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- PDB-1pdi: Fitting of the C-terminal part of the short tail fibers into the ... -

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Basic information

Entry
Database: PDB / ID: 1pdi
TitleFitting of the C-terminal part of the short tail fibers into the cryo-EM reconstruction of T4 baseplate
ComponentsShort tail fiber protein
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


virus tail, baseplate / virus tail, fiber / entry receptor-mediated virion attachment to host cell / symbiont entry into host cell / metal ion binding
Similarity search - Function
Bacteriophage T4, Gp12 / Short tail fibre protein, C-terminal / Short tail fibre protein, C-terminal superfamily / Phage short tail fibre protein gp12, middle domain / Short tail fibre protein receptor-binding domain / Phage tail collar domain / Phage tail collar domain superfamily / Phage Tail Collar Domain
Similarity search - Domain/homology
Short tail fiber protein gp12
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12 Å
AuthorsKostyuchenko, V.A. / Leiman, P.G. / Chipman, P.R. / Kanamaru, S. / van Raaij, M.J. / Arisaka, F. / Mesyanzhinov, V.V. / Rossmann, M.G.
Citation
Journal: Nat Struct Biol / Year: 2003
Title: Three-dimensional structure of bacteriophage T4 baseplate.
Authors: Victor A Kostyuchenko / Petr G Leiman / Paul R Chipman / Shuji Kanamaru / Mark J van Raaij / Fumio Arisaka / Vadim V Mesyanzhinov / Michael G Rossmann /
Abstract: The baseplate of bacteriophage T4 is a multiprotein molecular machine that controls host cell recognition, attachment, tail sheath contraction and viral DNA ejection. We report here the three- ...The baseplate of bacteriophage T4 is a multiprotein molecular machine that controls host cell recognition, attachment, tail sheath contraction and viral DNA ejection. We report here the three-dimensional structure of the baseplate-tail tube complex determined to a resolution of 12 A by cryoelectron microscopy. The baseplate has a six-fold symmetric, dome-like structure approximately 520 A in diameter and approximately 270 A long, assembled around a central hub. A 940 A-long and 96 A-diameter tail tube, coaxial with the hub, is connected to the top of the baseplate. At the center of the dome is a needle-like structure that was previously identified as a cell puncturing device. We have identified the locations of six proteins with known atomic structures, and established the position and shape of several other baseplate proteins. The baseplate structure suggests a mechanism of baseplate triggering and structural transition during the initial stages of T4 infection.
#1: Journal: J.Mol.Biol. / Year: 2001
Title: Crystal Structure of a Heat-and Protease-Stable Part of the Bacteriophage T4 Short Tail Fibre
Authors: van Raaij, M.J. / Schoehn, G. / Burda, M.R. / Miller, S.
#2: Journal: To be published
Title: Structure of the receptor-binding domain of the bacteriophage T4 short tail fibre
Authors: Thomassen, E. / Gielen, G. / Schuetz, M. / Miller, S. / van Raaij, M.J.
History
DepositionMay 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 9, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: 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 / 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
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
Remark 999SEQUENCE The differences between the database reference sequence and the deposited sequence arise ...SEQUENCE The differences between the database reference sequence and the deposited sequence arise because the source of the fitted model is bacteriophage T4alc7, whereas the protein used in the structural solution is from bacteriophage T4D. The sequence of the protein from T4D has not yet been deposited. Only coordinates for CA atoms were submitted.
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS A PORTION OF THE BIOLOGICALLY SIGNIFICANT MULTIMER. ASSEMBLY ...BIOMOLECULE: 1 THIS ENTRY CONTAINS A PORTION OF THE BIOLOGICALLY SIGNIFICANT MULTIMER. ASSEMBLY COMPONENTS COM_ID: 1 NAME:GP12 IPR_ID: NULL GO_ID: NULL OTHER_DETAILS: TRIMER

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Structure visualization

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Assembly

Deposited unit
A: Short tail fiber protein
B: Short tail fiber protein
C: Short tail fiber protein
D: Short tail fiber protein
E: Short tail fiber protein
F: Short tail fiber protein
G: Short tail fiber protein
H: Short tail fiber protein
I: Short tail fiber protein
J: Short tail fiber protein
K: Short tail fiber protein
L: Short tail fiber protein
M: Short tail fiber protein
N: Short tail fiber protein
O: Short tail fiber protein
P: Short tail fiber protein
Q: Short tail fiber protein
R: Short tail fiber protein


Theoretical massNumber of molelcules
Total (without water)537,40818
Polymers537,40818
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
SymmetryPoint symmetry: (Schoenflies symbol: C6 (6 fold cyclic))

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Components

#1: Protein
Short tail fiber protein / Protein Gp12 / p12 / Coordinate model: Cα atoms only


Mass: 29856.020 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Strain: T4D / References: UniProt: P10930

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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
1T4 baseplate-tail tube complexVIRUST4 double mutant, 18-,23-, produces baseplate-tail tube assemblies0
2gp12trimer1
Buffer solutionName: water / pH: 7 / Details: water
SpecimenConc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: holey carbon
VitrificationCryogen name: ETHANE / Details: ethane vitrification
Crystal grow
*PLUS
Method: electron microscopy

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/T / Date: Jan 30, 2001
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 45000 X / Calibrated magnification: 47000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm / Cs: 2 mm
Specimen holderTemperature: 70 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameVersionCategory
1SITUS COLORES2model fitting
2SPIDER3D reconstruction
CTF correctionDetails: CTF correction of individual particles with Wiener filtering
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionMethod: model-based projection matching / Resolution: 12 Å / Num. of particles: 945 / Nominal pixel size: 3.11 Å / Actual pixel size: 2.98 Å / Magnification calibration: TMV particles images
Details: modifed version of program SPIDER was used for the reconstruction
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: Correlation Coefficient maximization
Details: REFINEMENT PROTOCOL--Laplacian transform real space
Atomic model buildingPDB-ID: 1OCY
Accession code: 1OCY / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms5004 0 0 0 5004

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