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

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ID or keywords:

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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: To Be Published
Title: HPV16 neutralizing monoclonal antibodies show evidence for common developmental pathways and public epitopes
Authors: Carter JJ / Hurlburt NK
History
DepositionDec 18, 2024-
Header (metadata) releaseAug 20, 2025-
Map releaseAug 20, 2025-
UpdateAug 20, 2025-
Current statusAug 20, 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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