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- EMDB-39194: HPV11 L1 pentamer in complex with Fab F5-187 -

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Basic information

Entry
Database: EMDB / ID: EMD-39194
TitleHPV11 L1 pentamer in complex with Fab F5-187
Map data
Sample
  • Complex: HPV11 L1 pentamer in complex with Fab F5-187
    • Complex: Fab F5-187
      • Protein or peptide: heavy chain of F5-187
      • Protein or peptide: light chain of F5-187
    • Complex: HPV11 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) / human papillomavirus 11
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 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_39194.png

Downloads & links

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Map

FileDownload / File: emd_39194.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 200 pix.
= 214. Å		1.07 Å/pix.
x 200 pix.
= 214. Å		1.07 Å/pix.
x 200 pix.
= 214. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.097022876 - 0.15367119
Average (Standard dev.)-0.00049807574 (±0.007119039)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 214.00002 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_39194_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_39194_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 : HPV11 L1 pentamer in complex with Fab F5-187

EntireName: HPV11 L1 pentamer in complex with Fab F5-187
Components
  • Complex: HPV11 L1 pentamer in complex with Fab F5-187
    • Complex: Fab F5-187
      • Protein or peptide: heavy chain of F5-187
      • Protein or peptide: light chain of F5-187
    • Complex: HPV11 L1 pentamer
      • Protein or peptide: Major capsid protein L1

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Supramolecule #1: HPV11 L1 pentamer in complex with Fab F5-187

SupramoleculeName: HPV11 L1 pentamer in complex with Fab F5-187 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Fab F5-187

SupramoleculeName: Fab F5-187 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1, #3
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: HPV11 L1 pentamer

SupramoleculeName: HPV11 L1 pentamer / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: human papillomavirus 11

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Macromolecule #1: heavy chain of F5-187

MacromoleculeName: heavy chain of F5-187 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.179688 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLLESGGG LVQPGGSLRL SCAASGLTFS SYAMSWVRQA PGKGLEWVSS ISASGGSTYY ADSVRGRFTI SRDNSRTTLY LQMNILRAE DTAVYYCAKD RMGVRGSGWF DYWGQGTLVT VSS

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Macromolecule #2: Major capsid protein L1

MacromoleculeName: Major capsid protein L1 / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: human papillomavirus 11
Molecular weightTheoretical: 50.384586 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AVVATDAYVK RTNIFYHASS SRLLAVGHPY YSIKKVNKTV VPKVSGYQYR VFKVVLPDPN KFALPDSSLF DPTTQRLVWA CTGLEVGRG QPLGVGVSGH PLLNKYDDVE NSGGYGGNPG QDNRVNVGMD YKQTQLCMVG CAPPLGEHWG KGTQCSNTSV Q NGDCPPLE ...String:
AVVATDAYVK RTNIFYHASS SRLLAVGHPY YSIKKVNKTV VPKVSGYQYR VFKVVLPDPN KFALPDSSLF DPTTQRLVWA CTGLEVGRG QPLGVGVSGH PLLNKYDDVE NSGGYGGNPG QDNRVNVGMD YKQTQLCMVG CAPPLGEHWG KGTQCSNTSV Q NGDCPPLE LITSVIQDGD MVDTGFGAMN FADLQTNKSD VPLDICGTVC KYPDYLQMAA DPYGDRLFFY LRKEQMFARH FF NRAGTVG EPVPDDLLVK GGNNRSSVAS SIYVHTPSGS LVSSEAQLFN KPYWLQKAQG HNNGICWGNH LFVTVVDTTR STN MTLCAS VSKSATYTNS DYKEYMRHVE EFDLQFIFQL CSITLSAEVM AYIHTMNPSV LEDWNFGLSP PPNGTLEDTY RYVQ SQAIT CQKPTPEKEK QDPYKDMSFW EVNLKEKFSS ELDQFPLGRK FLLQSGY

UniProtKB: Major capsid protein L1

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Macromolecule #3: light chain of F5-187

MacromoleculeName: light chain of F5-187 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.51592 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DIVMTQSPDS LAVSLGERAT INCKSSQSIL YSSSNKNYLA WYQQKPGQPP KLLIYWASTR ESGVPDRFSG SGSGTDFTLT ISSLLPEDV AVYYCQQYHS TPWTFGQGTK VEIK

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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: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 216722
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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