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- PDB-1tja: Fitting of gp8, gp9, and gp11 into the cryo-EM reconstruction of ... -

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Basic information

Entry
Database: PDB / ID: 1tja
TitleFitting of gp8, gp9, and gp11 into the cryo-EM reconstruction of the bacteriophage T4 contracted tail
Components
  • Baseplate structural protein Gp11
  • Baseplate structural protein Gp8
  • Baseplate structural protein Gp9
KeywordsVIRAL PROTEIN / fitting / docking / cryo-EM / gp8 / gp9 / gp11 / circular symmetry
Function / homology
Function and homology information


virus tail, baseplate / viral tail assembly / viral release from host cell
Similarity search - Function
Baseplate structural protein Gp11 / Bacteriophage T4, Gp11, C-terminal finger domain / Baseplate structural protein Gp11, N-terminal domain superfamily / Baseplate structural protein Gp11 superfamily / Baseplate structural protein Gp11, C-terminal domain / GP11 baseplate wedge protein / Baseplate structural protein Gp9 C-terminal domain superfamily / Bacteriophage T4, Gp8 / Bacteriophage T4, Gp8 superfamily / Bacteriophage T4, Gp8 ...Baseplate structural protein Gp11 / Bacteriophage T4, Gp11, C-terminal finger domain / Baseplate structural protein Gp11, N-terminal domain superfamily / Baseplate structural protein Gp11 superfamily / Baseplate structural protein Gp11, C-terminal domain / GP11 baseplate wedge protein / Baseplate structural protein Gp9 C-terminal domain superfamily / Bacteriophage T4, Gp8 / Bacteriophage T4, Gp8 superfamily / Bacteriophage T4, Gp8 / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / Bacteriophage T4 gp9/10-like protein
Similarity search - Domain/homology
Baseplate protein gp9 / Baseplate wedge protein gp11 / Baseplate wedge protein gp8
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 16 Å
AuthorsLeiman, P.G. / Chipman, P.R. / Kostyuchenko, V.A. / Mesyanzhinov, V.V. / Rossmann, M.G.
CitationJournal: Cell / Year: 2004
Title: Three-dimensional rearrangement of proteins in the tail of bacteriophage T4 on infection of its host.
Authors: Petr G Leiman / Paul R Chipman / Victor A Kostyuchenko / Vadim V Mesyanzhinov / Michael G Rossmann /
Abstract: The contractile tail of bacteriophage T4 undergoes major structural transitions when the virus attaches to the host cell surface. The baseplate at the distal end of the tail changes from a hexagonal ...The contractile tail of bacteriophage T4 undergoes major structural transitions when the virus attaches to the host cell surface. The baseplate at the distal end of the tail changes from a hexagonal to a star shape. This causes the sheath around the tail tube to contract and the tail tube to protrude from the baseplate and pierce the outer cell membrane and the cell wall before reaching the inner cell membrane for subsequent viral DNA injection. Analogously, the T4 tail can be contracted by treatment with 3 M urea. The structure of the T4 contracted tail, including the head-tail joining region, has been determined by cryo-electron microscopy to 17 A resolution. This 1200 A-long, 20 MDa structure has been interpreted in terms of multiple copies of its approximately 20 component proteins. A comparison with the metastable hexagonal baseplate of the mature virus shows that the baseplate proteins move as rigid bodies relative to each other during the structural change.
History
DepositionJun 3, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_image_scans / em_software / Item: _em_software.image_processing_id
Revision 1.4Feb 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 / pdbx_struct_oper_list
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 / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Remark 999SEQUENCE COORDINATES FOR CA ATOMS ONLY WERE SUBMITTED.

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Structure visualization

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Assembly

Deposited unit
A: Baseplate structural protein Gp8
B: Baseplate structural protein Gp8
C: Baseplate structural protein Gp9
D: Baseplate structural protein Gp9
E: Baseplate structural protein Gp9
F: Baseplate structural protein Gp11
G: Baseplate structural protein Gp11
H: Baseplate structural protein Gp11


Theoretical massNumber of molelcules
Total (without water)240,3348
Polymers240,3348
Non-polymers00
Water0
1
A: Baseplate structural protein Gp8
B: Baseplate structural protein Gp8
C: Baseplate structural protein Gp9
D: Baseplate structural protein Gp9
E: Baseplate structural protein Gp9
F: Baseplate structural protein Gp11
G: Baseplate structural protein Gp11
H: Baseplate structural protein Gp11
x 6


Theoretical massNumber of molelcules
Total (without water)1,442,00448
Polymers1,442,00448
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Hermann–Mauguin notation: 6 / Schoenflies symbol: C6 (6 fold cyclic))

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Components

#1: Protein Baseplate structural protein Gp8 / Baseplate wedge protein 8 / Coordinate model: Cα atoms only


Mass: 38041.668 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Strain: D / References: UniProt: P19062
#2: Protein Baseplate structural protein Gp9 / Baseplate wedge protein 9 / Coordinate model: Cα atoms only


Mass: 31024.725 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Strain: D / References: UniProt: P10927
#3: Protein Baseplate structural protein Gp11 / Baseplate wedge protein 11 / Coordinate model: Cα atoms only


Mass: 23725.523 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Strain: D / References: UniProt: P10929

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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

Component
IDNameTypeDetailsParent-ID
1bacteriophage T4Escherichia virus T4VIRUSPhage treated with 3 M urea to contract tails0
2gene product 8dimer1
3gene product 9trimer1
4gene product 11trimer1
Details of virusHost category: BACTERIA(EUBACTERIA) / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Escherichia coli
Buffer solutionName: H2O / pH: 7.5 / Details: H2O
SpecimenConc.: 20 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/T / Date: Jan 6, 2002
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 45000 X / Calibrated magnification: 47000 X / Nominal defocus max: 3400 nm / Nominal defocus min: 500 nm / Cs: 1.4 mm
Specimen holderTemperature: 100 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameVersionCategory
1Situsmodel fitting
2SPIDER23D reconstruction
CTF correctionDetails: CTF correction of each particle
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionMethod: Back projection / Resolution: 16 Å / Num. of particles: 1965 / Nominal pixel size: 4.10442 Å / Actual pixel size: 3.93285 Å / Magnification calibration: Catalase crystals diffraction / Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Details: METHOD--Laplacian filtered real space
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
11N7Z

1n7z

11N7Z1PDBexperimental model
21S2E

1s2e

11S2E2PDBexperimental model
31EL6

1el6

11EL63PDBexperimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms2144 0 0 0 2144

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