEIN / IMMUNE SYSTEM-VIRAL PROTEIN complex
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
Similarity search - Component
Biological speciesHuman papillomavirus type 58
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.41 Å
AuthorsHe, M.Z. / Chi, X. / Zha, Z.H. / Zheng, Q.B. / Gu, Y. / Li, S.W. / Xia, N.S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U1705283 China
CitationJournal: J Virol / Year: 2021
Title: Structural basis for the shared neutralization mechanism of three classes of human papillomavirus type 58 antibodies with disparate modes of binding.
Authors: Maozhou He / Xin Chi / Zhenghui Zha / Yunbing Li / Jie Chen / Yang Huang / Shiwen Huang / Miao Yu / Zhiping Wang / Shuo Song / Xinlin Liu / Shuangping Wei / Zekai Li / Tingting Li / Yingbin ...Authors: Maozhou He / Xin Chi / Zhenghui Zha / Yunbing Li / Jie Chen / Yang Huang / Shiwen Huang / Miao Yu / Zhiping Wang / Shuo Song / Xinlin Liu / Shuangping Wei / Zekai Li / Tingting Li / Yingbin Wang / Hai Yu / Qinjian Zhao / Jun Zhang / Qingbing Zheng / Ying Gu / Shaowei Li / Ningshao Xia /
Abstract: Human papillomavirus type 58 (HPV58) is associated with cervical cancer and poses a significant health burden worldwide. Although the commercial 9-valent HPV vaccine covers HPV58, the structural and ...Human papillomavirus type 58 (HPV58) is associated with cervical cancer and poses a significant health burden worldwide. Although the commercial 9-valent HPV vaccine covers HPV58, the structural and molecular-level neutralization sites of the HPV58 complete virion are not fully understood. Here, we report the high-resolution (∼3.5 Å) structure of the complete HPV58 pseudovirus (PsV58) using cryo-electron microscopy (cryo-EM). Three representative neutralizing monoclonal antibodies (nAbs 5G9, 2H3 and A4B4) were selected through clustering from a nAb panel against HPV58. Bypassing the steric hindrance and symmetry-mismatch in the HPV Fab-capsid immune-complex, we present three different neutralizing epitopes in the PsV58, and show that, despite differences in binding, these nAbs share a common neutralization mechanism. These results offer insight into HPV58 genotype specificity and broaden our understanding of HPV58 neutralization sites for antiviral research. Cervical cancer primarily results from persistent infection with high-risk types of human papillomavirus (HPV). HPV type 58 (HPV58) is an important causative agent, especially within Asia. Despite this, we still have limited data pertaining to the structural and neutralizing epitopes of HPV58, and this encumbers our in-depth understanding of the virus mode of infection. Here, we show that representative nAbs (5G9, 10B11, 2H3, 5H2 and A4B4) from three different groups share a common neutralization mechanism that appears to prohibit the virus from associating with the extracellular matrix and cell surface. Furthermore, we identify that the nAbs engage via three different binding patterns: top-center binding (5G9 and 10B11), top-fringe binding (2H3 and 5H2), and fringe binding (A4B4). Our work shows that, despite differences in the pattern in binding, nAbs against HPV58 share a common neutralization mechanism. These results provide new insight into the understanding of HPV58 infection.
History
DepositionDec 9, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 3, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 7, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation_author.identifier_ORCID ..._citation.journal_volume / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure viewerMolecule:
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Assembly

Deposited unit
L: The light chain of 5G9 Fab fragment
H: The heavy chain of 5G9 Fab fragment
B: Major capsid protein L1
A: Major capsid protein L1
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1


Theoretical massNumber of molelcules
Total (without water)341,8837
Polymers341,8837
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area38460 Å2
ΔGint-213 kcal/mol
Surface area139630 Å2

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Components

#1: Antibody The light chain of 5G9 Fab fragment


Mass: 23739.164 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody The heavy chain of 5G9 Fab fragment


Mass: 22627.357 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein
Major capsid protein L1


Mass: 59103.199 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human papillomavirus type 58 / Gene: L1 / Production host: Homo sapiens (human) / References: UniProt: P26535

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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

Component
IDNameTypeEntity IDParent-IDSource
12-fold sub-articles refinement of human papillomavirus type 58 pseudpvirus in complexed with the Fab fragment of 5G9COMPLEXall0MULTIPLE SOURCES
2Fab fragment of 5G9COMPLEX#1-#21NATURAL
3human papillomavirus type 58 pseudpvirusCOMPLEX#31RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Mus musculus (house mouse)10090
32Human papillomavirus type 5810598
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: NO / Enveloped: NO / Isolate: OTHER / Type: VIRION
Buffer solutionpH: 7.4
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 30 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

EM softwareName: cisTEM / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 6.41 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 14464 / Symmetry type: POINT

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