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- EMDB-39193: HPV6 L1 pentamer in complex with Fab F5-77 -

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Basic information

Entry
Database: EMDB / ID: EMD-39193
TitleHPV6 L1 pentamer in complex with Fab F5-77
Map data
Sample
  • Complex: HPV6 L1 pentamer in complex with Fab F5-77
    • Complex: FabF5-77
      • Protein or peptide: Heavy chain of F5-77
      • Protein or peptide: Light chain of F5-77
    • Complex: HPV6 L1 pentamer
      • Protein or peptide: Major capsid protein L1
KeywordsHPV / 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) / Alphapapillomavirus 10
Methodsingle particle reconstruction / cryo EM / Resolution: 4.3 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_39193.png

Downloads & links

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Map

FileDownload / File: emd_39193.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: 0.24
Minimum - Maximum-0.60027087 - 1.0550728
Average (Standard dev.)0.00040832523 (±0.048770227)
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_39193_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_39193_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 : HPV6 L1 pentamer in complex with Fab F5-77

EntireName: HPV6 L1 pentamer in complex with Fab F5-77
Components
  • Complex: HPV6 L1 pentamer in complex with Fab F5-77
    • Complex: FabF5-77
      • Protein or peptide: Heavy chain of F5-77
      • Protein or peptide: Light chain of F5-77
    • Complex: HPV6 L1 pentamer
      • Protein or peptide: Major capsid protein L1

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Supramolecule #1: HPV6 L1 pentamer in complex with Fab F5-77

SupramoleculeName: HPV6 L1 pentamer in complex with Fab F5-77 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: FabF5-77

SupramoleculeName: FabF5-77 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: HPV6 L1 pentamer

SupramoleculeName: HPV6 L1 pentamer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Alphapapillomavirus 10

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Macromolecule #1: Heavy chain of F5-77

MacromoleculeName: Heavy chain of F5-77 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.505018 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLVQSGSE VKKPGASVTV SCKASGYVFT GQYIHWVRQA PGQGLEWIGW ITPNTGGTNY GQKFEDRVSM TRETSISTAY MELRSLRSD DTAVYYCLTR RYGHYDLFEY WGQGTLVTVS S

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Macromolecule #2: Light chain of F5-77

MacromoleculeName: Light chain of F5-77 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.821146 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIQMTQSPST LSASVGDRVT ITCRASQTIY NWLAWYQQKP GKAPNILIYK ASTLQNGVPA RFSGGGSGTE FTLTISGLQP DDFATYYCQ QYNSYPWTFG QGTKVEIK

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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: Alphapapillomavirus 10
Molecular weightTheoretical: 49.993113 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: KVVATDAYVT RTNIFYHASS SRLLAVGHPY FSIKRANKTV VPKVSGYQYR VFKVVLPDPN KFALPDSSLF DPTTQRLVWA CTGLEVGRG QPLGVGVSGH PFLNKYDDVE NSGSGGNPGQ DNRVNVGMDY KQTQLCMVGC APPLGEHWGK GKQCTNTPVQ A GDCPPLEL ...String:
KVVATDAYVT RTNIFYHASS SRLLAVGHPY FSIKRANKTV VPKVSGYQYR VFKVVLPDPN KFALPDSSLF DPTTQRLVWA CTGLEVGRG QPLGVGVSGH PFLNKYDDVE NSGSGGNPGQ DNRVNVGMDY KQTQLCMVGC APPLGEHWGK GKQCTNTPVQ A GDCPPLEL ITSVIQDGDM VDTGFGAMNF ADLQTNKSDV PIDICGTTCK YPDYLQMAAD PYGDRLFFFL RKEQMFARHF FN RAGEVGE PVPDTLIIKG SGNRTSVGSS IYVNTPSGSL VSSEAQLFNK PYWLQKAQGH NNGICWGNQL FVTVVDTTRS TNM TLCASV TTSSTYTNSD YKEYMRHVEE YDLQFIFQLC SITLSAEVVA YIHTMNPSVL EDWNFGLSPP PNGTLEDTYR YVQS QAITC QKPTPEKEKP DPYKNLSFWE VNLKEKFSSE LDQYPLGRKF LLQS

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 K2 QUANTUM (4k 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: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 66519
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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