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- EMDB-0793: The cryo-EM map of virus like particle of human papillomavirus ty... -

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Basic information

Entry
Database: EMDB / ID: EMD-0793
TitleThe cryo-EM map of virus like particle of human papillomavirus type 16 in I3 symmetry
Map datahuman papillomavirus 16
Sample
  • Virus: Human papillomavirus type 16
Biological speciesHuman papillomavirus type 16
Methodsingle particle reconstruction / cryo EM / Resolution: 4.9 Å
AuthorsZhu Y / Tai L / Sun F
CitationJournal: To Be Published
Title: A triple-helix region of human collagen type II inhibits the infection of human papillomavirus: structures and mechanisms
Authors: Zhu Y / Hua C / Tai L / Ye S / Zhang R / Sun F / Lu L / Jiang S
History
DepositionSep 25, 2019-
Header (metadata) releaseSep 30, 2020-
Map releaseSep 30, 2020-
UpdateSep 30, 2020-
Current statusSep 30, 2020Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00241
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.00241
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0793.png

Downloads & links

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Map

FileDownload / File: emd_0793.map.gz / Format: CCP4 / Size: 1.4 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman papillomavirus 16
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.32 Å/pix.
x 720 pix.
= 950.4 Å		1.32 Å/pix.
x 720 pix.
= 950.4 Å		1.32 Å/pix.
x 720 pix.
= 950.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00241 / Movie #1: 0.00241
Minimum - Maximum-0.008729978 - 0.019354885
Average (Standard dev.)0.00014855931 (±0.0009793987)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions720720720
Spacing720720720
CellA=B=C: 950.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.321.321.32
M x/y/z720720720
origin x/y/z0.0000.0000.000
length x/y/z950.400950.400950.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS720720720
D min/max/mean-0.0090.0190.000

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Supplemental data

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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

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Supramolecule #1: Human papillomavirus type 16

SupramoleculeName: Human papillomavirus type 16 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 333760 / Sci species name: Human papillomavirus type 16 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SUBSPECIES / Virus enveloped: No / Virus empty: Yes
Host systemOrganism: Homo sapiens (human)

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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: 7.5
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k 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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2980
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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