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- EMDB-48344: D24.1M01 Fab bound to HPV16 L1 pentamer -

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Basic information

Entry
Database: EMDB / ID: EMD-48344
TitleD24.1M01 Fab bound to HPV16 L1 pentamer
Map dataSharpened map of D24.M01 Fab bound to HPV16 L1 pentamer
Sample
  • Complex: HPV16 L1 pentamer bound to five D24.1M01 Fabs
    • Protein or peptide: Major capsid protein L1
    • Protein or peptide: D24.1M01 Heavy Chain
    • Protein or peptide: D24.1M01 Light Chain
KeywordsHPV / antibody / IMMUNE SYSTEM
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 16 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsHurlburt NK / Singh S / Rodarte JV / Pancera M
Funding support United States, 1 items
OrganizationGrant numberCountry
Other private United States
CitationJournal: PLoS Pathog / Year: 2025
Title: Human monoclonal antibodies to HPV16 show evidence for common developmental pathways and public epitopes.
Authors: Joseph J Carter / Nicholas K Hurlburt / Erin M Scherer / Suruchi Singh / Justas V Rodarte / Robin A Smith / Peter Lewis / Rachel Kinzelman / Jacqueline Kieltyka / Madelyn E Cabãn / Gregory ...Authors: Joseph J Carter / Nicholas K Hurlburt / Erin M Scherer / Suruchi Singh / Justas V Rodarte / Robin A Smith / Peter Lewis / Rachel Kinzelman / Jacqueline Kieltyka / Madelyn E Cabãn / Gregory C Wipf / Marie Pancera / Denise A Galloway /
Abstract: Antibodies to human papillomavirus (HPV) primarily recognize surface exposed residues on five loops of the major capsid protein (L1) that vary significantly among HPV types. We determined which loops ...Antibodies to human papillomavirus (HPV) primarily recognize surface exposed residues on five loops of the major capsid protein (L1) that vary significantly among HPV types. We determined which loops were required for neutralization for 68 HPV16 specific human monoclonal antibodies (mAbs) cloned from participants who received an HPV vaccine and describe molecular features of those antibodies. Chimeric HPV16 pseudovirus (cpsV), each having one surface loop bearing multiple amino acid substitutions, were used to determine neutralization specificity. The HPV16-FG-loop was the loop most frequently required for neutralization (42 of 68, 61.8%), however, all surface loops were required for neutralization by multiple mAbs: HI (13, 19.1%), DE (15, 22.1%), EF (five, 7.4%), BC (four, 5.9%). Antibodies that required multiple loops were common (17, 25.0%). Three mAbs (4.4%) required sequences on the c-terminus of L1 and for another three mAbs the neutralization specificity could not be determined. Two types of mAbs appeared to be overrepresented: ten mAbs used immunoglobin heavy chain variable region 2-70 (IGHV2-70) with immunoglobin light chain variable region 1-40 (IGLV1-40), having characteristic mutations in complementarity determining region two (CDRL2) of the light chain. Cryogenic electron microscopy (Cryo-EM) revealed that two of these antibodies bound five Fabs per capsomer interacting with all five L1-surface loops. The other type of mAbs that appeared to be overrepresented were nine mAbs using IGHV4-34, six of which also used DH3-16*02 with conserved CDRH3 sequences. Cryo-EM for one of these mAbs, that required the FG-loop for neutralization, was shown to bind one Fab per capsomer at the apex, interacting with the DE- and FG-loops, with sequences of the Fab CDRH3 inserted between the DE- and FG-loops from two L1 proteins. These two types of mAbs were found in the four participants suggesting that these antibodies shared developmental pathways and bound to similar immunodominant epitopes on the virus.
History
DepositionDec 18, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48344.png

Downloads & links

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Map

FileDownload / File: emd_48344.map.gz / Format: CCP4 / Size: 40.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of D24.M01 Fab bound to HPV16 L1 pentamer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 220 pix.
= 231.88 Å		1.05 Å/pix.
x 220 pix.
= 231.88 Å		1.05 Å/pix.
x 220 pix.
= 231.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.054 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-3.816326 - 5.069594
Average (Standard dev.)0.008156201 (±0.17159878)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions220220220
Spacing220220220
CellA=B=C: 231.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A

