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- PDB-1zku: Fitting of the gp9 structure in the EM density of bacteriophage T... -

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Basic information

Entry
Database: PDB / ID: 1zku
TitleFitting of the gp9 structure in the EM density of bacteriophage T4 extended tail
ComponentsBaseplate structural protein Gp9
KeywordsVIRAL PROTEIN / Structural protein
Function / homologyBaseplate structural protein Gp9 C-terminal domain superfamily / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / Bacteriophage T4 gp9/10-like protein / virus tail, baseplate / viral tail assembly / viral release from host cell / Baseplate protein gp9
Function and homology information
Biological speciesEnterobacteria phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 15 Å
AuthorsKostyuchenko, V.A.
CitationJournal: Nat Struct Mol Biol / Year: 2005
Title: The tail structure of bacteriophage T4 and its mechanism of contraction.
Authors: Victor A Kostyuchenko / Paul R Chipman / Petr G Leiman / Fumio Arisaka / Vadim V Mesyanzhinov / Michael G Rossmann /
Abstract: Bacteriophage T4 and related viruses have a contractile tail that serves as an efficient mechanical device for infecting bacteria. A three-dimensional cryo-EM reconstruction of the mature T4 tail ...Bacteriophage T4 and related viruses have a contractile tail that serves as an efficient mechanical device for infecting bacteria. A three-dimensional cryo-EM reconstruction of the mature T4 tail assembly at 15-A resolution shows the hexagonal dome-shaped baseplate, the extended contractile sheath, the long tail fibers attached to the baseplate and the collar formed by six whiskers that interact with the long tail fibers. Comparison with the structure of the contracted tail shows that tail contraction is associated with a substantial rearrangement of the domains within the sheath protein and results in shortening of the sheath to about one-third of its original length. During contraction, the tail tube extends beneath the baseplate by about one-half of its total length and rotates by 345 degrees , allowing it to cross the host's periplasmic space.
History
DepositionMay 4, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 3, 2013Group: Database references
Revision 1.4Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id
Revision 1.5Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

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Assembly

Deposited unit
A: Baseplate structural protein Gp9
B: Baseplate structural protein Gp9
C: Baseplate structural protein Gp9
D: Baseplate structural protein Gp9
E: Baseplate structural protein Gp9
F: Baseplate structural protein Gp9
G: Baseplate structural protein Gp9
H: Baseplate structural protein Gp9
I: Baseplate structural protein Gp9
J: Baseplate structural protein Gp9
K: Baseplate structural protein Gp9
L: Baseplate structural protein Gp9
M: Baseplate structural protein Gp9
N: Baseplate structural protein Gp9
O: Baseplate structural protein Gp9
P: Baseplate structural protein Gp9
Q: Baseplate structural protein Gp9
R: Baseplate structural protein Gp9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)562,73536
Polymers558,44518
Non-polymers4,28918
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Baseplate structural protein Gp9 / Baseplate wedge protein 9


Mass: 31024.725 Da / Num. of mol.: 18
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: 9 / References: UniProt: P10927
#2: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM

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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: T4 / Type: VIRUS
Buffer solutionpH: 7 / Details: H2O
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: COPPER GRID
VitrificationCryogen name: ETHANE / Details: LIQUID ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/T / Date: Jan 10, 2003
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 45000 X / Calibrated magnification: 47000 X / Nominal defocus max: 3.2 nm / Nominal defocus min: 0.8 nm / Cs: 2 mm
Specimen holderTemperature: 100 K
Image recordingFilm or detector model: GENERIC FILM
Image scansNum. digital images: 75
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1SITUS COLORESmodel fitting
2XFITmodel fitting
3SPIDER3D reconstruction
CTF correctionDetails: EACH IMAGE
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionMethod: REAL SPACE SIRT / Resolution: 15 Å / Num. of particles: 3029 / Nominal pixel size: 3.97 Å / Actual pixel size: 3.97 Å / Magnification calibration: 47000 / Details: EM MAP DEPOSITED AS EMD-1126 / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL
Details: REFINEMENT PROTOCOL--MANUAL FITTING FOLLOWED BY REFINEMENT IN COLORES
Atomic model buildingPDB-ID: 1S2E

1s2e


Accession code: 1S2E / Source name: PDB / Type: experimental model
RefinementHighest resolution: 15 Å
Refinement stepCycle: LAST / Highest resolution: 15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms39150 0 270 0 39420

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