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- EMDB-49960: Atomic resolution cryoEM structure of HPV16 bound to heparin -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-49960
TitleAtomic resolution cryoEM structure of HPV16 bound to heparin
Map dataComposite map generated from two subparticles, one copy of the pentavalent subparticle and six copies of the hexavalent subparticle.
Sample
  • Virus: Human papillomavirus 16
    • Protein or peptide: Major capsid protein L1
  • Ligand: MAGNESIUM ION
  • Ligand: water
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: 1.9 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 1, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_49960.png

Downloads & links

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Map

FileDownload / File: emd_49960.map.gz / Format: CCP4 / Size: 1.6 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map generated from two subparticles, one copy of the pentavalent subparticle and six copies of the hexavalent 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: 0.9
Minimum - Maximum-0.2735523 - 7.9058557
Average (Standard dev.)0.12660898 (±0.21094131)
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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Sample components

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Entire : Human papillomavirus 16

EntireName: Human papillomavirus 16
Components
  • Virus: Human papillomavirus 16
    • Protein or peptide: Major capsid protein L1
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: Human papillomavirus 16

SupramoleculeName: Human papillomavirus 16 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1 / 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: 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 16
Molecular weightTheoretical: 54.160387 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MSLWLPSEAT VYLPPVPVSK VVSTDEYVAR TNIYYHAGTS RLLAVGHPYF PIKKPNNNKI LVPKVSGLQY RVFRIHLPDP NKFGFPDTS FYNPDTQRLV WACVGVEVGR GQPLGVGISG HPLLNKLDDT ENASAYAANA GVDNRECISM DYKQTQLCLI G CKPPIGEH ...String:
MSLWLPSEAT VYLPPVPVSK VVSTDEYVAR TNIYYHAGTS RLLAVGHPYF PIKKPNNNKI LVPKVSGLQY RVFRIHLPDP NKFGFPDTS FYNPDTQRLV WACVGVEVGR GQPLGVGISG HPLLNKLDDT ENASAYAANA GVDNRECISM DYKQTQLCLI G CKPPIGEH WGKGSPCTNV AVNPGDCPPL ELINTVIQDG DMVDTGFGAM DFTTLQANKS EVPLDICTSI CKYPDYIKMV SE PYGDSLF FYLRREQMFV RHLFNRAGAV GENVPDDLYI KGSGSTANLA SSNYFPTPSG SMVTSDAQIF NKPYWLQRAQ GHN NGICWG NQLFVTVVDT TRSTNMSLCA AISTSETTYK NTNFKEYLRH GEEYDLQFIF QLCKITLTAD VMTYIHSMNS TILE DWNFG LQPPPGGTLE DTYRFVTSQA IACQKHTPPA PKEDPLKKYT FWEVNLKEKF SADLDQFPLG RKFLLQAGLK AKPKF TLGK R

UniProtKB: Major capsid protein L1

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 189 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 1369 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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 reconstructionResolution.type: BY AUTHOR / Resolution: 1.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44159
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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