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- PDB-7t4f: Structure of bacteriophage lambda tube protein V in C3 -

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Basic information

Entry
Database: PDB / ID: 7t4f
TitleStructure of bacteriophage lambda tube protein V in C3
ComponentsTail tube protein
KeywordsVIRUS / Phage / Lambda / Siphoviridae / Tail / Tube
Function / homology
Function and homology information


virus tail, tube / symbiont genome ejection through host cell envelope, long flexible tail mechanism / viral tail assembly / host cell cytoplasm
Similarity search - Function
Factor Xa Inhibitor - #40 / Immunoglobulin-like - #1080 / Lambda phage tail tube protein / Lambda phage tail tube protein, TTP / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Factor Xa Inhibitor / Few Secondary Structures / Irregular ...Factor Xa Inhibitor - #40 / Immunoglobulin-like - #1080 / Lambda phage tail tube protein / Lambda phage tail tube protein, TTP / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Factor Xa Inhibitor / Few Secondary Structures / Irregular / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesEscherichia virus Lambda
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.7 Å
AuthorsProkhorov, N.S. / Yang, Q. / Catalano, C.E. / Morais, M.C.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM127365 United States
CitationJournal: To Be Published
Title: Structure of bacteriophage lambda tube protein V in C6
Authors: Prokhorov, N.S. / Yang, Q. / Catalano, C.E. / Morais, M.C.
History
DepositionDec 9, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 14, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tail tube protein
B: Tail tube protein
C: Tail tube protein
D: Tail tube protein


Theoretical massNumber of molelcules
Total (without water)102,8024
Polymers102,8024
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Tail tube protein / TTP / Gene product V / gpV / Major tail protein V


Mass: 25700.582 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia virus Lambda / Gene: V, lambdap13 / Production host: Escherichia coli (E. coli) / References: UniProt: P03733

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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: Escherichia virus Lambda / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Escherichia virus Lambda
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 35.6 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.20rc3_4406refinement
PHENIX1.20rc3_4406refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C3 (3 fold cyclic)
3D reconstructionResolution: 2.7 Å / Resolution method: FSC 3 SIGMA CUT-OFF / Num. of particles: 653608 / Symmetry type: POINT
RefinementCross valid method: NONE

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