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- EMDB-30142: phage t7 capsid-II -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-30142
Titlephage t7 capsid-II
Map data
Sample
  • Complex: phage t7 capsid-II
    • Other: bacteriophage T7 capsid II
Biological speciesEscherichia phage T7 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 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 /
History
DepositionMar 21, 2020-
Header (metadata) releaseMar 17, 2021-
Map releaseMar 17, 2021-
UpdateMar 17, 2021-
Current statusMar 17, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 15
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 15
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30142.png

Downloads & links

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Map

FileDownload / File: emd_30142.map.gz / Format: CCP4 / Size: 600.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.27 Å/pix.
x 540 pix.
= 685.8 Å		1.27 Å/pix.
x 540 pix.
= 685.8 Å		1.27 Å/pix.
x 540 pix.
= 685.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.27 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 7.0 / Movie #1: 15
Minimum - Maximum-20.00159 - 56.2649
Average (Standard dev.)0.0077179396 (±5.6805844)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-270-270-270
Dimensions540540540
Spacing540540540
CellA=B=C: 685.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.271.271.27
M x/y/z540540540
origin x/y/z0.0000.0000.000
length x/y/z685.800685.800685.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-270-270-270
NC/NR/NS540540540
D min/max/mean-20.00256.2650.008

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Supplemental data

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Sample components

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Entire : phage t7 capsid-II

EntireName: phage t7 capsid-II
Components
  • Complex: phage t7 capsid-II
    • Other: bacteriophage T7 capsid II

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Supramolecule #1: phage t7 capsid-II

SupramoleculeName: phage t7 capsid-II / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage T7 (virus)
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria) / Recombinant strain: BL21

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Macromolecule #1: bacteriophage T7 capsid II

MacromoleculeName: bacteriophage T7 capsid II / type: other / ID: 1 / Classification: other
SequenceString: MASMTGGQQM GTNQGKGVVA AGDKLALFLK VFGGEVLTAF ARTSVTTSRH MVRSISSGKS AQFPVLGRTQ AAYLAPGENL DDKRKDIKHT EKVITIDGLL TADVLIYDIE DAMNHYDVRS EYTSQLGESL AMAADGAVLA EIAGLCNVES KYNENIEGLG TATVIETTQN ...String:
MASMTGGQQM GTNQGKGVVA AGDKLALFLK VFGGEVLTAF ARTSVTTSRH MVRSISSGKS AQFPVLGRTQ AAYLAPGENL DDKRKDIKHT EKVITIDGLL TADVLIYDIE DAMNHYDVRS EYTSQLGESL AMAADGAVLA EIAGLCNVES KYNENIEGLG TATVIETTQN KAALTDQVAL GKEIIAALTK ARAALTKNYV PAADRVFYCD PDSYSAILAA LMPNAANYAA LIDPEKGSIR NVMGFEVVEV PHLTAGGAGT AREGTTGQKH VFPANKGEGN VKVAKDNVIG LFMHRSAVGT VKLRDLALER ARRANFQADQ IIAKYAMGHG GLRPEAAGAV VFKVE

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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
VitrificationCryogen name: NITROGEN

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Electron microscopy

MicroscopeFEI TECNAI ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 24.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 84318
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING

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