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- EMDB-30104: The density map of the dodecameric terminase complex in the prese... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-30104
TitleThe density map of the dodecameric terminase complex in the presence of the ADP-BeF3
Map data
Sample
  • Complex: HSV-1 terminase complex
Biological speciesHuman herpesvirus 1 (Herpes simplex virus type 1)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.6 Å
AuthorsYang YX / Yang P / Wang N / Chen ZH / Zhou ZH / Rao ZH / Wang XX
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, China)31800145 and 31570717 China
CitationJournal: To Be Published
Title: The density map of the dodecameric terminase complex in the presence of the ADP-BeF3
Authors: Yang YX / Yang P / Wang N / Chen ZH / Zhou ZH / Rao ZH / Wang XX
History
DepositionMar 12, 2020-
Header (metadata) releaseJan 13, 2021-
Map releaseJan 13, 2021-
UpdateJan 13, 2021-
Current statusJan 13, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0561
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0561
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30104.png

Downloads & links

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Map

FileDownload / File: emd_30104.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.0561 / Movie #1: 0.0561
Minimum - Maximum-0.14000297 - 0.2631587
Average (Standard dev.)0.0023451804 (±0.01918811)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 187.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z187.200187.200187.200
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.1400.2630.002

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Supplemental data

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Sample components

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Entire : HSV-1 terminase complex

EntireName: HSV-1 terminase complex
Components
  • Complex: HSV-1 terminase complex

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Supramolecule #1: HSV-1 terminase complex

SupramoleculeName: HSV-1 terminase complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Human herpesvirus 1 (Herpes simplex virus type 1)
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)

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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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Average electron dose: 2.0 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 reconstructionResolution.type: BY AUTHOR / Resolution: 4.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 3890
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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