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- EMDB-48346: B25M05 Fab bound to HPV16 L1 pentamer -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-48346
TitleB25M05 Fab bound to HPV16 L1 pentamer
Map dataSharpened map of B25M05 bound to HPV16 L1 pentamer
Sample
  • Complex: HPV16 L1 pentamer bound to B25M05 Fab
    • Protein or peptide: Major capsid protein L1
    • Protein or peptide: B25M05 Fab Heavy Chain
    • Protein or peptide: B25M05 Fab 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: 2.9 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_48346.png

Downloads & links

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Map

FileDownload / File: emd_48346.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of B25M05 bound to HPV16 L1 pentamer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 224 pix.
= 251.328 Å		1.12 Å/pix.
x 224 pix.
= 251.328 Å		1.12 Å/pix.
x 224 pix.
= 251.328 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.122 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.7
Minimum - Maximum-3.7184224 - 7.435181
Average (Standard dev.)0.004965778 (±0.28962582)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 251.328 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map B

Fileemd_48346_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_48346_half_map_2.map
AnnotationHalf map A
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 B25M05 Fab

EntireName: HPV16 L1 pentamer bound to B25M05 Fab
Components
  • Complex: HPV16 L1 pentamer bound to B25M05 Fab
    • Protein or peptide: Major capsid protein L1
    • Protein or peptide: B25M05 Fab Heavy Chain
    • Protein or peptide: B25M05 Fab Light Chain

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Supramolecule #1: HPV16 L1 pentamer bound to B25M05 Fab

SupramoleculeName: HPV16 L1 pentamer bound to B25M05 Fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Human papillomavirus 16
Molecular weightTheoretical: 280 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: 47.534574 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 VQPGDCPP ...String:
AVVSTDEYVA RTNIYYHAGT SRLLAVGHPY FPIKKPNNNK ILVPKVSGLQ YRVFRIHLPD PNKFGFPDTS FYNPDTQRLV WACVGVEVG RGQPLGVGIS GHPLLNKLDD TENASAYAAN AGVDNRECIS MDYKQTQLCL IGCKPPIGEH WGKGSPCTNV A VQPGDCPP LELINTVIQD GDMVDTGFGA MDFTTLQANK SEVPLDICTS ICKYPDYIKM VSEPYGDSLF FYLRREQMFV RH LFNRAGT VGENVPDDLY IKGSGSTANL ASSNYFPTPS GSMVTSDAQI FNKPYWLQRA QGHNNGICWG NQLFVTVVDT TRS TNMSLC AAISTSETTY KNTNFKEYLR HGEEYDLQFI FQLCKITLTA DVMTYIHSMN STILEDWNGG SGGEDPLKKY TFWE VNLKE KFSADLDQFP LGRKFLLQLG L

UniProtKB: Major capsid protein L1

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Macromolecule #2: B25M05 Fab Heavy Chain

MacromoleculeName: B25M05 Fab Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 25.864021 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLQQWGAG LLKPSETLSL TCAVNGGSFS IYYWSWIRQP PGKGLDWIGE INQSGSTNYN PSLKSRVTMS VDTSKSQFSL RMTSVTAAD TAIYYCARAP RIRWGSYRLK QTNFDSWGQG TLVTVSSRST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN ...String:
QVQLQQWGAG LLKPSETLSL TCAVNGGSFS IYYWSWIRQP PGKGLDWIGE INQSGSTNYN PSLKSRVTMS VDTSKSQFSL RMTSVTAAD TAIYYCARAP RIRWGSYRLK QTNFDSWGQG TLVTVSSRST KGPSVFPLAP SSKSTSGGTA ALGCLVKDYF P EPVTVSWN SGALTSGVHT FPAVLQSSGL YSLSSVVTVP SSSLGTQTYI CNVNHKPSNT KVDKRVEPKS CDKTHHHHHH

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Macromolecule #3: B25M05 Fab Light Chain

MacromoleculeName: B25M05 Fab Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 22.902104 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QSALTQPASV SGSPGQSITI SCTGTSNDVG DYDYVSWYQL HPGKAPKLLI FDVSRRPSGV SDRFSGSKSG DTASLTISGL QAEDEADYY CSSYTGSSTY VFGTGTKVSV LSQPKANPTV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP ...String:
QSALTQPASV SGSPGQSITI SCTGTSNDVG DYDYVSWYQL HPGKAPKLLI FDVSRRPSGV SDRFSGSKSG DTASLTISGL QAEDEADYY CSSYTGSSTY VFGTGTKVSV LSQPKANPTV TLFPPSSEEL QANKATLVCL ISDFYPGAVT VAWKADSSPV K AGVETTTP SKQSNNKYAA SSYLSLTPEQ WKSHRSYSCQ VTHEGSTVEK TVAPTECS

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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

Concentration0.6 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.8 µm / Nominal magnification: 36000

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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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 83711
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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