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- EMDB-39196: HPV18 L1 pentamer in complex with Fab F5-203 -

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Basic information

Entry
Database: EMDB / ID: EMD-39196
TitleHPV18 L1 pentamer in complex with Fab F5-203
Map data
Sample
  • Complex: HPV18 L1 pentamer in complex with Fab F5-203
    • Complex: Fab F5-203
      • Protein or peptide: heavy chain of antibody F5-203
      • Protein or peptide: light chain of antibody F5-203
    • Complex: HPV18 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 / membrane
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 18
Methodsingle particle reconstruction / cryo EM / Resolution: 2.93 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_39196.png

Downloads & links

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Map

FileDownload / File: emd_39196.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: 0.307
Minimum - Maximum-2.3499134 - 4.1510077
Average (Standard dev.)0.004184859 (±0.13126455)
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_39196_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_39196_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 : HPV18 L1 pentamer in complex with Fab F5-203

EntireName: HPV18 L1 pentamer in complex with Fab F5-203
Components
  • Complex: HPV18 L1 pentamer in complex with Fab F5-203
    • Complex: Fab F5-203
      • Protein or peptide: heavy chain of antibody F5-203
      • Protein or peptide: light chain of antibody F5-203
    • Complex: HPV18 L1 pentamer
      • Protein or peptide: Major capsid protein L1

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Supramolecule #1: HPV18 L1 pentamer in complex with Fab F5-203

SupramoleculeName: HPV18 L1 pentamer in complex with Fab F5-203 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Fab F5-203

SupramoleculeName: Fab F5-203 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: HPV18 L1 pentamer

SupramoleculeName: HPV18 L1 pentamer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: human papillomavirus 18

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Macromolecule #1: heavy chain of antibody F5-203

MacromoleculeName: heavy chain of antibody F5-203 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.406923 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QVQLQESGPG LVKPSETLSL TCTVSGGSIT RYHWSWIRQP PGKGLEWIGN IYNRGSTKYN PSLKSRVTIS IDISNNQFSL RLSSVTAAD TAVYHCARWD NGHSYAIGGF DYWGQGILVT VSS

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Macromolecule #2: light chain of antibody F5-203

MacromoleculeName: light chain of antibody F5-203 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.878074 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSVLTQPPSA SGTPGQRVTI SCSGSSFNIE SNYVYWYQHL PGTAPKLLIY RNNQRPSGVP DRFSGTKSGT SASLAISGLR SEDETDYFC ATWDDSLSVW VFGGGTKLTV L

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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 18
Molecular weightTheoretical: 50.605633 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AVVNTDDYVT RTSIFYHAGS SRLLTVGNPY FRVPAGGGNK QDIPKVSAYQ YRVFRVQLPD PNKFGLPDTS IYNPETQRLV WACAGVEIG RGQPLGVGLS GHPFYNKLDD TESSHAATSN VSEDVRDNVS VDYKQTQLCI LGCAPAIGEH WAKGTASKSR P LSQGDCPP ...String:
AVVNTDDYVT RTSIFYHAGS SRLLTVGNPY FRVPAGGGNK QDIPKVSAYQ YRVFRVQLPD PNKFGLPDTS IYNPETQRLV WACAGVEIG RGQPLGVGLS GHPFYNKLDD TESSHAATSN VSEDVRDNVS VDYKQTQLCI LGCAPAIGEH WAKGTASKSR P LSQGDCPP LELKNTVLED GDMVDTGYGA MDFSTLQDTK CEVPLDICQS ICKYPDYLQM SADPYGDSMF FCLRREQLFA RH FWNRAGT MGDTVPQSLY IKGTGMRASP GSCVYSPSPS GSIVTSDSQL FNKPYWLHKA QGHNNGVCWH NQLFVTVVDT TRS TNLTIC ASTQSPVPGQ YDATKFKQYS RHVEEYDLQF IFQLCTITLT ADVMSYIHSM NSSILEDWNF GVPPPPTTSL VDTY RFVQS VAITCQKDAA PAENKDPYDK LKFWNVDLKE KFSLDLDQYP LGRKFLVQA

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: 2.93 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 224760
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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