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- PDB-7boy: Mature bacteriorphage t7 tail nozzle protein gp12 -

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Basic information

Entry
Database: PDB / ID: 7boy
TitleMature bacteriorphage t7 tail nozzle protein gp12
ComponentsTail tubular protein gp12
KeywordsSTRUCTURAL PROTEIN / phage / portal / mature / 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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsChen, W.Y. / Xiao, H.
Funding support2items
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, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 17, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
s: Tail tubular protein gp12
t: Tail tubular protein gp12
u: Tail tubular protein gp12
v: Tail tubular protein gp12
w: Tail tubular protein gp12
x: Tail tubular protein gp12


Theoretical massNumber of molelcules
Total (without water)536,8846
Polymers536,8846
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area44370 Å2
ΔGint-98 kcal/mol
Surface area172200 Å2

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Components

#1: Protein
Tail tubular protein gp12 / Gene product 12 / Gp12


Mass: 89480.594 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage T7 (virus) / Gene: 12 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P03747

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Mature bacteriorphage t7 tail nozzle protein gp12 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Escherichia phage T7 (virus)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: NITROGEN

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TECNAI ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 24 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55212 / Symmetry type: POINT

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