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- EMDB-30122: Asymmetric reconstrcution of HSV2 C capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-30122
TitleAsymmetric reconstrcution of HSV2 C capsid
Map data
Sample
  • Virus: Human alphaherpesvirus 2
Biological speciesHuman alphaherpesvirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsWang XX / Wang N
CitationJournal: Protein Cell / Year: 2020
Title: Structures of the portal vertex reveal essential protein-protein interactions for Herpesvirus assembly and maturation.
Authors: Nan Wang / Wenyuan Chen / Ling Zhu / Dongjie Zhu / Rui Feng / Jialing Wang / Bin Zhu / Xinzheng Zhang / Xiaoqing Chen / Xianjie Liu / Runbin Yan / Dongyao Ni / Grace Guoying Zhou / Hongrong ...Authors: Nan Wang / Wenyuan Chen / Ling Zhu / Dongjie Zhu / Rui Feng / Jialing Wang / Bin Zhu / Xinzheng Zhang / Xiaoqing Chen / Xianjie Liu / Runbin Yan / Dongyao Ni / Grace Guoying Zhou / Hongrong Liu / Zihe Rao / Xiangxi Wang /
History
DepositionMar 14, 2020-
Header (metadata) releaseFeb 17, 2021-
Map releaseFeb 17, 2021-
UpdateFeb 17, 2021-
Current statusFeb 17, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.74
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4.74
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4.74
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30122.png

Downloads & links

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Map

FileDownload / File: emd_30122.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.76 Å/pix.
x 512 pix.
= 1413.12 Å		2.76 Å/pix.
x 512 pix.
= 1413.12 Å		2.76 Å/pix.
x 512 pix.
= 1413.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.76 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.74 / Movie #1: 4.74
Minimum - Maximum-13.478878 - 19.892067
Average (Standard dev.)0.31781787 (±2.662943)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions512512512
Spacing512512512
CellA=B=C: 1413.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.762.762.76
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z1413.1201413.1201413.120
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-180-180-180
NC/NR/NS512512512
D min/max/mean-13.47919.8920.318

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Supplemental data

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Sample components

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Entire : Human alphaherpesvirus 2

EntireName: Human alphaherpesvirus 2
Components
  • Virus: Human alphaherpesvirus 2

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Supramolecule #1: Human alphaherpesvirus 2

SupramoleculeName: Human alphaherpesvirus 2 / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 10310 / Sci species name: Human alphaherpesvirus 2 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: 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: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 71956
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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