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- PDB-9vz8: Local refinement region of HPV45 in complex with antibody 10G2 -

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Basic information

Entry
Database: PDB / ID: 9vz8
TitleLocal refinement region of HPV45 in complex with antibody 10G2
Components
  • 10G2 Fab heavy chain
  • 10G2 Fab light chain
  • Major capsid protein L1
KeywordsVIRUS LIKE PARTICLE / Human papillomavirus / Cryo-EM / structural protein
Function / homology
Function and homology information


T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / 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 45
Mus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.81 Å
AuthorsJiang, Y. / Sun, H. / Zheng, Q. / Li, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Structure / Year: 2026
Title: Structural and biochemical characterization of neutralizing antibodies targeting human papillomavirus type 45.
Authors: Yanan Jiang / Zhiping Wang / Qin Xu / Shuyue Zhang / Jinfu Su / Hui Sun / Chengzong Zhang / Lizhi Zhou / Tingting Li / Zhibo Kong / Hai Yu / Jun Zhang / Qingbing Zheng / Ying Gu / Ningshao Xia / Shaowei Li /
Abstract: Human papillomavirus type 45 (HPV45) is a high-risk genotype and the third most prevalent HPV type associated with cervical cancer worldwide, posing a significant public health concern. Although ...Human papillomavirus type 45 (HPV45) is a high-risk genotype and the third most prevalent HPV type associated with cervical cancer worldwide, posing a significant public health concern. Although HPV45 is included in the commercial 9-valent HPV vaccine, its complete virion structure and the molecular basis of antibody-mediated neutralization remain incompletely understood. Here, we report the near-atomic resolution structure of the HPV45 pseudovirus (PsV45) determined by cryo-electron microscopy. We also isolated and structurally characterized several neutralizing monoclonal antibodies (nAbs) targeting PsV45. Our analysis reveals two distinct neutralizing epitopes on PsV45, and these nAbs likely neutralize the virus by a common mechanism involving the inhibition of viral attachment, despite differences in their binding interfaces. Biochemical assays confirmed that antibodies with non-overlapping binding modes can engage PsV45 simultaneously, indicating potential for synergistic combinations. These findings elucidate the structural basis of HPV45 type specificity and provide insights into HPV neutralization mechanisms.
History
DepositionJul 22, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: Major capsid protein L1
D: Major capsid protein L1
E: Major capsid protein L1
L: 10G2 Fab light chain
H: 10G2 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)197,7215
Polymers197,7215
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Major capsid protein L1


Mass: 57379.891 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) human papillomavirus 45 / Gene: L1 / Production host: Escherichia coli (E. coli) / References: UniProt: P36741
#2: Antibody 10G2 Fab light chain


Mass: 12215.571 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Antibody 10G2 Fab heavy chain


Mass: 13365.791 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
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

Component
IDNameTypeEntity IDParent-IDSource
1Local refinement region of HPV45 in complex with antibody 10G2COMPLEXall0MULTIPLE SOURCES
2Human papillomavirus type 45COMPLEX#11RECOMBINANT
3The Fab fragment of 10G2COMPLEX#2-#31NATURAL
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22human papillomavirus 4510593
33Mus musculus (house mouse)10090
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Escherichia coli (E. coli)562
33Homo sapiens (human)9606
Buffer solutionpH: 7.5
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCparticle selection
2PHENIX1.20_4459model refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 993420 / Symmetry type: POINT
RefinementHighest resolution: 3.81 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0047843
ELECTRON MICROSCOPYf_angle_d0.56510697
ELECTRON MICROSCOPYf_dihedral_angle_d4.1161076
ELECTRON MICROSCOPYf_chiral_restr0.0441184
ELECTRON MICROSCOPYf_plane_restr0.0061370

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