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- EMDB-70164: Subparticle map of HPV16 hexavalent capsomer -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-70164
TitleSubparticle map of HPV16 hexavalent capsomer
Map dataHPV16 hexavalent capsomer subparticle
Sample
  • Virus: Human papillomavirus 16
    • Protein or peptide: HPV16 L1
KeywordsHPV / heparin / VIRUS
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
Methodsingle particle reconstruction / cryo EM / Resolution: 1.92 Å
AuthorsLangley CH / Hafenstein SL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)7R01AI134910-04 United States
CitationJournal: To Be Published
Title: Atomic resolution structure of human papillomavirus bound to heparin
Authors: Langley CH / Hafenstein SL
History
DepositionApr 11, 2025-
Header (metadata) releaseMay 6, 2026-
Map releaseMay 6, 2026-
UpdateMay 6, 2026-
Current statusMay 6, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70164.png

Downloads & links

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Map

FileDownload / File: emd_70164.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHPV16 hexavalent capsomer subparticle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.52 Å/pix.
x 760 pix.
= 392.92 Å		0.52 Å/pix.
x 760 pix.
= 392.92 Å		0.52 Å/pix.
x 760 pix.
= 392.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.517 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.65
Minimum - Maximum-4.8219275 - 7.9058557
Average (Standard dev.)0.0015560118 (±0.15171844)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions760760760
Spacing760760760
CellA=B=C: 392.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half map A of HPV16 hexavalent capsomer subparticle

Fileemd_70164_half_map_1.map
AnnotationHalf map A of HPV16 hexavalent capsomer subparticle
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B of HPV16 hexavalent capsomer subparticle

Fileemd_70164_half_map_2.map
AnnotationHalf map B of HPV16 hexavalent capsomer subparticle
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human papillomavirus 16

EntireName: Human papillomavirus 16
Components
  • Virus: Human papillomavirus 16
    • Protein or peptide: HPV16 L1

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Supramolecule #1: Human papillomavirus 16

SupramoleculeName: Human papillomavirus 16 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 333760 / Sci species name: Human papillomavirus 16 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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Macromolecule #1: HPV16 L1

MacromoleculeName: HPV16 L1 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Human papillomavirus 16
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSLWLPSEAT VYLPPVPVSK VVSTDEYVAR TNIYYHAGTS RLLAVGHPYF PIKKPNNNKI LVPKVSGLQY RVFRIHLPDP NKFGFPDTSF YNPDTQRLVW ACVGVEVGRG QPLGVGISGH PLLNKLDDTE NASAYAANAG VDNRECISMD YKQTQLCLIG CKPPIGEHWG ...String:
MSLWLPSEAT VYLPPVPVSK VVSTDEYVAR TNIYYHAGTS RLLAVGHPYF PIKKPNNNKI LVPKVSGLQY RVFRIHLPDP NKFGFPDTSF YNPDTQRLVW ACVGVEVGRG QPLGVGISGH PLLNKLDDTE NASAYAANAG VDNRECISMD YKQTQLCLIG CKPPIGEHWG KGSPCTNVAV NPGDCPPLEL INTVIQDGDM VDTGFGAMDF TTLQANKSEV PLDICTSICK YPDYIKMVSE PYGDSLFFYL RREQMFVRHL FNRAGAVGEN VPDDLYIKGS GSTANLASSN YFPTPSGSMV TSDAQIFNKP YWLQRAQGHN NGICWGNQLF VTVVDTTRST NMSLCAAIST SETTYKNTNF KEYLRHGEEY DLQFIFQLCK ITLTADVMTY IHSMNSTILE DWNFGLQPPP GGTLEDTYRF VTSQAIACQK HTPPAPKEDP LKKYTFWEVN LKEKFSADLD QFPLGRKFLL QAGLKAKPKF TLGKRKATPT TSSTSTTAKR KKRKL

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 / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 39.75 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
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: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 1.92 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2649540
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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