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- EMDB-30145: Phage t7 capsid-II core -

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Basic information

Database: EMDB / ID: EMD-30145
TitlePhage t7 capsid-II core
Map data
SamplePhage t7 capsid-II core
Biological speciesEscherichia phage T7 (bacteriophage)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.9 Å
AuthorsChen WY / Xiao H
Funding support1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)
CitationJournal: Protein Cell / Year: 2020
Title: Structural changes of a bacteriophage upon DNA packaging and maturation.
Authors: Wenyuan Chen / Hao Xiao / Xurong Wang / Shuanglin Song / Zhen Han / Xiaowu Li / Fan Yang / Li Wang / Jingdong Song / Hongrong Liu / Lingpeng Cheng /
DepositionMar 21, 2020-
Header (metadata) releaseJan 27, 2021-
Map releaseJan 27, 2021-
UpdateMar 17, 2021-
Current statusMar 17, 2021Processing site: PDBj / Status: Released

Structure visualization

  • Surface view with section colored by density value
  • Surface level: 7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 7
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


FileDownload / File: emd_30145.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
1.27 Å/pix.
x 320 pix.
= 406.4 Å
1.27 Å/pix.
x 320 pix.
= 406.4 Å
1.27 Å/pix.
x 320 pix.
= 406.4 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.27 Å
Contour LevelBy AUTHOR: 7.0 / Movie #1: 7
Minimum - Maximum-12.747104 - 17.694763
Average (Standard dev.)-0.3008876 (±1.1827341)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
CellA=B=C: 406.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.271.271.27
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z406.400406.400406.400
MAP C/R/S123
start NC/NR/NS-252-252-252
D min/max/mean-12.74717.695-0.301

Supplemental data

Sample components

Entire Phage t7 capsid-II core

EntireName: Phage t7 capsid-II core / Number of components: 1

Component #1: protein, Phage t7 capsid-II core

ProteinName: Phage t7 capsid-II core / Recombinant expression: No
SourceSpecies: Escherichia phage T7 (bacteriophage)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

Experimental details

Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7
VitrificationCryogen name: NITROGEN

Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 24 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 69964
3D reconstructionResolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF

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