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- PDB-3j2o: Model of the bacteriophage T4 fibritin based on the cryo-EM recon... -

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Basic information

Entry
Database: PDB / ID: 3j2o
TitleModel of the bacteriophage T4 fibritin based on the cryo-EM reconstruction of the contracted T4 tail containing the phage collar and whiskers
ComponentsFibritin
KeywordsVIRAL PROTEIN / Bacteriophage T4 / phage neck / collar whiskers / fibritin / gpwac
Function / homologyFibritin C-terminal / Fibritin C-terminal region / virion component / Fibritin
Function and homology information
Biological speciesEnterobacteria phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 25 Å
AuthorsFokine, A. / Zhang, Z. / Kanamaru, S. / Bowman, V.D. / Aksyuk, A.A. / Arisaka, F. / Rao, V.B. / Rossmann, M.G.
CitationJournal: 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.
History
DepositionNov 12, 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
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Assembly

Deposited unit
A: Fibritin
B: Fibritin
C: Fibritin
D: Fibritin
E: Fibritin
F: Fibritin


Theoretical massNumber of molelcules
Total (without water)310,6686
Polymers310,6686
Non-polymers00
Water00
1


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

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Components

#1: Protein
Fibritin / Collar protein / Whisker antigen control protein / Coordinate model: Cα atoms only


Mass: 51777.973 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: wac / Production host: Escherichia coli (E. coli) / References: UniProt: P10104

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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
2fibritin1Twelve fibritin molecules attach to the bacteriophage T4 neck with six molecules forming the phage collar and six molecules forming the whiskers. The model of fibritin comprises the crystal structure of the N-terminal comain (Boudko et al., 2004, J. Mol. Biol. 339, 927-935), the crystal structure of the C-terminal domain (Tao et al., 1997, Structure 5, 789-798), and the central region, modeled with segments of triple-helical coiled coil (Letarov et al., 2005, J. Bacteriol. 187, 1055-1066).
Buffer solutionName: 50 mM Tris-HCl, pH 8.0, 0.2 M NaCl, 8 mM MgCl2 / pH: 8 / Details: 50 mM Tris-HCl, pH 8.0, 0.2 M NaCl, 8 mM MgCl2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Details: plunged into liquid ethane (homemade plunger)

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM200FEG / Date: Mar 7, 2007
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal magnification: 38000 X / Calibrated magnification: 39190 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1500 nm / Cs: 2 mm
Specimen holderSpecimen holder model: GATAN LIQUID NITROGEN
Image recordingElectron dose: 16 e/Å2 / Film or detector model: KODAK SO-163 FILM / Details: Kodak film
Image scansNum. digital images: 97
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1UCSF Chimeramodel fitting
2EMAN3D reconstruction
CTF correctionDetails: phase flipping
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: projection matching / Resolution: 25 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 2727 / Nominal pixel size: 3.572 Å / Actual pixel size: 3.572 Å / Symmetry type: POINT
Atomic model buildingSpace: REAL
Details: DETAILS--The model of fibritin comprises the crystal structure of the N-terminal domain (Boudko et al., 2004, J. Mol. Biol. 339, 927-935), the crystal structure of the C-terminal domain (Tao ...Details: DETAILS--The model of fibritin comprises the crystal structure of the N-terminal domain (Boudko et al., 2004, J. Mol. Biol. 339, 927-935), the crystal structure of the C-terminal domain (Tao et al., 1997, Structure 5, 789-798), and the central region, modeled with segments of triple-helical coiled coil (Letarov et al., 2005, J. Bacteriol. 187, 1055-1066). These parts of the fibritin structure were fitted into the cryo-EM density using the program CHIMERA (Pettersen et al., 2004, J. Computat. Chem. 25, 1605-1612). Chains A, B, and C correspond to one fibritin molecule located in the phage collar. Chains D, E, and F correspond to one fibritin molecule forming the whisker.
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 0 0 1518

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