Fileemd_48344_half_map_1.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_48344_half_map_2.map
AnnotationHalf map B
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 bound to five D24.1M01 Fabs

EntireName: HPV16 L1 pentamer bound to five D24.1M01 Fabs
Components
  • Complex: HPV16 L1 pentamer bound to five D24.1M01 Fabs
    • Protein or peptide: Major capsid protein L1
    • Protein or peptide: D24.1M01 Heavy Chain
    • Protein or peptide: D24.1M01 Light Chain

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Supramolecule #1: HPV16 L1 pentamer bound to five D24.1M01 Fabs

SupramoleculeName: HPV16 L1 pentamer bound to five D24.1M01 Fabs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human papillomavirus 16
Molecular weightTheoretical: 50 KDa

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Macromolecule #1: Major capsid protein L1

MacromoleculeName: Major capsid protein L1 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Human papillomavirus 16
Molecular weightTheoretical: 47.492496 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: AVVSTDEYVA RTNIYYHAGT SRLLAVGHPY FPIKKPNNNK ILVPKVSGLQ YRVFRIHLPD PNKFGFPDTS FYNPDTQRLV WACVGVEVG RGQPLGVGIS GHPLLNKLDD TENASAYAAN AGVDNRECIS MDYKQTQLCL IGCKPPIGEH WGKGSPCTNV A VNPGDCPP ...String:
AVVSTDEYVA 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 LFNRAGT VGENVPDDLY IKGSGSTANL ASSNYFPTPS GSMVTSDAQI FNKPYWLQRA QGHNNGICWG NQLFVTVVDT TRS TNMSLC AAISTSETTY KNTNFKEYLR HGEEYDLQFI FQLCKITLTA DVMTYIHSMN STILEDWNGG SGAEDPLKKY TFWE VNLKE KFSADLDQFP LGRKFLLQAG L

UniProtKB: Major capsid protein L1

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Macromolecule #2: D24.1M01 Heavy Chain

MacromoleculeName: D24.1M01 Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.534828 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVTLRESGPA LVKPTQTLTL TCTISGLSLT TSGVCVSWIR QPPGKALEWL ALIDWDDDKY YSTSLRTRLT ISKDISKNQV VLTMTNMDP VDTATFFCAR TRCTSNWGYY FDSWGRGTRV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA ...String:
QVTLRESGPA LVKPTQTLTL TCTISGLSLT TSGVCVSWIR QPPGKALEWL ALIDWDDDKY YSTSLRTRLT ISKDISKNQV VLTMTNMDP VDTATFFCAR TRCTSNWGYY FDSWGRGTRV TVSSASTKGP SVFPLAPSSK STSGGTAALG CLVKDYFPEP V TVSWNSGA LTSGVHTFPA VLQSSGLYSL SSVVTVPSSS LGTQTYICNV NHKPSNTKVD KRVEPKSCDK THHHHHH

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Macromolecule #3: D24.1M01 Light Chain

MacromoleculeName: D24.1M01 Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.866293 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSVLTQPPSV SGAPGQRVTI SCTGSASNIG AGYDVHWYQQ VPGAAPKLLI FVYSNRPSGV PDRISGSKSG TSASLAISGL QAEDEADYY CQSYDDSLRG WVFGGGTKLT VLGQPKAAPS VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT ...String:
QSVLTQPPSV SGAPGQRVTI SCTGSASNIG AGYDVHWYQQ VPGAAPKLLI FVYSNRPSGV PDRISGSKSG TSASLAISGL QAEDEADYY CQSYDDSLRG WVFGGGTKLT VLGQPKAAPS VTLFPPSSEE LQANKATLVC LISDFYPGAV TVAWKADSSP V KAGVETTT PSKQSNNKYA ASSYLSLTPE QWKSHRSYSC QVTHEGSTVE KTVAPTECS

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (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: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 96000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

2r5h

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 188743
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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