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- EMDB-39195: HPV16 L1 pentamer in complex with Fab F5-196 -

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Basic information

Entry
Database: EMDB / ID: EMD-39195
TitleHPV16 L1 pentamer in complex with Fab F5-196
Map data
Sample
  • Complex: HPV16 L1 pentamer in complex with Fab F5-196
    • Complex: FabF5-196
      • Protein or peptide: heavy chain of F5-196
      • Protein or peptide: light chain of F5-196
    • Complex: HPV16 L1 pentamer
      • Protein or peptide: Major capsid protein L1
KeywordsHPV16 / L1 / antibody / VIRAL PROTEIN / VIRAL 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 speciesHomo sapiens (human) / Human papillomavirus 16 / Human papillomavirus type 16
Methodsingle particle reconstruction / cryo EM / Resolution: 2.86 Å
AuthorsWang X / Fu W
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: NPJ Vaccines / Year: 2025
Title: Establishing a universal IVRP method for quadrivalent HPV vaccines to replace in vivo potency tests.
Authors: Jinpan Hu / Zijing Jia / Meng Wang / Lingling Nie / Wangjun Fu / Qingfeng Zhang / Haiyang Qin / Jianhui Nie / Xiaoyu Xu / Lingjie Xu / Fengze Wang / Yingping Chen / Bo Xing / Tao Li / ...Authors: Jinpan Hu / Zijing Jia / Meng Wang / Lingling Nie / Wangjun Fu / Qingfeng Zhang / Haiyang Qin / Jianhui Nie / Xiaoyu Xu / Lingjie Xu / Fengze Wang / Yingping Chen / Bo Xing / Tao Li / Danfeng Li / Shaowei Li / Ningshao Xia / Xiangxi Wang / Weijin Huang /
Abstract: Several human papillomavirus (HPV) L1-based virus-like particle (VLP) vaccines are in development to meet future global vaccination needs. Type-specific monoclonal antibodies with good reactivity to ...Several human papillomavirus (HPV) L1-based virus-like particle (VLP) vaccines are in development to meet future global vaccination needs. Type-specific monoclonal antibodies with good reactivity to all types of vaccines are urgently needed to evaluate vaccine potency. In this study, binding activity, neutralizing activity, conformational sensitivity, immunodominance in human serum, and versatility were compared among antibodies. A broad-spectrum binding antibody (C4-F5-127) was selected as the capture antibody; four type-specific neutralizing antibodies (6-F5-77, 11-F5-187, 16-F5-196, and 18-F5-203) were selected as detection antibodies for HPV6, 11, 16, and 18, respectively. These antibodies formed a standardized and universal in vitro relative potency (IVRP) assay kit. High-resolution cryo-electron microscopy (cryo-EM) structures of HPV6-6-F5-77, HPV11-11-F5-187, HPV16-16-F5-196 and HPV18-18-F5-203 complexes define the location and nature of epitopes, revealing serotype specific binding modes and neutralization mechanisms. The IVRP results were correlated with potency data from mouse models, offering an efficient alternative to in vivo potency experiments.
History
DepositionFeb 22, 2024-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateSep 10, 2025-
Current statusSep 10, 2025Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_39195.png

Downloads & links

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Map

FileDownload / File: emd_39195.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å		1.04 Å/pix.
x 256 pix.
= 266.24 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.585
Minimum - Maximum-4.1831527 - 6.81985
Average (Standard dev.)0.0014595857 (±0.18918245)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 266.24 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39195_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_39195_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HPV16 L1 pentamer in complex with Fab F5-196

EntireName: HPV16 L1 pentamer in complex with Fab F5-196
Components
  • Complex: HPV16 L1 pentamer in complex with Fab F5-196
    • Complex: FabF5-196
      • Protein or peptide: heavy chain of F5-196
      • Protein or peptide: light chain of F5-196
    • Complex: HPV16 L1 pentamer
      • Protein or peptide: Major capsid protein L1

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Supramolecule #1: HPV16 L1 pentamer in complex with Fab F5-196

SupramoleculeName: HPV16 L1 pentamer in complex with Fab F5-196 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: FabF5-196

SupramoleculeName: FabF5-196 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: HPV16 L1 pentamer

SupramoleculeName: HPV16 L1 pentamer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Human papillomavirus 16

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Macromolecule #1: heavy chain of F5-196

MacromoleculeName: heavy chain of F5-196 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.34587 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGAE VKKPGSSVKV SCKASGGTFN SYATGWVRQA PGQGLEWMGV IVPIFGTEDY PQRFQGRVTI TADESTATAY MELRSLRSD DTAVYYCARS RLGSSSWFLF EYWGQGTLVT VSS

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Macromolecule #2: light chain of F5-196

MacromoleculeName: light chain of F5-196 / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.692977 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPSS LSASVGDRVT ITCRASDMIS NYLNWYQHKP GEAPKLLIYS ASSLQTGVPS RFSGSGSGTD FTLTINNLQP EDFATYYCQ QSYITRLSFG GGTKVEIK

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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 type 16
Molecular weightTheoretical: 50.647133 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: KVVSTDEYVA RTNIYYHAGT SRLLAVGHPY FPIKKPNNNK ILVPKVSGLQ YRVFRIHLPD PNKFGFPDTS FYNPDTQRLV WACVGVEVG RGQPLGVGIS GHPLLNKLDD TENASAYAAN AGVDNRECIS MDYKQTQLCL IGCKPPIGEH WGKGSPCTNV A VNPGDCPP ...String:
KVVSTDEYVA RTNIYYHAGT SRLLAVGHPY FPIKKPNNNK ILVPKVSGLQ YRVFRIHLPD PNKFGFPDTS FYNPDTQRLV WACVGVEVG RGQPLGVGIS GHPLLNKLDD TENASAYAAN AGVDNRECIS MDYKQTQLCL IGCKPPIGEH WGKGSPCTNV A VNPGDCPP LELINTVIQD GDMVDTGFGA MDFTTLQANK SEVPLDICTS ICKYPDYIKM VSEPYGDSLF FYLRREQMFV RH LFNRAGA VGDNVPDDLY IKGSGSTANL ASSNYFPTPS GSMVTSDAQI FNKPYWLQRA QGHNNGICWG NQLFVTVVDT TRS TNMSLC AAISTSETTY KNTNFKEYLR HGEEYDLQFI FQLCKITLTA DVMTYIHSMN STILEDWNFG LQPPPGGTLE DTYR FVTSQ AIACQKHTPP APKEDPLKKY TFWEVNLKEK FSADLDQFPL GRKFLLQA

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 TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 498615
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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