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- PDB-2fl8: Fitting of the gp10 trimer structure into the cryoEM map of the b... -

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Basic information

Entry
Database: PDB / ID: 2fl8
TitleFitting of the gp10 trimer structure into the cryoEM map of the bacteriophage T4 baseplate in the hexagonal conformation.
ComponentsBaseplate structural protein Gp10
KeywordsVIRUS/VIRAL PROTEIN / Bacteriophage T4 / Baseplate / Tail / Evolution / gp10 / Structural comparisons / VIRUS-VIRAL PROTEIN COMPLEX
Function / homologyBaseplate wedge protein gp10 / Baseplate structural protein Gp9/Gp10 / Baseplate structural protein Gp9/Gp10 middle domain superfamily / Gp9-like superfamily / Bacteriophage T4 gp9/10-like protein / viral tail assembly / virus tail, baseplate / viral release from host cell / Baseplate wedge protein gp10
Function and homology information
Biological speciesEnterobacteria phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 12 Å
AuthorsLeiman, P.G. / Shneider, M.M. / Mesyanzhinov, V.V. / Rossmann, M.G.
CitationJournal: J Mol Biol / Year: 2006
Title: Evolution of bacteriophage tails: Structure of T4 gene product 10.
Authors: Petr G Leiman / Mikhail M Shneider / Vadim V Mesyanzhinov / Michael G Rossmann /
Abstract: The success of tailed bacteriophages to infect cells far exceeds that of most other viruses on account of their specialized tail and associated baseplate structures. The baseplate protein gene ...The success of tailed bacteriophages to infect cells far exceeds that of most other viruses on account of their specialized tail and associated baseplate structures. The baseplate protein gene product (gp) 10 of bacteriophage T4, whose structure was determined to 1.2 A resolution, was fitted into the cryo-electron microscopy structures of the pre and post-infection conformations of the virus. gp10 functions as a molecular lever that rotates and extends the hinged short tail fibers to facilitate cell attachment. The central folding motif of the gp10 trimer is similar to that of the baseplate protein gp11 and to the receptor-binding domain of the short tail fiber, gp12. The three proteins comprise the periphery of the baseplate and interact with each other. The structural and functional similarities of gp10, gp11, and gp12 and their sequential order in the T4 genome suggest that they evolved separately, subsequent to gene triplication from a common ancestor. Such events are usual in the evolution of complex organelles from a common primordial molecule.
History
DepositionJan 5, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 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 1.4Nov 6, 2019Group: Data collection / Other / Category: atom_sites / cell
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.Z_PDB / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.5Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.6Feb 14, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._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 300 BIOMOLECULE: 1 ASSEMBLY COMPONENTS COM_ID: 1 NAME:THE TRIMERIC GENE PRODUCT 10 IS A STRUCTURAL ... BIOMOLECULE: 1 ASSEMBLY COMPONENTS COM_ID: 1 NAME:THE TRIMERIC GENE PRODUCT 10 IS A STRUCTURAL COMPONENT OF THE SIXFOLD-SYMMETRIC T4 BASEPLATE IPR_ID: NULL GO_ID: NULL OTHER_DETAILS: THE ENTRY CONTAINS THE FIT OF THE GP10 C- TERMINAL DOMAIN CRYSTAL STRUCTURE (RESIDUES 406-602) AND THE HOMOLOGY MODEL OF THE GP10 N-TERMINAL DOMAIN (RESIDUES 1-160) INTO THE CRYOEM MAP OF THE T4 BASEPLATE IN THE HEXAGONAL CONFORMATION (EMDB ID 1048). THE HOMOLOGY MODEL OF THE N-TERMINAL DOMAINS IS BASED ON THE CRYSTAL STRUCTURE OF T4 GP9 (PDB ID 1S2E). VIRUS PARTICULARS COM_ID: 1 VIRUS_HOST_CATEGORY: BACTERIA VIRUS_HOST_SPECIES: ESCHERICHIA COLI VIRUS_HOST_GROWTH_CELL: ESCHERICHIA COLI VIRUS_TYPE: VIRION VIRUS_ISOLATE: STRAIN ICTVDB_ID: 02.043.0.01.005

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Structure visualization

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Assembly

Deposited unit
A: Baseplate structural protein Gp10
B: Baseplate structural protein Gp10
C: Baseplate structural protein Gp10
D: Baseplate structural protein Gp10
E: Baseplate structural protein Gp10
F: Baseplate structural protein Gp10
G: Baseplate structural protein Gp10
H: Baseplate structural protein Gp10
I: Baseplate structural protein Gp10
J: Baseplate structural protein Gp10
K: Baseplate structural protein Gp10
L: Baseplate structural protein Gp10
M: Baseplate structural protein Gp10
N: Baseplate structural protein Gp10
O: Baseplate structural protein Gp10
P: Baseplate structural protein Gp10
Q: Baseplate structural protein Gp10
R: Baseplate structural protein Gp10


Theoretical massNumber of molelcules
Total (without water)1,194,65518
Polymers1,194,65518
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
SymmetryPoint symmetry: (Schoenflies symbol: C6 (6 fold cyclic))

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Components

#1: Protein
Baseplate structural protein Gp10 / Baseplate wedge protein 10 / Coordinate model: Cα atoms only


Mass: 66369.742 Da / Num. of mol.: 18 / Mutation: A442E, A530T
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 / Strain: D / Gene: 10 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3 / References: UniProt: P10928

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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: bacteriophage T4 baseplate / Type: VIRUS
Details: The trimeric gene product 10 is a structural component of the sixfold-symmetric T4 baseplate. The entry contains the fit of the gp10 C-terminal domain crystal structure (residues 406-602) ...Details: The trimeric gene product 10 is a structural component of the sixfold-symmetric T4 baseplate. The entry contains the fit of the gp10 C-terminal domain crystal structure (residues 406-602) and the homology model of the gp10 N-terminal domain (residues 1-160) into the cryoEM map of the T4 baseplate in the hexagonal conformation (EMDB ID 1048). The homology model of the N-terminal domains is based on the crystal structure of T4 gp9 (PDB ID 1S2E).
Source: NATURAL
Source (natural)Organism: Enterobacteria phage T4 (virus)
Details of virusHost category: BACTERIA / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Escherichia coli
Buffer solutionpH: 7 / Details: water
SpecimenEmbedding 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 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 / Nominal defocus max: 5000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM

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Processing

EM software
IDNameCategory
1SITUS COLORESmodel fitting
2SPIDER3D reconstruction
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 12 Å / Num. of particles: 945
Details: THE COORDINATES CONTAIN CA ONLY. RESIDUES 161-405 ARE MISSING. PLEASE SEE THE RELATED EMDB ENTRY FOR DETAILS OF THE EM RECONSTRUCTION.
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Target criteria: correlation coefficient as defined by the program COLORES/SITUS
Details: METHOD--laplacian filtered real space REFINEMENT PROTOCOL--rigid body
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
12FKK12FKK1PDBexperimental model
21S2E11S2E2PDBexperimental model
RefinementHighest resolution: 12 Å
Details: THE COORDINATES CONTAIN CA ONLY. RESIDUES 161-405 ARE MISSING.
Refinement stepCycle: LAST / Highest resolution: 12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6192 0 0 0 6192

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