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- PDB-6iab: Tail fiber of Staphylococcus aureus phage P68 -

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Basic information

Entry
Database: PDB / ID: 6iab
TitleTail fiber of Staphylococcus aureus phage P68
ComponentsTail Fiber of phage P68
KeywordsSUGAR BINDING PROTEIN / structural protein / receptor binding protein / beta-propeller
Function / homology: / Phage 5-bladed beta propeller receptor binding platform domain / Minor structural protein / Minor structural protein
Function and homology information
Biological speciesStaphylococcus aureus phage P68 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsHrebik, D. / Karel, S. / Plevka, P.
Funding support Czech Republic, 4items
OrganizationGrant numberCountry
Czech Science Foundation15-21631Y Czech Republic
Czech Science Foundation18-17810S Czech Republic
European Molecular Biology Organization3041 Czech Republic
16-29916A Czech Republic
CitationJournal: Sci Adv / Year: 2019
Title: Structure and genome ejection mechanism of phage P68.
Authors: Dominik Hrebík / Dana Štveráková / Karel Škubník / Tibor Füzik / Roman Pantůček / Pavel Plevka /
Abstract: Phages infecting can be used as therapeutics against antibiotic-resistant bacterial infections. However, there is limited information about the mechanism of genome delivery of phages that infect ...Phages infecting can be used as therapeutics against antibiotic-resistant bacterial infections. However, there is limited information about the mechanism of genome delivery of phages that infect Gram-positive bacteria. Here, we present the structures of native phage P68, genome ejection intermediate, and empty particle. The P68 head contains 72 subunits of inner core protein, 15 of which bind to and alter the structure of adjacent major capsid proteins and thus specify attachment sites for head fibers. Unlike in the previously studied phages, the head fibers of P68 enable its virion to position itself at the cell surface for genome delivery. The unique interaction of one end of P68 DNA with one of the 12 portal protein subunits is disrupted before the genome ejection. The inner core proteins are released together with the DNA and enable the translocation of phage genome across the bacterial membrane into the cytoplasm.
History
DepositionNov 26, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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

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Assembly

Deposited unit
A: Tail Fiber of phage P68


Theoretical massNumber of molelcules
Total (without water)75,6631
Polymers75,6631
Non-polymers00
Water7,855436
1
A: Tail Fiber of phage P68

A: Tail Fiber of phage P68

A: Tail Fiber of phage P68


Theoretical massNumber of molelcules
Total (without water)226,9883
Polymers226,9883
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area23030 Å2
ΔGint-104 kcal/mol
Surface area50990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.733, 100.733, 125.462
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
Components on special symmetry positions
IDModelComponents
11A-706-

HOH

21A-711-

HOH

31A-945-

HOH

41A-958-

HOH

51A-1017-

HOH

61A-1080-

HOH

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Components

#1: Protein Tail Fiber of phage P68


Mass: 75662.641 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus phage P68 (virus)
Plasmid: pMUH17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q859K8, UniProt: Q859I6*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 1.62 Å3/Da / Density % sol: 24.18 %
Crystal growTemperature: 293.16 K / Method: vapor diffusion, hanging drop
Details: 200 mM magnesium chloride, 100 mM HEPES, 20% (w/v) polyethylene glycol 6000
PH range: 7.0 - 7.5

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 19, 2017
RadiationMonochromator: channel cut cryogenically cooled monochromator crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2→19.968 Å / Num. obs: 32065 / % possible obs: 99.99 % / Redundancy: 5.1 % / Net I/σ(I): 13.5
Reflection shellResolution: 2.0002→2.0502 Å / Num. unique obs: 2146 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_3042refinement
XDS0.73data reduction
Aimless0.5.32data scaling
PHASER2.5.7phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EFV

5efv


Resolution: 2→19.968 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.59 / Phase error: 18.9
RfactorNum. reflection% reflection
Rfree0.2019 1895 5.91 %
Rwork0.1642 --
obs0.1663 32065 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→19.968 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4021 0 0 436 4457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0034109
X-RAY DIFFRACTIONf_angle_d0.5745550
X-RAY DIFFRACTIONf_dihedral_angle_d19.0321517
X-RAY DIFFRACTIONf_chiral_restr0.047589
X-RAY DIFFRACTIONf_plane_restr0.003721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.05020.22891580.21452146X-RAY DIFFRACTION100
2.0502-2.10560.2351440.20042176X-RAY DIFFRACTION100
2.1056-2.16740.25041240.19852155X-RAY DIFFRACTION100
2.1674-2.23730.22082060.18732100X-RAY DIFFRACTION100
2.2373-2.31720.19931350.18372125X-RAY DIFFRACTION100
2.3172-2.40980.20781310.1892147X-RAY DIFFRACTION100
2.4098-2.51930.21281200.17162172X-RAY DIFFRACTION100
2.5193-2.65180.21461450.17532172X-RAY DIFFRACTION100
2.6518-2.81750.23751310.1732133X-RAY DIFFRACTION100
2.8175-3.03440.21121160.16962155X-RAY DIFFRACTION100
3.0344-3.33850.19831030.1662198X-RAY DIFFRACTION100
3.3385-3.81860.17291670.1442124X-RAY DIFFRACTION100
3.8186-4.80.16241070.12182184X-RAY DIFFRACTION100
4.8-19.96890.19931080.1592183X-RAY DIFFRACTION100

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