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- PDB-6xgr: YSD1 major tail protein -

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Basic information

Entry
Database: PDB / ID: 6xgr
TitleYSD1 major tail protein
ComponentsYSD1_22 major tail protein
KeywordsVIRAL PROTEIN / Bacteriophage tail / helical assembly
Function / homologyBacterial Ig-like domain (group 1) / Bacterial Ig-like domain (group 1) / Big-1 (bacterial Ig-like domain 1) domain / Big-1 (bacterial Ig-like domain 1) domain profile. / Invasin/intimin cell-adhesion fragments / Immunoglobulin-like fold / Bacterial+Ig-like+domain+(Group+1)
Function and homology information
Biological speciesBacteriophage sp. (virus)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsHardy, J.M. / Dunstan, R. / Venugopal, H. / Lithgow, T.J. / Coulibaly, F.J.
Funding support Australia, United Kingdom, 3items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)1092262 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 1.2Nov 29, 2023Group: 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

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  • Simplified surface model + fitted atomic model
  • EMDB-22183
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  • EMDB-22183
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Structure viewerMolecule:
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Assembly

Deposited unit
A: YSD1_22 major tail protein
B: YSD1_22 major tail protein
C: YSD1_22 major tail protein
D: YSD1_22 major tail protein
E: YSD1_22 major tail protein
F: YSD1_22 major tail protein
G: YSD1_22 major tail protein
H: YSD1_22 major tail protein
I: YSD1_22 major tail protein
J: YSD1_22 major tail protein
K: YSD1_22 major tail protein
L: YSD1_22 major tail protein
M: YSD1_22 major tail protein
N: YSD1_22 major tail protein
O: YSD1_22 major tail protein
P: YSD1_22 major tail protein
Q: YSD1_22 major tail protein
R: YSD1_22 major tail protein


Theoretical massNumber of molelcules
Total (without water)727,04518
Polymers727,04518
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
YSD1_22 major tail protein


Mass: 40391.363 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Source: (natural) Bacteriophage sp. (virus) / References: UniProt: A0A498U5Z3

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Bacteriophage sp. / Type: VIRUS
Details: From environmental water samples taken during a phage survey of the waterways of Cambridge UK, the phage YSD1 was isolated using the attenuated S. enterica serovar Typhi BRD948. The virus ...Details: From environmental water samples taken during a phage survey of the waterways of Cambridge UK, the phage YSD1 was isolated using the attenuated S. enterica serovar Typhi BRD948. The virus was then amplified by infecting S. Typhimurium SL3261 delta-fljB.
Entity ID: all / Source: NATURAL
Molecular weightValue: 56.3 kDa/nm / Experimental value: NO
Source (natural)Organism: Bacteriophage sp. (virus) / Strain: YSD1
Details of virusEmpty: NO / Enveloped: NO / Isolate: SUBSPECIES / Type: VIRION
Natural hostOrganism: Salmonella enterica subsp. enterica serovar Typhi
Virus shellName: YSD1 capsid / Diameter: 650 nm / Triangulation number (T number): 7
Buffer solutionpH: 7.5
Buffer component
IDConc.NameFormulaBuffer-ID
1100 mMSodium chlorideNaClSodium chloride1
28 mMMagnesium SulfateMgSO41
310 mMTris pH 7.5Tris-HClTris1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R2/2
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K
Details: The grid was blotted for 2 seconds with a blot force of -3 and no drain time.

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Calibrated magnification: 105000 X / Calibrated defocus min: 500 nm / Calibrated defocus max: 2500 nm / Cs: 2.7 mm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 12 sec. / Electron dose: 27.24 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1881
Image scansMovie frames/image: 30 / Used frames/image: 1-30

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Processing

EM software
IDNameVersionCategory
4CTFFIND4.1.8CTF correction
7Coot0.8.9.1model fitting
8Rosetta1.16model fitting
10SPRING0.86.1661initial Euler assignment
11RELION2.1initial Euler assignment
12RELION2.1final Euler assignment
13RELION2.1classification
14RELION2.13D reconstruction
15PHENIX1.14model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 19.7 ° / Axial rise/subunit: 41.2 Å / Axial symmetry: C6
Particle selectionNum. of particles selected: 184501
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 147809 / Algorithm: BACK PROJECTION / Symmetry type: HELICAL
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL

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