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- PDB-1pdf: Fitting of gp11 crystal structure into 3D cryo-EM reconstruction ... -

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Basic information

Entry
Database: PDB / ID: 1pdf
TitleFitting of gp11 crystal structure into 3D cryo-EM reconstruction of bacteriophage T4 baseplate-tail tube complex
ComponentsBaseplate structural protein Gp11
KeywordsSTRUCTURAL PROTEIN
Function / homologyBaseplate 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 / virus tail, baseplate / viral tail assembly / Baseplate wedge protein gp11
Function and homology information
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: 2000
Title: Structure of bacteriophage T4 gene product 11, the interface between the baseplate and short tail fibers
Authors: Leiman, P.G. / Kostyuchenko, V.A. / Shneider, M.M. / Kurochkina, L.P. / Mesyanzhinov, V.V. / 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 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:GP11 IPR_ID: NULL GO_ID: NULL OTHER_DETAILS: TRIMER

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Structure visualization

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Assembly

Deposited unit
A: Baseplate structural protein Gp11
B: Baseplate structural protein Gp11
C: Baseplate structural protein Gp11
D: Baseplate structural protein Gp11
E: Baseplate structural protein Gp11
F: Baseplate structural protein Gp11
G: Baseplate structural protein Gp11
H: Baseplate structural protein Gp11
I: Baseplate structural protein Gp11
J: Baseplate structural protein Gp11
K: Baseplate structural protein Gp11
L: Baseplate structural protein Gp11
M: Baseplate structural protein Gp11
N: Baseplate structural protein Gp11
O: Baseplate structural protein Gp11
P: Baseplate structural protein Gp11
Q: Baseplate structural protein Gp11
R: Baseplate structural protein Gp11


Theoretical massNumber of molelcules
Total (without water)427,05918
Polymers427,05918
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 Gp11 / Baseplate wedge protein 11 / Coordinate model: Cα atoms only


Mass: 23725.523 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 / 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
1T4 18-,23-VIRUSDouble amber mutants of bacteriophage T4 producing baseplate and tail tube assembly only0
2gp11trimer1
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 correction of each particle using 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 program SPIDER was used for the reconstruction
Symmetry type: POINT
Atomic model buildingProtocol: OTHER / Space: REAL / Target criteria: Correlation coefficient maximum / Details: REFINEMENT PROTOCOL--Laplacian-filtered real space
Atomic model buildingPDB-ID: 1EL6

1el6


Accession code: 1EL6 / Source name: PDB / Type: experimental model
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms3744 0 0 0 3744

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