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- PDB-3j2m: The X-ray structure of the gp15 hexamer and the model of the gp18... -

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Basic information

Entry
Database: PDB / ID: 3j2m
TitleThe X-ray structure of the gp15 hexamer and the model of the gp18 protein fitted into the cryo-EM reconstruction of the extended T4 tail
Components
  • Tail connector protein Gp15
  • Tail sheath protein Gp18
KeywordsVIRAL PROTEIN / bacteriophage T4 / phage tail terminator protein / phage sheath protein
Function / homology
Function and homology information


virus tail, sheath / symbiont genome ejection through host cell envelope, contractile tail mechanism / virion component
Similarity search - Function
Myoviridae tail sheath stabiliser / Myoviridae tail sheath stabiliser superfamily / T4-like virus Myoviridae tail sheath stabiliser / Phage tail sheath protein, beta-sandwich domain / Phage tail sheath protein beta-sandwich domain / Tail sheath protein, subtilisin-like domain / Phage tail sheath protein subtilisin-like domain / Tail sheath protein, C-terminal domain / Phage tail sheath C-terminal domain
Similarity search - Domain/homology
Tail completion protein gp15 / Tail sheath protein
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 15 Å
AuthorsFokine, A. / Zhang, Z. / Kanamaru, S. / Bowman, V.D. / Aksyuk, A. / Arisaka, F. / Rao, V.B. / Rossmann, M.G.
Citation
Journal: J Mol Biol / Year: 2013
Title: The molecular architecture of the bacteriophage T4 neck.
Authors: Andrei Fokine / Zhihong Zhang / Shuji Kanamaru / Valorie D Bowman / Anastasia A Aksyuk / Fumio Arisaka / Venigalla B Rao / Michael G Rossmann /
Abstract: A hexamer of the bacteriophage T4 tail terminator protein, gp15, attaches to the top of the phage tail stabilizing the contractile sheath and forming the interface for binding of the independently ...A hexamer of the bacteriophage T4 tail terminator protein, gp15, attaches to the top of the phage tail stabilizing the contractile sheath and forming the interface for binding of the independently assembled head. Here we report the crystal structure of the gp15 hexamer, describe its interactions in T4 virions that have either an extended tail or a contracted tail, and discuss its structural relationship to other phage proteins. The neck of T4 virions is decorated by the "collar" and "whiskers", made of fibritin molecules. Fibritin acts as a chaperone helping to attach the long tail fibers to the virus during the assembly process. The collar and whiskers are environment-sensing devices, regulating the retraction of the long tail fibers under unfavorable conditions, thus preventing infection. Cryo-electron microscopy analysis suggests that twelve fibritin molecules attach to the phage neck with six molecules forming the collar and six molecules forming the whiskers.
#1: Journal: Nat Struct Mol Biol / Year: 2005
Title: The tail structure of bacteriophage T4 and its mechanism of contraction.
Authors: Victor A Kostyuchenko / Paul R Chipman / Petr G Leiman / Fumio Arisaka / Vadim V Mesyanzhinov / Michael G Rossmann /
Abstract: Bacteriophage T4 and related viruses have a contractile tail that serves as an efficient mechanical device for infecting bacteria. A three-dimensional cryo-EM reconstruction of the mature T4 tail ...Bacteriophage T4 and related viruses have a contractile tail that serves as an efficient mechanical device for infecting bacteria. A three-dimensional cryo-EM reconstruction of the mature T4 tail assembly at 15-A resolution shows the hexagonal dome-shaped baseplate, the extended contractile sheath, the long tail fibers attached to the baseplate and the collar formed by six whiskers that interact with the long tail fibers. Comparison with the structure of the contracted tail shows that tail contraction is associated with a substantial rearrangement of the domains within the sheath protein and results in shortening of the sheath to about one-third of its original length. During contraction, the tail tube extends beneath the baseplate by about one-half of its total length and rotates by 345 degrees , allowing it to cross the host's periplasmic space.
History
DepositionNov 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2013Provider: repository / Type: Initial release
Revision 1.1May 15, 2013Group: Database references
Revision 1.2Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id / _em_software.name
Revision 1.3Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Assembly

Deposited unit
A: Tail connector protein Gp15
B: Tail connector protein Gp15
C: Tail connector protein Gp15
D: Tail connector protein Gp15
E: Tail connector protein Gp15
F: Tail connector protein Gp15
U: Tail sheath protein Gp18
V: Tail sheath protein Gp18
W: Tail sheath protein Gp18
X: Tail sheath protein Gp18
Y: Tail sheath protein Gp18
Z: Tail sheath protein Gp18


Theoretical massNumber of molelcules
Total (without water)617,26212
Polymers617,26212
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Tail connector protein Gp15 / Tail completion protein 15


Mass: 31587.486 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 15 / Production host: Escherichia coli (E. coli) / References: UniProt: P11112
#2: Protein
Tail sheath protein Gp18


Mass: 71289.484 Da / Num. of mol.: 6 / Mutation: R510P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 18 / Production host: Escherichia coli (E. coli) / References: UniProt: P13332
Sequence detailsTHE AUTHORS STATE THAT D100E, G148A, N150I, Y151I, E301G, A399V, AND H454Y ARE NATURAL VARIANTS AS ...THE AUTHORS STATE THAT D100E, G148A, N150I, Y151I, E301G, A399V, AND H454Y ARE NATURAL VARIANTS AS PER PDB ENTRY 3FOA.

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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
1Bacteriophage T4 tailVIRUS0
2Bacteriophage T4 tail terminator protein, gp151
3Bacteriophage T4 tail sheath protein, gp181Model of the entire gp18 molecule based on the crystal structure of the gp18M truncation mutant (PDB IDs: 3FOA, 3FOH) and the crystal structure of the Lin1278 protein (PDB ID: 3LML)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 200 mesh copper grids
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/ST / Date: Jan 10, 2003
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: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN
Image scansNum. digital images: 89
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategoryDetails
1EMfitmodel fitting
2SPIDER3D reconstructionSPIDER-like
CTF correctionDetails: each particle image
SymmetryPoint symmetry: C6 (6 fold cyclic)
3D reconstructionResolution: 15 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 3029 / Nominal pixel size: 3.97 Å / Actual pixel size: 3.97 Å
Details: reconstruction done with in-house implementation of BP RP algorithm from SPIDER to support non-cubic reconstruction volumes
Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL / Details: REFINEMENT PROTOCOL--rigid body
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms38334 0 0 0 38334

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