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- PDB-5ngj: Crystal structure of pb6, major tail tube protein of bacteriophage T5 -

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Basic information

Entry
Database: PDB / ID: 5ngj
TitleCrystal structure of pb6, major tail tube protein of bacteriophage T5
ComponentsTail tube protein
KeywordsVIRAL PROTEIN / bacteriophage / tube protein / virion protein
Function / homologyvirus tail, tube / symbiont genome ejection through host cell envelope, long flexible tail mechanism / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain (group 2) / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / virus tail / viral release from host cell by cytolysis / Tail tube protein pb6
Function and homology information
Biological speciesEscherichia phage T5 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsArnaud, C.-A. / Effantin, G. / Vives, C. / Engilberge, S. / Bacia, M. / Boulanger, P. / Girard, E. / Schoehn, G. / Breyton, C.
Funding support France, 2items
OrganizationGrant numberCountry
French National Research AgencyANR-10-INSB-05-02 France
LABEX GRALANR-10-LABX-49-01 France
CitationJournal: Nat Commun / Year: 2017
Title: Bacteriophage T5 tail tube structure suggests a trigger mechanism for Siphoviridae DNA ejection.
Authors: Charles-Adrien Arnaud / Grégory Effantin / Corinne Vivès / Sylvain Engilberge / Maria Bacia / Pascale Boulanger / Eric Girard / Guy Schoehn / Cécile Breyton /
Abstract: The vast majority of phages, bacterial viruses, possess a tail ensuring host recognition, cell wall perforation and safe viral DNA transfer from the capsid to the host cytoplasm. Long flexible tails ...The vast majority of phages, bacterial viruses, possess a tail ensuring host recognition, cell wall perforation and safe viral DNA transfer from the capsid to the host cytoplasm. Long flexible tails are formed from the tail tube protein (TTP) polymerised as hexameric rings around and stacked along the tape measure protein (TMP). Here, we report the crystal structure of T5 TTP pb6 at 2.2 Å resolution. Pb6 is unusual in forming a trimeric ring, although structure analysis reveals homology with all classical TTPs and related tube proteins of bacterial puncturing devices (type VI secretion system and R-pyocin). Structures of T5 tail tubes before and after interaction with the host receptor were determined by cryo-electron microscopy at 6 Å resolution. Comparison of these two structures reveals that host-binding information is not propagated to the capsid through conformational changes in the tail tube, suggesting a role of the TMP in this information transduction process.
History
DepositionMar 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2May 8, 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

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Assembly

Deposited unit
A: Tail tube protein
B: Tail tube protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,4577
Polymers104,2802
Non-polymers1775
Water4,107228
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-46 kcal/mol
Surface area41190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.790, 115.081, 83.366
Angle α, β, γ (deg.)90.00, 111.88, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tail tube protein / TTP / Tail protein pb6


Mass: 52139.984 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage T5 (virus) / Gene: N4, ORF134, T5.145, T5p141 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q6QGE2
#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 1

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Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.48 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 10 % 3350 PEG, 0.2 M HEPES pH 7.5, 0.3 M LiSO4, 0.1 mM MgCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.97965 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97965 Å / Relative weight: 1
ReflectionResolution: 2.2→57.54 Å / Num. obs: 68061 / % possible obs: 99.7 % / Redundancy: 7.5 % / Biso Wilson estimate: 60.54 Å2 / Net I/σ(I): 14.4

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→44 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.931 / SU R Cruickshank DPI: 0.318 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.181 / SU Rfree Blow DPI: 0.16 / SU Rfree Cruickshank DPI: 0.165
RfactorNum. reflection% reflectionSelection details
Rfree0.235 3399 5 %RANDOM
Rwork0.205 ---
obs0.206 67990 99.7 %-
Displacement parametersBiso mean: 86.23 Å2
Baniso -1Baniso -2Baniso -3
1--3.4064 Å20 Å2-7.1015 Å2
2---10.7647 Å20 Å2
3---14.1711 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: 1 / Resolution: 2.2→44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6667 0 5 228 6900
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0113407HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1924225HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2972SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes187HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1968HARMONIC5
X-RAY DIFFRACTIONt_it13407HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.73
X-RAY DIFFRACTIONt_other_torsion16.18
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion984SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact14322SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2756 247 5 %
Rwork0.2451 4696 -
all0.2465 4943 -
obs--97.8 %
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)
10.8736-0.2369-1.13670.78990.62953.19670.00380.07360.0718-0.02480.01080.1041-0.2008-0.195-0.0146-0.09540.01120.0385-0.0371-0.0479-0.19267.833515.134654.1985
21.3430.34850.64171.45090.41073.9436-0.05630.0150.02980.0207-0.02970.03310.1971-0.00040.086-0.21130.05530.005-0.0690.0123-0.184425.047631.920152.0983
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }

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