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

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Basic information

Entry
Database: PDB / ID: 4huh
TitleStructure of the bacteriophage T4 tail terminator protein, gp15 (C-terminal truncation mutant 1-261).
ComponentsTail connector protein Gp15
KeywordsVIRAL PROTEIN
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 / SIRAS (using Pt derivative) / Resolution: 3.2 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 / Item: _software.name
Revision 1.4Feb 28, 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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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)182,7556
Polymers182,7556
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13520 Å2
ΔGint-99 kcal/mol
Surface area54820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.874, 76.305, 93.893
Angle α, β, γ (deg.)109.04, 104.62, 89.30
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain B and ((resseq 5:28)) or chain B and ((resseq...
21chain A and ((resseq 5:28)) or chain A and ((resseq...
31chain C and ((resseq 5:28)) or chain C and ((resseq...
41chain D and ((resseq 5:28)) or chain D and ((resseq...
51chain E and ((resseq 5:28)) or chain E and ((resseq...
61chain F and ((resseq 5:28)) or chain F and ((resseq...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'B' and ((resseq 5:28)) or chain 'B' and ((resseq...B0
211chain 'A' and ((resseq 5:28)) or chain 'A' and ((resseq...A0
311chain 'C' and ((resseq 5:28)) or chain 'C' and ((resseq...C0
411chain 'D' and ((resseq 5:28)) or chain 'D' and ((resseq...D0
511chain 'E' and ((resseq 5:28)) or chain 'E' and ((resseq...E0
611chain 'F' and ((resseq 5:28)) or chain 'F' and ((resseq...F0

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Components

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


Mass: 30459.240 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

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.6
Details: 20% w/v Polyethylene glycol 3,350, 0.2 M Ammonium formate., pH 6.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97941 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Dec 3, 2011
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
ReflectionResolution: 3.2→45.911 Å / Num. all: 25229 / Num. obs: 25229 / % possible obs: 91.72 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 18.7
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 5.9 / % possible all: 72

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Processing

Software
NameVersionClassification
JBluIce-EPICS- EPICSdata collection
PHENIXAutoSolmodel building
PHENIX(phenix.refine: 1.8_1069)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXAutoSolphasing
RefinementMethod to determine structure: SIRAS (using Pt derivative) / Resolution: 3.2→45.911 Å / SU ML: 0.25 / σ(F): 0 / σ(I): 0 / Phase error: 26.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2021 1276 5.06 %The test set was selected in thin resolution shells because of presence of NCS.
Rwork0.1711 ---
all0.1727 25229 --
obs0.1727 25229 91.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.2→45.911 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10145 0 0 0 10145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00910410
X-RAY DIFFRACTIONf_angle_d1.22314097
X-RAY DIFFRACTIONf_dihedral_angle_d17.7573823
X-RAY DIFFRACTIONf_chiral_restr0.0821501
X-RAY DIFFRACTIONf_plane_restr0.0051813
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11B1512X-RAY DIFFRACTIONPOSITIONAL0.04
12A1512X-RAY DIFFRACTIONPOSITIONAL0.04
13C1512X-RAY DIFFRACTIONPOSITIONAL0.038
14D1512X-RAY DIFFRACTIONPOSITIONAL0.042
15E1512X-RAY DIFFRACTIONPOSITIONAL0.041
16F1512X-RAY DIFFRACTIONPOSITIONAL0.041
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.32810.2832930.20952113X-RAY DIFFRACTION72
3.3281-3.47950.21011020.1922332X-RAY DIFFRACTION79
3.4795-3.66290.20631830.16752464X-RAY DIFFRACTION87
3.6629-3.89230.19441330.16042686X-RAY DIFFRACTION93
3.8923-4.19260.19791390.15242857X-RAY DIFFRACTION98
4.1926-4.61420.13971390.1362868X-RAY DIFFRACTION99
4.6142-5.2810.18662080.13772856X-RAY DIFFRACTION99
5.281-6.65030.23251390.19412913X-RAY DIFFRACTION99
6.6503-45.91560.23361400.20672864X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -11.3821 Å / Origin y: -10.0467 Å / Origin z: -7.3768 Å
111213212223313233
T-0.2398 Å2-0.3124 Å20.0782 Å2--0.2343 Å20.0536 Å2--0.2837 Å2
L1.4005 °2-1.2629 °20.3334 °2-1.8164 °20.001 °2--3.2859 °2
S0.0363 Å °0.071 Å °-0.17 Å °0.0949 Å °0.0569 Å °0.1744 Å °0.1987 Å °-0.0747 Å °-0.0344 Å °
Refinement TLS groupSelection details: all

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