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- PDB-4hud: Structure of the bacteriophage T4 tail terminator protein, gp15. -

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Basic information

Entry
Database: PDB / ID: 4hud
TitleStructure of the bacteriophage T4 tail terminator protein, gp15.
ComponentsTail connector protein Gp15
KeywordsVIRAL PROTEIN / Bacteriophage T4 / phage tail terminator protein / gp15
Function / homologyMyoviridae tail sheath stabiliser / STM4215-like / Myoviridae tail sheath stabiliser / Myoviridae tail sheath stabiliser superfamily / T4-like virus Myoviridae tail sheath stabiliser / virion component / 2-Layer Sandwich / Alpha Beta / Tail completion protein gp15
Function and homology information
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7001 Å
AuthorsFokine, A. / Zhang, Z. / Kanamaru, S. / Bowman, V.D. / Aksyuk, 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 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 27, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2013Group: Database references
Revision 1.2May 22, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4Sep 20, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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


Theoretical massNumber of molelcules
Total (without water)189,5256
Polymers189,5256
Non-polymers00
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13530 Å2
ΔGint-103 kcal/mol
Surface area57910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.682, 100.682, 155.891
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.9 %
Crystal growTemperature: 301 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.15 M ammonium sulfate, 10.5 % isopropanol, 0.085 M Na Hepes pH 7.5, 20% PEG 4000, 15% glycerol., VAPOR DIFFUSION, HANGING DROP, temperature 301K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 23, 2001
RadiationMonochromator: NA / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→33 Å / Num. all: 45176 / Num. obs: 45176 / % possible obs: 93.03 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 20
Reflection shellResolution: 2.7→2.75 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 3.3 / % possible all: 85

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Processing

Software
NameVersionClassification
PHASERphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4HUH

4huh


Resolution: 2.7001→32.956 Å / SU ML: 0.31 / σ(F): 0 / Phase error: 34.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2521 2536 5.61 %The test set was chosen in thin resolution shells because of presence of NCS.
Rwork0.2066 ---
all0.2092 45176 --
obs0.2092 45176 93.03 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7001→32.956 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10452 0 0 72 10524
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0110722
X-RAY DIFFRACTIONf_angle_d1.29814526
X-RAY DIFFRACTIONf_dihedral_angle_d17.4043948
X-RAY DIFFRACTIONf_chiral_restr0.0791548
X-RAY DIFFRACTIONf_plane_restr0.0061878
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7001-2.79650.37963210.31813945X-RAY DIFFRACTION87
2.7965-2.90840.32453410.30244074X-RAY DIFFRACTION91
2.9084-3.04070.3792740.28764299X-RAY DIFFRACTION94
3.0407-3.20090.28612590.25164309X-RAY DIFFRACTION95
3.2009-3.40130.29582230.22744424X-RAY DIFFRACTION96
3.4013-3.66360.21841960.19514439X-RAY DIFFRACTION95
3.6636-4.03160.23762200.19284418X-RAY DIFFRACTION95
4.0316-4.61370.22492350.15874276X-RAY DIFFRACTION94
4.6137-5.80760.17772100.16444306X-RAY DIFFRACTION93
5.8076-32.95840.21922570.20394150X-RAY DIFFRACTION91
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.4636-0.2789-0.15792.2382-0.22450.3119-0.0813-0.0464-0.60510.28230.0427-0.97720.08670.22780.0620.35290.0416-0.09250.2215-0.01340.908231.113612.707513.091
21.3515-0.0703-0.15213.2065-0.01871.02430.0182-0.0005-1.01780.1375-0.07870.15530.26050.06940.03140.37340.00970.05840.16580.06531.1930.06390.408413.1879
31.85210.1142-0.1723.28410.45640.2866-0.0945-0.1025-0.57920.04070.07170.97390.1458-0.19150.030.324-0.00130.14130.2832-0.00561.2285-26.046421.110213.2968
43.3161-0.0975-0.06212.75580.49350.6645-0.0733-0.06580.28610.24510.00191.0366-0.0956-0.16660.05870.3290.0720.04180.2169-0.08890.6978-21.169354.098613.3021
53.0487-0.3157-0.11612.23340.28040.6222-0.03680.02690.95220.041-0.15640.0489-0.1930.04750.08640.41340.0255-0.150.1851-0.20720.14739.826266.361313.0912
62.1610.17350.52483.63350.20430.7941-0.21490.06330.3003-0.11280.0149-1.04110.00910.2639-0.18560.2846-0.0074-0.21410.2411-0.11270.309935.964345.661112.9616
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A'
2X-RAY DIFFRACTION2chain 'B'
3X-RAY DIFFRACTION3chain 'C'
4X-RAY DIFFRACTION4chain 'D'
5X-RAY DIFFRACTION5chain 'E'
6X-RAY DIFFRACTION6chain 'F'

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