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- EMDB-65403: Local refinement region of HPV45 in complex with antibody A16E6 -

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Basic information

Entry
Database: EMDB / ID: EMD-65403
TitleLocal refinement region of HPV45 in complex with antibody A16E6
Map data
Sample
  • Complex: Local refinement region of HPV45 in complex with antibody A16E6
    • Complex: Human papillomavirus type 45
      • Protein or peptide: Major capsid protein L1
    • Complex: The Fab fragment of A16E6
      • Protein or peptide: A16E6 Fab light chain
      • Protein or peptide: A16E6 Fab heavy chain
KeywordsHuman papillomavirus / Cryo-EM / STRUCTURAL PROTEIN/IMMUNE SYSTEM / STRUCTURAL PROTEIN-IMMUNE SYSTEM complex
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) / human papillomavirus 45
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsJiang Y / Sun H / 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
DepositionJul 17, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateJul 1, 2026-
Current statusJul 1, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65403.png

Downloads & links

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Map

FileDownload / File: emd_65403.map.gz / Format: CCP4 / Size: 282.6 MB / 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 Å/pix.
x 420 pix.
= 420. Å		1 Å/pix.
x 420 pix.
= 420. Å		1 Å/pix.
x 420 pix.
= 420. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.5622063 - 0.9028291
Average (Standard dev.)0.00011327845 (±0.02557095)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 420.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_65403_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_65403_half_map_2.map
Projections & Slices
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Histogram

Histogram (log scale)

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Sample components

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Entire : Local refinement region of HPV45 in complex with antibody A16E6

EntireName: Local refinement region of HPV45 in complex with antibody A16E6
Components
  • Complex: Local refinement region of HPV45 in complex with antibody A16E6
    • Complex: Human papillomavirus type 45
      • Protein or peptide: Major capsid protein L1
    • Complex: The Fab fragment of A16E6
      • Protein or peptide: A16E6 Fab light chain
      • Protein or peptide: A16E6 Fab heavy chain

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Supramolecule #1: Local refinement region of HPV45 in complex with antibody A16E6

SupramoleculeName: Local refinement region of HPV45 in complex with antibody A16E6
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human papillomavirus 45

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Supramolecule #2: Human papillomavirus type 45

SupramoleculeName: Human papillomavirus type 45 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Human papillomavirus 45

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Supramolecule #3: The Fab fragment of A16E6

SupramoleculeName: The Fab fragment of A16E6 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: A16E6 Fab light chain

MacromoleculeName: A16E6 Fab light chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 11.390643 KDa
SequenceString:
QIVLTQSPAI MSASPGEKVT ISCSASSSVS YMYWYQQKPG SSPKPWIYRT SNLASGVPAR FSGSGSGTSY SLTISSMEAE DAATYYCQQ YHSYPPTFGG GTKLEIK

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Macromolecule #2: A16E6 Fab heavy chain

MacromoleculeName: A16E6 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 13.618193 KDa
SequenceString:
QVQLQQSGPE LVRPGVSVKI SCKGSGYTFT DYSMHWVKQS HTKSLEWIGV ISTYYGKTNY NQRFKGKATM TVDKSSSTAY MELARLTSE DSAIYYCARR YDGKADYGMD YWGQGTSVTV SS

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Macromolecule #3: Major capsid protein L1

MacromoleculeName: Major capsid protein L1 / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: human papillomavirus 45
Molecular weightTheoretical: 57.379891 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MALWRPSDST VYLPPPSVAR VVSTDDYVSR TSIFYHAGSS RLLTVGNPYF RVVPNGAGNK QAVPKVSAYQ YRVFRVALPD PNKFGLPDS TIYNPETQRL VWACVGMEIG RGQPLGIGLS GHPFYNKLDD TESAHAATAV ITQDVRDNVS VDYKQTQLCI L GCVPAIGE ...String:
MALWRPSDST VYLPPPSVAR VVSTDDYVSR TSIFYHAGSS RLLTVGNPYF RVVPNGAGNK QAVPKVSAYQ YRVFRVALPD PNKFGLPDS TIYNPETQRL VWACVGMEIG RGQPLGIGLS GHPFYNKLDD TESAHAATAV ITQDVRDNVS VDYKQTQLCI L GCVPAIGE HWAKGTLCKP AQLQPGDCPP LELKNTIIED GDMVDTGYGA MDFSTLQDTK CEVPLDICQS ICKYPDYLQM SA DPYGDSM FFCLRREQLF ARHFWNRAGV MGDTVPTDLY IKGTSANMRE TPGSCVYSPS PSGSIITSDS QLFNKPYWLH KAQ GHNNGI CWHNQLFVTV VDTTRSTNLT LCASTQNPVP STYDPTKFKQ YSRHVEEYDL QFIFQLCTIT LTAEVMSYIH SMNS SILEN WNFGVPPPPT TSLVDTYRFV QSVAVTCQKD TTPPEKQDPY DKLKFWTVDL KEKFSSDLDQ YPLGRKFLVQ AGLRR RPTI GPRKRPAAST STASTASRPA KRVRIRSKK

UniProtKB: Major capsid protein L1

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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: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.7 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: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 260276
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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