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- EMDB-6918: CryoEM structure of HPV52 L1-only VLP -

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Basic information

Entry
Database: EMDB / ID: 6918
TitleCryoEM structure of HPV52 L1-only VLP
Map data
SampleHPV52 L1-only VLP:
virus
SourceHuman papillomavirus type 52
Methodsingle particle reconstruction / cryo EM / 7 Å resolution
AuthorsLi SW / Li ZH / He MZ
CitationJournal: Emerg Microbes Infect / Year: 2018
Title: N-terminal truncations on L1 proteins of human papillomaviruses promote their soluble expression in Escherichia coli and self-assembly in vitro.
Authors: Minxi Wei / Daning Wang / Zhihai Li / Shuo Song / Xianglin Kong / Xiaobing Mo / Yurou Yang / Maozhou He / Zhongyi Li / Bo Huang / Zhijie Lin / Huirong Pan / Qingbing Zheng / Hai Yu / Ying Gu / Jun Zhang / Shaowei Li / Ningshao Xia
DateDeposition: Feb 24, 2018 / Header (metadata) release: Oct 10, 2018 / Map release: Oct 10, 2018 / Last update: Oct 10, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6918.map.gz (map file in CCP4 format, 275685 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
410 pix
2.22 Å/pix.
= 910.2 Å
410 pix
2.22 Å/pix.
= 910.2 Å
410 pix
2.22 Å/pix.
= 910.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.22 Å
Density
Contour Level:2.0 (by author), 2 (movie #1):
Minimum - Maximum-7.5382047 - 12.818773999999999
Average (Standard dev.)0.000000002334276 (0.99999994)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions410410410
Origin-205.0-205.0-205.0
Limit204.0204.0204.0
Spacing410410410
CellA=B=C: 910.2 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.222.222.22
M x/y/z410410410
origin x/y/z0.0000.0000.000
length x/y/z910.200910.200910.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-205-205-205
NC/NR/NS410410410
D min/max/mean-7.53812.8190.000

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Supplemental data

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Sample components

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Entire HPV52 L1-only VLP

EntireName: HPV52 L1-only VLP / Number of components: 1

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Component #1: virus, Human papillomavirus type 52

VirusName: Human papillomavirus type 52 / Class: VIRUS-LIKE PARTICLE / Empty: Yes / Enveloped: No / Isolate: OTHER
SpeciesSpecies: Human papillomavirus type 52
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 6.5
VitrificationCryogen name: ETHANE

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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: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON I (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 6100
3D reconstructionResolution: 7 Å / Resolution method: FSC 0.5 CUT-OFF

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