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- EMDB-22182: YSD1 bacteriophage capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-22182
TitleYSD1 bacteriophage capsid
Map dataSharpened masked map
Sample
  • Virus: Bacteriophage sp. (virus)
    • Protein or peptide: YSD1_17
    • Protein or peptide: YSD1_16
KeywordsBacteriophage capsid / VIRUS
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsHardy JM / Dunstan R
Funding support Australia, United Kingdom, 3 items
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, 2020-
Header (metadata) releaseJul 1, 2020-
Map releaseJul 1, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6xgq
  • Surface level: 0.015
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6xgq
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22182.png

Downloads & links

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Map

FileDownload / File: emd_22182.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened masked map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.34 Å/pix.
x 600 pix.
= 804. Å		1.34 Å/pix.
x 600 pix.
= 804. Å		1.34 Å/pix.
x 600 pix.
= 804. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.34 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.015 / Movie #1: 0.015
Minimum - Maximum-0.037067343 - 0.079657204
Average (Standard dev.)0.00084995694 (±0.0051737824)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin100100100
Dimensions600600600
Spacing600600600
CellA=B=C: 804.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z600600600
origin x/y/z0.0000.0000.000
length x/y/z804.000804.000804.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ400400400
MAP C/R/S123
start NC/NR/NS100100100
NC/NR/NS600600600
D min/max/mean-0.0370.0800.001

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Supplemental data

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Mask #1

Fileemd_22182_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map

Fileemd_22182_additional.map
AnnotationSharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1

Fileemd_22182_half_map_1.map
AnnotationHalf map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_22182_half_map_2.map
AnnotationHalf map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Bacteriophage sp.

EntireName: Bacteriophage sp. (virus)
Components
  • Virus: Bacteriophage sp. (virus)
    • Protein or peptide: YSD1_17
    • Protein or peptide: YSD1_16

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Supramolecule #1: Bacteriophage sp.

SupramoleculeName: Bacteriophage sp. / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all
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.
NCBI-ID: 38018 / Sci species name: Bacteriophage sp. / Sci species strain: YSD1 / Virus type: VIRION / Virus isolate: SUBSPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Salmonella enterica subsp. enterica serovar Typhi (bacteria)
Molecular weightTheoretical: 22.8 MDa
Virus shellShell ID: 1 / Name: YSD1 capsid / Diameter: 650.0 Å / T number (triangulation number): 7

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Macromolecule #1: YSD1_17

MacromoleculeName: YSD1_17 / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Bacteriophage sp. (virus)
Molecular weightTheoretical: 39.945598 KDa
SequenceString: MAGLYTTYQL LEVQRKLKTL PAFFLQWFPR QINFQEDMIA FDKVIQDVTR VAPFVAPNVQ GRVIKESGYN TKTFKPAYVK PKHVIDPNM IIPRQPGEAL GTGTLSIAQR RDRVIAYLLM KHRAMHENTW EWMAAQAAQY GYVDVQGQDY PLVRVDFGRD A ALTMTTDW ...String:
MAGLYTTYQL LEVQRKLKTL PAFFLQWFPR QINFQEDMIA FDKVIQDVTR VAPFVAPNVQ GRVIKESGYN TKTFKPAYVK PKHVIDPNM IIPRQPGEAL GTGTLSIAQR RDRVIAYLLM KHRAMHENTW EWMAAQAAQY GYVDVQGQDY PLVRVDFGRD A ALTMTTDW TAAGVTLMDM IADLRDGQRL VSDKSMSGTV IRDYVFGGDA WDQFVKVGGK ELWGKDGLMD STIRGSETNV TR LWDDVEG VQYMGELVGA NGAGRMRIWV NTQKYRDQND QEQFLMKQKA VMGISSAIEG VRCFGAILDK GAGYQALDYF PKM WDQEDP SVEYLMSQGA PLMVPADPNA SFLLTVMS

UniProtKB: Major capsid protein

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Macromolecule #2: YSD1_16

MacromoleculeName: YSD1_16 / type: protein_or_peptide / ID: 2 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Bacteriophage sp. (virus)
Molecular weightTheoretical: 14.401047 KDa
SequenceString:
MNLLTMMAAT SLPNYLAGNG DLGSWEPTQI FAGEADIVTE GGAAGADIEI YQVIAKNAAG AMVPHDPTAT TGTSPDEVPA PQSVAIGIA AQPAKSGQNV PYYIGGVFNH AALGWHASLD TLAKRQAVFD RTNIHIGNLY

UniProtKB: Putative+head+decorative+protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Component:
ConcentrationFormulaName
100.0 mMNaClSodium chloride
8.0 mMMgSO4Magnesium Sulfate
10.0 mMTris-HClTris pH 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
Details: The grid was blotted for 2 seconds with a blot force of -3 and no drain time..

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-30 / Number grids imaged: 1 / Number real images: 1881 / Average exposure time: 12.0 sec. / Average electron dose: 27.24 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 2.5 µm / Calibrated defocus min: 0.5 µm / Calibrated magnification: 105000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 7366
Startup modelType of model: INSILICO MODEL / In silico model: Soft sphere
Final reconstructionNumber classes used: 11 / Applied symmetry - Point group: I (icosahedral) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number images used: 5449
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final 3D classificationNumber classes: 50 / Avg.num./class: 126 / Software - Name: RELION (ver. 2.1)
Details: 2D classification was used to remove particles with contamination features and poor signal-to-noise. Particles from 11 classes were selected for 3D reconstruction.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6xgp


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-6xgq:
YSD1 bacteriophage capsid

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