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- EMDB-30134: GP8 of Mature Bacteriophage T7 -

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Basic information

Database: EMDB / ID: EMD-30134
TitleGP8 of Mature Bacteriophage T7
Map data
SampleMature GP8:
Portal protein
Function / homologyHead-to-tail connector protein, podovirus-type / Portal protein, Caudovirales / Bacteriophage head to tail connecting protein / viral portal complex / viral genome ejection through host cell envelope, short tail mechanism / viral DNA genome packaging / Portal protein
Function and homology information
Biological speciesEscherichia phage T7 (bacteriophage)
Methodsingle particle reconstruction / Resolution: 3.6 Å
AuthorsChen WY / Xiao H
Funding support China, 2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971122 China
National Natural Science Foundation of China (NSFC)31570742 China
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 19, 2020-
Header (metadata) releaseMar 17, 2021-
Map releaseMar 17, 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
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  • Surface view colored by cylindrical radius
  • Surface level: 7
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7bou
  • Surface level: 7
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7bou
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
Supplemental images

Downloads & links


FileDownload / File: emd_30134.map.gz / Format: CCP4 / Size: 166.4 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 352 pix.
= 447.04 Å
1.27 Å/pix.
x 352 pix.
= 447.04 Å
1.27 Å/pix.
x 352 pix.
= 447.04 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-17.02163 - 33.935318
Average (Standard dev.)0.038269434 (±0.73607147)
SymmetrySpace group: 1


Map geometry
Axis orderXYZ
CellA=B=C: 447.03998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.271.271.27
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z447.040447.040447.040
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-17.02233.9350.038

Supplemental data

Sample components

Entire Mature GP8

EntireName: Mature GP8 / Number of components: 2

Component #1: protein, Mature GP8

ProteinName: Mature GP8 / Recombinant expression: No
SourceSpecies: Escherichia phage T7 (bacteriophage)

Component #2: protein, Portal protein

ProteinName: Portal protein / Number of Copies: 12 / Recombinant expression: No
MassTheoretical: 59.173984 kDa
SourceSpecies: Escherichia phage T7 (bacteriophage)
Source (engineered)Expression System: Escherichia coli BL21 (bacteria)

Experimental details

Sample preparation

SpecimenSpecimen state: Particle
Sample solutionpH: 7
VitrificationCryogen name: NONE

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
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 50000
3D reconstructionResolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF

Atomic model buiding

Output model

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