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- EMDB-66072: Cryo-EM structure of human papillomavirus type 45 -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-66072
TitleCryo-EM structure of human papillomavirus type 45
Map data
Sample
  • Virus: human papillomavirus 45
    • Protein or peptide: Major capsid protein L1
KeywordsHuman papillomavirus / Cryo-EM / STRUCTURAL PROTEIN / VIRAL PROTEIN
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 45
Methodsingle particle reconstruction / cryo EM / Resolution: 3.95 Å
AuthorsJiang Y / Sun H / Zheng Q / Li S / Xia N
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Cryo-EM structure of human papillomavirus type 45
Authors: Jiang Y / Sun H / Zheng Q / Li S
History
DepositionSep 2, 2025-
Header (metadata) releaseMar 4, 2026-
Map releaseMar 4, 2026-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66072.png

Downloads & links

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Map

FileDownload / File: emd_66072.map.gz / Format: CCP4 / Size: 1.7 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.12 Å/pix.
x 768 pix.
= 860.16 Å		1.12 Å/pix.
x 768 pix.
= 860.16 Å		1.12 Å/pix.
x 768 pix.
= 860.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.12 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.06990555 - 2.1827834
Average (Standard dev.)0.0067076045 (±0.056624033)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions768768768
Spacing768768768
CellA=B=C: 860.16003 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66072_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66072_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 : human papillomavirus 45

EntireName: human papillomavirus 45
Components
  • Virus: human papillomavirus 45
    • Protein or peptide: Major capsid protein L1

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Supramolecule #1: human papillomavirus 45

SupramoleculeName: human papillomavirus 45 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10593 / Sci species name: human papillomavirus 45 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Major capsid protein L1

MacromoleculeName: Major capsid protein L1 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: human papillomavirus 45
Molecular weightTheoretical: 57.379891 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MALWRPSDST VYLPPPSVAR VVSTDDYVSR TSIFYHAGSS RLLTVGNPYF RVVPNGAGNK QAVPKVSAYQ YRVFRVALPD PNKFGLPDS TIYNPETQRL VWACVGMEIG RGQPLGIGLS GHPFYNKLDD TESAHAATAV ITQDVRDNVS VDYKQTQLCI L GCVPAIGE ...String:
MALWRPSDST VYLPPPSVAR VVSTDDYVSR TSIFYHAGSS RLLTVGNPYF RVVPNGAGNK QAVPKVSAYQ YRVFRVALPD PNKFGLPDS TIYNPETQRL VWACVGMEIG RGQPLGIGLS GHPFYNKLDD TESAHAATAV ITQDVRDNVS VDYKQTQLCI L GCVPAIGE HWAKGTLCKP AQLQPGDCPP LELKNTIIED GDMVDTGYGA MDFSTLQDTK CEVPLDICQS ICKYPDYLQM SA DPYGDSM FFCLRREQLF ARHFWNRAGV MGDTVPTDLY IKGTSANMRE TPGSCVYSPS PSGSIITSDS QLFNKPYWLH KAQ GHNNGI CWHNQLFVTV VDTTRSTNLT LCASTQNPVP STYDPTKFKQ YSRHVEEYDL QFIFQLCTIT LTAEVMSYIH SMNS SILEN WNFGVPPPPT TSLVDTYRFV QSVAVTCQKD TTPPEKQDPY DKLKFWTVDL KEKFSSDLDQ YPLGRKFLVQ AGLRR RPTI GPRKRPAAST STASTASRPA KRVRIRSKK

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

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Electron microscopy

MicroscopeFEI TECNAI F30
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 32.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.95 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 30327
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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