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- PDB-1pdj: Fitting of gp27 into cryoEM reconstruction of bacteriophage T4 ba... -

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Basic information

Entry
Database: PDB / ID: 1pdj
TitleFitting of gp27 into cryoEM reconstruction of bacteriophage T4 baseplate
ComponentsBaseplate structural protein Gp27
KeywordsSTRUCTURAL PROTEIN
Function / homology
Function and homology information


virus tail, baseplate / viral tail assembly / virus tail
Similarity search - Function
Bacteriophage T4, Gp27, baseplate hub, C-terminal / Bacteriophage T4, Gp27, baseplate hub, N-terminal / Gp27, baseplate hub, domain 3 / Gp27, baseplate hub, domain 4 / Gp27, baseplate hub, domain 2 / Baseplate structural protein, domain 2 / Baseplate structural protein, domain 1 / Peptidase S1, PA clan, chymotrypsin-like fold
Similarity search - Domain/homology
Baseplate central spike complex protein gp27
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: Nature / Year: 2002
Title: Structure of the cell-puncturing device of bacteriophage T4
Authors: Kanamaru, S. / Leiman, P.G. / Kostyuchenko, V.A. / Chipman, P.R. / Mesyanzhinov, V.V. / Arisaka, F. / Rossmann, M.G.
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 ONLY COORDINTES FOR CA ATOMS 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:GP27 IPR_ID: NULL GO_ID: NULL OTHER_DETAILS: TRIMER

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Structure visualization

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Assembly

Deposited unit
D: Baseplate structural protein Gp27
E: Baseplate structural protein Gp27
F: Baseplate structural protein Gp27


Theoretical massNumber of molelcules
Total (without water)133,2933
Polymers133,2933
Non-polymers00
Water00
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 Baseplate structural protein Gp27 / Hub protein 27 / Coordinate model: Cα atoms only


Mass: 44431.062 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 / References: UniProt: P17172

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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
IDNameTypeParent-IDDetails
1T4 baseplate-tail tube complexVIRUS0
2gp271trimer
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 FIELD / 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 was corrected for each particle 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 images
Details: a modified version of SPIDER was used for the reconstruction
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: Correlation coefficient maximization / Details: REFINEMENT PROTOCOL--laplacian filtered real space
Atomic model buildingPDB-ID: 1K28

1k28


Accession code: 1K28 / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1092 0 0 0 1092

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