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- EMDB-30135: Mature bacteriorphage t7 tail adaptor protein gp11 -

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Basic information

Entry
Database: EMDB / ID: EMD-30135
TitleMature bacteriorphage t7 tail adaptor protein gp11
Map dataGP11 mature viron particle
Sample
  • Complex: Mature bacteriorphage t7 tail adaptor protein gp11
    • Protein or peptide: Tail adaptor protein gp11
KeywordsPhage / portal / mature / complex / STRUCTURAL PROTEIN
Function / homologyTail tubular protein Gp11 / Tail tubular protein / virus tail, tube / symbiont genome ejection through host cell envelope, short tail mechanism / Tail tubular protein gp11
Function and homology information
Biological speciesEscherichia phage T7 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 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 /
History
DepositionMar 20, 2020-
Header (metadata) releaseMar 17, 2021-
Map releaseMar 17, 2021-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • 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-7box
  • Surface level: 7
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7box
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30135.png

Downloads & links

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Map

FileDownload / File: emd_30135.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGP11 mature viron particle
Projections & slices

Image control

Size
Brightness
Contrast
Others
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

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: 7
Minimum - Maximum-18.459064000000001 - 33.935310000000001
Average (Standard dev.)0.018783214 (±0.5735686)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
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
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-18.45933.9350.019

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Supplemental data

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Sample components

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Entire : Mature bacteriorphage t7 tail adaptor protein gp11

EntireName: Mature bacteriorphage t7 tail adaptor protein gp11
Components
  • Complex: Mature bacteriorphage t7 tail adaptor protein gp11
    • Protein or peptide: Tail adaptor protein gp11

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Supramolecule #1: Mature bacteriorphage t7 tail adaptor protein gp11

SupramoleculeName: Mature bacteriorphage t7 tail adaptor protein gp11 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage T7 (virus)

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Macromolecule #1: Tail adaptor protein gp11

MacromoleculeName: Tail adaptor protein gp11 / type: protein_or_peptide / ID: 1 / Number of copies: 12 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T7 (virus)
Molecular weightTheoretical: 22.30765 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MRSYDMNVET AAELSAVNDI LASIGEPPVS TLEGDANADA ANARRILNKI NRQIQSRGWT FNIEEGITLL PDVYSNLIVY SDDYLSLMS TSGQSIYVNR GGYVYDRTSQ SDRFDSGITV NIIRLRDYDE MPECFRYWIV TKASRQFNNR FFGAPEVEGV L QEEEDEAR ...String:
MRSYDMNVET AAELSAVNDI LASIGEPPVS TLEGDANADA ANARRILNKI NRQIQSRGWT FNIEEGITLL PDVYSNLIVY SDDYLSLMS TSGQSIYVNR GGYVYDRTSQ SDRFDSGITV NIIRLRDYDE MPECFRYWIV TKASRQFNNR FFGAPEVEGV L QEEEDEAR RLCMEYEMDY GGYNMLDGDA FTSGLLTR

UniProtKB: Tail tubular protein gp11

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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 II (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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55212
Initial angle assignmentType: COMMON LINE
Final angle assignmentType: PROJECTION MATCHING

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