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- PDB-6xgp: YSD1_17 major capsid protein -

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Basic information

Entry
Database: PDB / ID: 6xgp
TitleYSD1_17 major capsid protein
ComponentsYSD1_17 major capsid protein
KeywordsVIRAL PROTEIN / capsid protein
Function / homologyMajor capsid protein GpE / Phage major capsid protein E / viral capsid / host cell cytoplasm / Major capsid protein
Function and homology information
Biological speciesBacteriophage sp. (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGrinter, R. / Hardy, J.M. / Dunstan, R. / Lithgow, T.J. / Coulibaly, F.J.
Funding support Australia, United Kingdom, 4items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1092262 Australia
Australian Research Council (ARC)FL130100038 Australia
Australian Research Council (ARC)FL130100038 Australia
Wellcome Trust106077/Z/14/Z United Kingdom
CitationJournal: Nat Commun / Year: 2020
Title: The architecture and stabilisation of flagellotropic tailed bacteriophages.
Authors: Joshua M Hardy / Rhys A Dunstan / Rhys Grinter / Matthew J Belousoff / Jiawei Wang / Derek Pickard / Hariprasad Venugopal / Gordon Dougan / Trevor Lithgow / Fasséli Coulibaly /
Abstract: Flagellotropic bacteriophages engage flagella to reach the bacterial surface as an effective means to increase the capture radius for predation. Structural details of these viruses are of great ...Flagellotropic bacteriophages engage flagella to reach the bacterial surface as an effective means to increase the capture radius for predation. Structural details of these viruses are of great interest given the substantial drag forces and torques they face when moving down the spinning flagellum. We show that the main capsid and auxiliary proteins form two nested chainmails that ensure the integrity of the bacteriophage head. Core stabilising structures are conserved in herpesviruses suggesting their ancestral origin. The structure of the tail also reveals a robust yet pliable assembly. Hexameric rings of the tail-tube protein are braced by the N-terminus and a β-hairpin loop, and interconnected along the tail by the splayed β-hairpins. By contrast, we show that the β-hairpin has an inhibitory role in the tail-tube precursor, preventing uncontrolled self-assembly. Dyads of acidic residues inside the tail-tube present regularly-spaced motifs well suited to DNA translocation into bacteria through the tail.
History
DepositionJun 17, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 12, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 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

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Assembly

Deposited unit
A: YSD1_17 major capsid protein
B: YSD1_17 major capsid protein


Theoretical massNumber of molelcules
Total (without water)79,8912
Polymers79,8912
Non-polymers00
Water82946
1
A: YSD1_17 major capsid protein


Theoretical massNumber of molelcules
Total (without water)39,9461
Polymers39,9461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: YSD1_17 major capsid protein


Theoretical massNumber of molelcules
Total (without water)39,9461
Polymers39,9461
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.396, 91.994, 89.032
Angle α, β, γ (deg.)90.000, 102.420, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein YSD1_17 major capsid protein


Mass: 39945.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage sp. (virus) / Gene: YSD1_17, SAMEA3317914_00017 / Plasmid: pET21a / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): C41 / References: UniProt: A0A498U580
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.72 Å3/Da / Density % sol: 54.83 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 4 % PEG3350, 20 % glycerol, 0.2 M NaBr and 0.1 M MOPS-HEPES buffer (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 24, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.6→46.01 Å / Num. obs: 26350 / % possible obs: 99.6 % / Redundancy: 2 % / Biso Wilson estimate: 39.16 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.106 / Rrim(I) all: 0.149 / Net I/σ(I): 8
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 2 % / Rmerge(I) obs: 0.734 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 2620 / CC1/2: 0.438 / Rpim(I) all: 0.734 / Rrim(I) all: 1.038 / % possible all: 99.6

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Processing

Software
NameVersionClassification
BUSTERrefinement
XDS20151015data reduction
Aimless0.7.3data scaling
PDB_EXTRACT3.24data extraction
PHASER2.6.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BQW

3bqw


Resolution: 2.6→30.83 Å / Cor.coef. Fo:Fc: 0.8787 / Cor.coef. Fo:Fc free: 0.8277 / SU R Cruickshank DPI: 0.565 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.51 / SU Rfree Blow DPI: 0.289 / SU Rfree Cruickshank DPI: 0.299
RfactorNum. reflection% reflectionSelection details
Rfree0.2581 1285 4.88 %RANDOM
Rwork0.2193 ---
obs0.2211 26349 99.57 %-
Displacement parametersBiso max: 132.59 Å2 / Biso mean: 44.5 Å2 / Biso min: 7.07 Å2
Baniso -1Baniso -2Baniso -3
1--6.0913 Å20 Å20.6029 Å2
2--13.8105 Å20 Å2
3----7.7192 Å2
Refine analyzeLuzzati coordinate error obs: 0.378 Å
Refinement stepCycle: final / Resolution: 2.6→30.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5208 0 0 46 5254
Biso mean---28.54 -
Num. residues----657
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1825SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes138HARMONIC2
X-RAY DIFFRACTIONt_gen_planes760HARMONIC5
X-RAY DIFFRACTIONt_it5324HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion669SEMIHARMONIC5
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_contact5712SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5324HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg7209HARMONIC21.14
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion20.04
LS refinement shellResolution: 2.6→2.71 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2874 169 5.67 %
Rwork0.2343 2809 -
all0.2374 2978 -
obs--99.57 %

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