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- EMDB-30136: Mature bacteriorphage t7 tail nozzle protein gp12 -

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Basic information

Entry
Database: EMDB / ID: EMD-30136
TitleMature bacteriorphage t7 tail nozzle protein gp12
Map dataMature phage GP12
Sample
  • Complex: Mature bacteriorphage t7 tail nozzle protein gp12
    • Protein or peptide: Tail tubular protein gp12
Keywordsphage / portal / mature / protein / STRUCTURAL PROTEIN
Function / homologyvirus tail, tube / symbiont genome ejection through host cell envelope, short tail mechanism / Tail tubular protein gp12
Function and homology information
Biological speciesEscherichia phage T7 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsChen WY / Xiao H
Funding support2 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31971122
National Natural Science Foundation of China (NSFC)31570742
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-7boy
  • Surface level: 7
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7boy
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30136.png

Downloads & links

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Map

FileDownload / File: emd_30136.map.gz / Format: CCP4 / Size: 166.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMature phage GP12
Voxel sizeX=Y=Z: 1.27 Å
Density
Contour LevelBy AUTHOR: 7.0 / Movie #1: 7
Minimum - Maximum-14.838167 - 33.232543999999997
Average (Standard dev.)0.034514226 (±0.6505986)
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-14.83833.2330.035

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Supplemental data

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Sample components

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Entire : Mature bacteriorphage t7 tail nozzle protein gp12

EntireName: Mature bacteriorphage t7 tail nozzle protein gp12
Components
  • Complex: Mature bacteriorphage t7 tail nozzle protein gp12
    • Protein or peptide: Tail tubular protein gp12

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Supramolecule #1: Mature bacteriorphage t7 tail nozzle protein gp12

SupramoleculeName: Mature bacteriorphage t7 tail nozzle protein gp12 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage T7 (virus)

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Macromolecule #1: Tail tubular protein gp12

MacromoleculeName: Tail tubular protein gp12 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Escherichia phage T7 (virus)
Molecular weightTheoretical: 89.480594 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MALISQSIKN LKGGISQQPD ILRYPDQGSR QVNGWSSETE GLQKRPPLVF LNTLGDNGAL GQAPYIHLIN RDEHEQYYAV FTGSGIRVF DLSGNEKQVR YPNGSNYIKT ANPRNDLRMV TVADYTFIVN RNVVAQKNTK SVNLPNYNPN QDGLINVRGG Q YGRELIVH ...String:
MALISQSIKN LKGGISQQPD ILRYPDQGSR QVNGWSSETE GLQKRPPLVF LNTLGDNGAL GQAPYIHLIN RDEHEQYYAV FTGSGIRVF DLSGNEKQVR YPNGSNYIKT ANPRNDLRMV TVADYTFIVN RNVVAQKNTK SVNLPNYNPN QDGLINVRGG Q YGRELIVH INGKDVAKYK IPDGSQPEHV NNTDAQWLAE ELAKQMRTNL SDWTVNVGQG FIHVTAPSGQ QIDSFTTKDG YA DQLINPV THYAQSFSKL PPNAPNGYMV KIVGDASKSA DQYYVRYDAE RKVWTETLGW NTEDQVLWET MPHALVRAAD GNF DFKWLE WSPKSCGDVD TNPWPSFVGS SINDVFFFRN RLGFLSGENI ILSRTAKYFN FYPASIANLS DDDPIDVAVS TNRI AILKY AVPFSEELLI WSDEAQFVLT ASGTLTSKSV ELNLTTQFDV QDRARPFGIG RNVYFASPRS SFTSIHRYYA VQDVS SVKN AEDITSHVPN YIPNGVFSIC GSGTENFCSV LSHGDPSKIF MYKFLYLNEE LRQQSWSHWD FGENVQVLAC QSISSD MYV ILRNEFNTFL ARISFTKNAI DLQGEPYRAF MDMKIRYTIP SGTYNDDTFT TSIHIPTIYG ANFGRGKITV LEPDGKI TV FEQPTAGWNS DPWLRLSGNL EGRMVYIGFN INFVYEFSKF LIKQTADDGS TSTEDIGRLQ LRRAWVNYEN SGTFDIYV E NQSSNWKYTM AGARLGSNTL RAGRLNLGTG QYRFPVVGNA KFNTVYILSD ETTPLNIIGC GWEGNYLRRS SGI

UniProtKB: Tail tubular protein gp12

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

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Image processing

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

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