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- PDB-6xgq: YSD1 bacteriophage capsid -

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Basic information

Entry
Database: PDB / ID: 6xgq
TitleYSD1 bacteriophage capsid
Components
  • YSD1_16
  • YSD1_17
KeywordsVIRUS / Bacteriophage capsid
Function / homologyHead decoration protein D / Bacteriophage lambda head decoration protein D / Major capsid protein GpE / Phage major capsid protein E / viral capsid / host cell cytoplasm / Putative+head+decorative+protein / Major capsid protein
Function and homology information
Biological speciesBacteriophage sp. (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 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 1.2Mar 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-22182
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Structure viewerMolecule:
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Assembly

Deposited unit
A: YSD1_17
B: YSD1_17
C: YSD1_17
D: YSD1_17
E: YSD1_17
F: YSD1_17
G: YSD1_17
a: YSD1_16
b: YSD1_16
c: YSD1_16
d: YSD1_16
e: YSD1_16
f: YSD1_16
g: YSD1_16


Theoretical massNumber of molelcules
Total (without water)380,42714
Polymers380,42714
Non-polymers00
Water0
1
A: YSD1_17
B: YSD1_17
C: YSD1_17
D: YSD1_17
E: YSD1_17
F: YSD1_17
G: YSD1_17
a: YSD1_16
b: YSD1_16
c: YSD1_16
d: YSD1_16
e: YSD1_16
f: YSD1_16
g: YSD1_16
x 60


Theoretical massNumber of molelcules
Total (without water)22,825,591840
Polymers22,825,591840
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: YSD1_17
B: YSD1_17
C: YSD1_17
D: YSD1_17
E: YSD1_17
F: YSD1_17
G: YSD1_17
a: YSD1_16
b: YSD1_16
c: YSD1_16
d: YSD1_16
e: YSD1_16
f: YSD1_16
g: YSD1_16
x 5


  • icosahedral pentamer
  • 1.9 MDa, 70 polymers
Theoretical massNumber of molelcules
Total (without water)1,902,13370
Polymers1,902,13370
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: YSD1_17
B: YSD1_17
C: YSD1_17
D: YSD1_17
E: YSD1_17
F: YSD1_17
G: YSD1_17
a: YSD1_16
b: YSD1_16
c: YSD1_16
d: YSD1_16
e: YSD1_16
f: YSD1_16
g: YSD1_16
x 6


  • icosahedral 23 hexamer
  • 2.28 MDa, 84 polymers
Theoretical massNumber of molelcules
Total (without water)2,282,55984
Polymers2,282,55984
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
YSD1_17


Mass: 39945.598 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Bacteriophage sp. (virus) / References: UniProt: A0A498U580
#2: Protein
YSD1_16


Mass: 14401.047 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Source: (natural) Bacteriophage sp. (virus) / References: UniProt: A0A498TZZ8

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle 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: 22.8 MDa
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
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
IDNameVersionCategoryDetails
1RELION2.1particle selectionAutopicking from 2D template
4CTFFIND4.1.8CTF correction
7Coot0.8.9.1model fitting
9PHENIX1.14model refinement
10RELION2.1initial Euler assignment
11RELION2.1final Euler assignment
12RELION2.1classification
13RELION2.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 7366
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 5449 / Algorithm: BACK PROJECTION / Num. of class averages: 11 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 6XGP

6xgp


Pdb chain-ID: A / Accession code: 6XGP / Source name: PDB / Type: experimental model

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