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- EMDB-9920: The cryo-em structure of HPV18 VLP -

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Basic information

Entry
Database: EMDB / ID: EMD-9920
TitleThe cryo-em structure of HPV18 VLP
Map data
SampleHuman papillomavirus:
virus
Biological speciesHuman papillomavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 11.5 Å
AuthorsLi S / Zheng Q
CitationJournal: To Be Published
Title: The cryo-em structure of HPV18 VLP
Authors: Li S / Zheng Q
DateDeposition: Jun 1, 2019 / Header (metadata) release: Jul 10, 2019 / Map release: Jul 10, 2019 / Update: Jul 10, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 50
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 50
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9920.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 801 pix.
= 903.528 Å
1.13 Å/pix.
x 801 pix.
= 903.528 Å
1.13 Å/pix.
x 801 pix.
= 903.528 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.128 Å
Density
Contour LevelBy AUTHOR: 50.0 / Movie #1: 50
Minimum - Maximum-251.424589999999995 - 324.410129999999981
Average (Standard dev.)0.24942526 (±33.923729999999999)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-400-400-400
Dimensions801801801
Spacing801801801
CellA=B=C: 903.528 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.1281.1281.128
M x/y/z801801801
origin x/y/z0.0000.0000.000
length x/y/z903.528903.528903.528
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ480480480
MAP C/R/S123
start NC/NR/NS-400-400-400
NC/NR/NS801801801
D min/max/mean-251.425324.4100.249

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Supplemental data

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Sample components

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Entire Human papillomavirus

EntireName: Human papillomavirus / Number of components: 1

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Component #1: virus, Human papillomavirus

VirusName: Human papillomavirusPapillomaviridae / Class: VIRUS-LIKE PARTICLE / Empty: Yes / Enveloped: No / Isolate: OTHER
SpeciesSpecies: Human papillomavirus
Source (engineered)Expression System: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/mL / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F30
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 901
3D reconstructionResolution: 11.5 Å / Resolution method: FSC 0.143 CUT-OFF

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