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- PDB-5w5f: Cryo-EM structure of the T4 tail tube -

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Basic information

Entry
Database: PDB / ID: 5w5f
TitleCryo-EM structure of the T4 tail tube
ComponentsTail tube protein gp19
KeywordsVIRAL PROTEIN / T4 tail tube / dose limit / helical reconstruction
Function / homologysymbiont genome ejection through host cell envelope, contractile tail mechanism / Bacteriophage T4, Gp19, tail tube / T4-like virus tail tube protein gp19 / virus tail, tube / structural molecule activity / Tail tube protein gp19
Function and homology information
Biological speciesEnterobacteria phage T4 sensu lato (virus)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsZheng, W. / Wang, F. / Taylor, N.M. / Guerrero-Ferreira, R.C. / Leiman, P.G. / Egelman, E.H.
Funding support United States, Switzerland, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM122510 United States
Swiss National Science Foundation310030_144243 Switzerland
CitationJournal: Structure / Year: 2017
Title: Refined Cryo-EM Structure of the T4 Tail Tube: Exploring the Lowest Dose Limit.
Authors: Weili Zheng / Fengbin Wang / Nicholas M I Taylor / Ricardo C Guerrero-Ferreira / Petr G Leiman / Edward H Egelman /
Abstract: The bacteriophage T4 contractile tail (containing a tube and sheath) was the first biological assembly reconstructed in three dimensions by electron microscopy at a resolution of ∼35 Å in 1968. A ...The bacteriophage T4 contractile tail (containing a tube and sheath) was the first biological assembly reconstructed in three dimensions by electron microscopy at a resolution of ∼35 Å in 1968. A single-particle reconstruction of the T4 baseplate was able to generate a 4.1 Å resolution map for the first two rings of the tube using the overall baseplate for alignment. We have now reconstructed the T4 tail tube at a resolution of 3.4 Å, more than a 1,000-fold increase in information content for the tube from 1968. We have used legacy software (Spider) to show that we can do better than the typical 2/3 Nyquist frequency. A reasonable map can be generated with only 1.5 electrons/Å using the higher dose images for alignment, but increasing the dose results in a better map, consistent with other reports that electron dose does not represent the main limitation on resolution in cryo-electron microscopy.
History
DepositionJun 15, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Data collection / Category: em_software / pdbx_audit_support
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.2Sep 20, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.name
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Mar 13, 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
A: Tail tube protein gp19
R: Tail tube protein gp19
C: Tail tube protein gp19
B: Tail tube protein gp19
D: Tail tube protein gp19
E: Tail tube protein gp19
F: Tail tube protein gp19
G: Tail tube protein gp19
H: Tail tube protein gp19
I: Tail tube protein gp19
J: Tail tube protein gp19
K: Tail tube protein gp19
L: Tail tube protein gp19
M: Tail tube protein gp19
N: Tail tube protein gp19
O: Tail tube protein gp19
P: Tail tube protein gp19
Q: Tail tube protein gp19


Theoretical massNumber of molelcules
Total (without water)332,63318
Polymers332,63318
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area114990 Å2
ΔGint-495 kcal/mol
Surface area100050 Å2
SymmetryHelical symmetry: (Circular symmetry: 6 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 4 / Rise per n subunits: 40.2 Å / Rotation per n subunits: 18.2 °)

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Components

#1: Protein
Tail tube protein gp19 / Gene product 19 / gp19


Mass: 18479.613 Da / Num. of mol.: 18 / Source method: isolated from a natural source
Source: (natural) Enterobacteria phage T4 sensu lato (virus)
References: UniProt: P13333

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Enterobacteria Phage T4 sensu lato tail tube protein gp19 filament
Type: COMPLEX / Entity ID: all / Source: NATURAL
Molecular weightExperimental value: NO
Source (natural)Organism: Enterobacteria phage T4 sensu lato (virus)
Buffer solutionpH: 8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen 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
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)
EM imaging opticsEnergyfilter name: Gatan image filter
Image scansMovie frames/image: 40

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Processing

SoftwareName: PHENIX / Version: 1.11.1_2575: / Classification: refinement
EM software
IDNameCategory
1EMAN2particle selection
4CTFFIND3CTF correction
7UCSF Chimeramodel fitting
9SPIDERinitial Euler assignment
10SPIDERfinal Euler assignment
12SPIDER3D reconstruction
13PHENIXmodel refinement
14Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 18.2 ° / Axial rise/subunit: 40.2 Å / Axial symmetry: C6
Particle selectionNum. of particles selected: 26320
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 26320 / Symmetry type: HELICAL
Atomic model buildingSpace: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00723994
ELECTRON MICROSCOPYf_angle_d0.78432562
ELECTRON MICROSCOPYf_dihedral_angle_d13.8114112
ELECTRON MICROSCOPYf_chiral_restr0.0573510
ELECTRON MICROSCOPYf_plane_restr0.0064284

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