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- EMDB-23081: High resolution cryo EM analysis of HPV16 identifies minor struct... -

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Basic information

Entry
Database: EMDB / ID: EMD-23081
TitleHigh resolution cryo EM analysis of HPV16 identifies minor structural protein L2 and describes capsid flexibility
Map dataHPV16 quasivirus capsid. Recombined map from pentavalent and hexavalent subvolume refinements.
Sample
  • Virus: Human papillomavirus type 16
    • Protein or peptide: Major capsid protein L1
KeywordsHPV16 / quasivirus / L1 / capsomer / subparticle / 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 type 16
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsHartmann SR / Goetschius DJ
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the Director United States
CitationJournal: Sci Rep / Year: 2021
Title: High resolution cryo EM analysis of HPV16 identifies minor structural protein L2 and describes capsid flexibility.
Authors: Daniel J Goetschius / Samantha R Hartmann / Suriyasri Subramanian / Carol M Bator / Neil D Christensen / Susan L Hafenstein /
Abstract: Human papillomavirus (HPV) is a significant health burden and leading cause of virus-induced cancers. HPV is epitheliotropic and its replication is tightly associated with terminal keratinocyte ...Human papillomavirus (HPV) is a significant health burden and leading cause of virus-induced cancers. HPV is epitheliotropic and its replication is tightly associated with terminal keratinocyte differentiation making production and purification of high titer virus preparations for research problematic, therefore alternative HPV production methods have been developed for virological and structural studies. In this study we use HPV16 quasivirus, composed of HPV16 L1/L2 capsid proteins with a packaged cottontail rabbit papillomavirus genome. We have achieved the first high resolution, 3.1 Å, structure of HPV16 by using a local subvolume refinement approach. The high resolution enabled us to build L1 unambiguously and identify L2 protein strands. The L2 density is incorporated adjacent to conserved L1 residues on the interior of the capsid. Further interpretation with our own software for Icosahedral Subvolume Extraction and Correlated Classification revealed flexibility, on the whole-particle level through diameter analysis and local movement with inter-capsomer analysis. Inter-capsomer expansion or contraction, governed by the connecting arms, showed no bias in the magnitude or direction of capsomer movement. We propose that papillomavirus capsids are dynamic and capsomers move as rigid bodies connected by flexible linkers. The resulting virus structure will provide a framework for continuing biochemical, genetic and biophysical research for papillomaviruses. Furthermore, our approach has allowed insight into the resolution barrier that has previously been a limitation in papillomavirus structural studies.
History
DepositionDec 10, 2020-
Header (metadata) releaseFeb 24, 2021-
Map releaseFeb 24, 2021-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7kzf
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7kzf
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23081.png

Downloads & links

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Map

FileDownload / File: emd_23081.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHPV16 quasivirus capsid. Recombined map from pentavalent and hexavalent subvolume refinements.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 600 pix.
= 660. Å		1.1 Å/pix.
x 600 pix.
= 660. Å		1.1 Å/pix.
x 600 pix.
= 660. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.5 / Movie #1: 2.5
Minimum - Maximum-10.47067 - 17.655211999999999
Average (Standard dev.)0.000000002508377 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-300-300-300
Dimensions600600600
Spacing600600600
CellA=B=C: 660.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z660.000660.000660.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-300-300-300
NC/NR/NS600600600
D min/max/mean-10.47117.6550.000

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Supplemental data

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Additional map: HPV16 quasivirus pentavalent capsomer subvolume refinement.

Fileemd_23081_additional_1.map
AnnotationHPV16 quasivirus pentavalent capsomer subvolume refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: HPV16 quasivirus hexavalent capsomer subvolume refinement.

Fileemd_23081_additional_2.map
AnnotationHPV16 quasivirus hexavalent capsomer subvolume refinement.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: HPV16 quasivirus icosahedral refinement from which pentavalent and...

Fileemd_23081_additional_3.map
AnnotationHPV16 quasivirus icosahedral refinement from which pentavalent and hexavalent subvolumes were extracted.
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 type 16

EntireName: Human papillomavirus type 16
Components
  • Virus: Human papillomavirus type 16
    • Protein or peptide: Major capsid protein L1

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Supramolecule #1: Human papillomavirus type 16

SupramoleculeName: Human papillomavirus type 16 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 333760 / Sci species name: Human papillomavirus type 16 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No

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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 type 16
Molecular weightTheoretical: 56.098617 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 RKATPTTSST STTAKRKKR

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 / Component - Concentration: 1.0 X / Component - Name: PBS
GridPretreatment - Type: GLOW DISCHARGE / Details: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 10143 / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 202705
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 181299
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER

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