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- PDB-6hhk: Structure of gp105 of Listeria bacteriophage A511 -

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Basic information

Entry
Database: PDB / ID: 6hhk
TitleStructure of gp105 of Listeria bacteriophage A511
ComponentsGp105
KeywordsVIRAL PROTEIN / bacteriophage baseplate protein
Function / homologyGp105
Function and homology information
Biological speciesListeria phage A511 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 Å
AuthorsTaylor, N.M.I. / Guerrero-Ferreira, R.C. / Leiman, P.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_146284/1 Switzerland
CitationJournal: EMBO J / Year: 2019
Title: Structure and transformation of bacteriophage A511 baseplate and tail upon infection of  cells.
Authors: Ricardo C Guerrero-Ferreira / Mario Hupfeld / Sergey Nazarov / Nicholas Mi Taylor / Mikhail M Shneider / Jagan M Obbineni / Martin J Loessner / Takashi Ishikawa / Jochen Klumpp / Petr G Leiman /
Abstract: Contractile injection systems (bacteriophage tails, type VI secretions system, R-type pyocins, etc.) utilize a rigid tube/contractile sheath assembly for breaching the envelope of bacterial and ...Contractile injection systems (bacteriophage tails, type VI secretions system, R-type pyocins, etc.) utilize a rigid tube/contractile sheath assembly for breaching the envelope of bacterial and eukaryotic cells. Among contractile injection systems, bacteriophages that infect Gram-positive bacteria represent the least understood members. Here, we describe the structure of bacteriophage A511 tail in its pre- and post-host attachment states (extended and contracted, respectively) using cryo-electron microscopy, cryo-electron tomography, and X-ray crystallography. We show that the structure of the tube-baseplate complex of A511 is similar to that of phage T4, but the A511 baseplate is decorated with different receptor-binding proteins, which undergo a large structural transformation upon host attachment and switch the symmetry of the baseplate-tail fiber assembly from threefold to sixfold. For the first time under native conditions, we show that contraction of the phage tail sheath assembly starts at the baseplate and propagates through the sheath in a domino-like motion.
History
DepositionAug 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc / Item: _citation.journal_volume

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gp105
B: Gp105
C: Gp105
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,4804
Polymers64,4453
Non-polymers351
Water1,71195
1
A: Gp105
B: Gp105
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9993
Polymers42,9632
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-27 kcal/mol
Surface area16430 Å2
MethodPISA
2
C: Gp105

C: Gp105


Theoretical massNumber of molelcules
Total (without water)42,9632
Polymers42,9632
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area2550 Å2
ΔGint-16 kcal/mol
Surface area16480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.143, 75.143, 187.303
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Gp105


Mass: 21481.592 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria phage A511 (virus) / Production host: Escherichia coli (E. coli) / References: UniProt: A8AST9
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 95 / 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: 2.38 Å3/Da / Density % sol: 48.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 6,000, 0.1M MES pH 6.5 and 0.05 M sodium acetate cryoprotectant: 30% ethylene glycol

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.978713 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978713 Å / Relative weight: 1
ReflectionResolution: 2.38→46.8 Å / Num. obs: 46819 / % possible obs: 98.86 % / Redundancy: 10.33 % / Biso Wilson estimate: 51.32 Å2 / Net I/σ(I): 16.15
Reflection shellResolution: 2.38→2.53 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
SHELXDEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→45.05 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU R Cruickshank DPI: 0.345 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.347 / SU Rfree Blow DPI: 0.234 / SU Rfree Cruickshank DPI: 0.237
RfactorNum. reflection% reflectionSelection details
Rfree0.243 1254 5 %RANDOM
Rwork0.204 ---
obs0.206 25080 99.1 %-
Displacement parametersBiso mean: 83.85 Å2
Baniso -1Baniso -2Baniso -3
1--0.1713 Å20 Å20 Å2
2---0.1713 Å20 Å2
3---0.3426 Å2
Refine analyzeLuzzati coordinate error obs: 0.36 Å
Refinement stepCycle: 1 / Resolution: 2.38→45.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4091 0 1 95 4187
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094192HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.075731HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1382SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes705HARMONIC5
X-RAY DIFFRACTIONt_it4192HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.72
X-RAY DIFFRACTIONt_other_torsion18.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion563SEMIHARMONIC5
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_contact4799SEMIHARMONIC4
LS refinement shellResolution: 2.38→2.48 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2662 131 5.02 %
Rwork0.2589 2480 -
all0.2593 2611 -
obs--92.04 %
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)
10.07390.3266-0.42966.6306-0.6415.50960.12930.0713-0.04840.2285-0.15390.2711-0.067-0.22480.0246-0.3074-0.0850.00180.47-0.1158-0.273535.9021-22.816434.3981
21.9910.731-0.55591.8003-0.9233.49810.25510.16170.0258-0.284-0.2798-0.0042-0.3508-0.15870.02470.16730.13390.00670.4067-0.103-0.301438.316-16.57425.2567
31.917-0.178-0.02624.7401-0.37955.0122-0.4290.62530.165-0.2861-0.38720.609-0.7819-0.05780.81620.2597-0.1028-0.23930.1632-0.1485-0.29472.89083.167815.7957
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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