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- EMDB-66053: Cryo-EM structure of human papillomavirus type 45 in complexed wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-66053
TitleCryo-EM structure of human papillomavirus type 45 in complexed with the Fab fragment of A14D2
Map data
Sample
  • Complex: Human papillomavirus type 45 in complexed with the Fab fragment of A14D2
    • Complex: Human papillomavirus type 45
    • Complex: The Fab fragment of A14D2
KeywordsHuman papillomavirus / Cryo-EM / STRUCTURAL PROTEIN
Biological speciesHuman papillomavirus / Mus (mice)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.38 Å
AuthorsJiang Y / Sun H / Wang Z / Zheng Q / Li S / Xia N
Funding support1 items
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
DepositionSep 2, 2025-
Header (metadata) releaseJul 1, 2026-
Map releaseJul 1, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66053.png

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Map

FileDownload / File: emd_66053.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 768 pix.
= 860.16 Å		1.12 Å/pix.
x 768 pix.
= 860.16 Å		1.12 Å/pix.
x 768 pix.
= 860.16 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.25322992 - 1.3070195
Average (Standard dev.)0.027748603 (±0.14977503)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 860.16003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_66053_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66053_half_map_2.map
Projections & Slices
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Sample components

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Entire : Human papillomavirus type 45 in complexed with the Fab fragment o...

EntireName: Human papillomavirus type 45 in complexed with the Fab fragment of A14D2
Components
  • Complex: Human papillomavirus type 45 in complexed with the Fab fragment of A14D2
    • Complex: Human papillomavirus type 45
    • Complex: The Fab fragment of A14D2

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Supramolecule #1: Human papillomavirus type 45 in complexed with the Fab fragment o...

SupramoleculeName: Human papillomavirus type 45 in complexed with the Fab fragment of A14D2
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Human papillomavirus

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Supramolecule #2: Human papillomavirus type 45

SupramoleculeName: Human papillomavirus type 45 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Human papillomavirus

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Supramolecule #3: The Fab fragment of A14D2

SupramoleculeName: The Fab fragment of A14D2 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Mus (mice)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.6000000000000005 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.38 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 8748
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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