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- EMDB-5236: Capsid of Staphylococcus aureus bacteriophage 80alpha virion -

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Basic information

Entry
Database: EMDB / ID: EMD-5236
TitleCapsid of Staphylococcus aureus bacteriophage 80alpha virion
Map dataTwofold (222) view of isosurface representation of bacteriophage 80alpha virion icosahedral reconstruction.
Sample
  • Sample: Staphylococcus aureus RN10616 (Bacteriophage 80alpha)
  • Virus: bacteriophage 80alpha (virus)
KeywordsStaphylococcus aureus / bacteriophage / virion / capsid / maturation / pathogenicity island
Biological speciesbacteriophage 80alpha (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.2 Å
AuthorsSpilman MS / Dearborn AD / Chang JR / Damle PK / Christie GE / Dokland T
CitationJournal: J Mol Biol / Year: 2011
Title: A conformational switch involved in maturation of Staphylococcus aureus bacteriophage 80α capsids.
Authors: Michael S Spilman / Altaira D Dearborn / Jenny R Chang / Priyadarshan K Damle / Gail E Christie / Terje Dokland /
Abstract: Bacteriophages are involved in many aspects of the spread and establishment of virulence factors in Staphylococcus aureus, including the mobilization of genetic elements known as S. aureus ...Bacteriophages are involved in many aspects of the spread and establishment of virulence factors in Staphylococcus aureus, including the mobilization of genetic elements known as S. aureus pathogenicity islands (SaPIs), which carry genes for superantigen toxins and other virulence factors. SaPIs are packaged into phage-like transducing particles using proteins supplied by the helper phage. We have used cryo-electron microscopy and icosahedral reconstruction to determine the structures of the procapsid and the mature capsid of 80α, a bacteriophage that can mobilize several different SaPIs. The 80α capsid has T=7 icosahedral symmetry with the capsid protein organized into pentameric and hexameric clusters that interact via prominent trimeric densities. The 80α capsid protein was modeled based on the capsid protein fold of bacteriophage HK97 and fitted into the 80α reconstructions. The models show that the trivalent interactions are mediated primarily by a 22-residue β hairpin structure called the P loop that is not found in HK97. Capsid expansion is associated with a conformational switch in the spine helix that is propagated throughout the subunit, unlike the domain rotation mechanism in phage HK97 or P22.
History
DepositionOct 5, 2010-
Header (metadata) releaseMar 9, 2011-
Map releaseMar 9, 2011-
UpdateMar 9, 2011-
Current statusMar 9, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.66
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.66
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5236_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5236.map.gz / Format: CCP4 / Size: 210.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTwofold (222) view of isosurface representation of bacteriophage 80alpha virion icosahedral reconstruction.
Voxel sizeX=Y=Z: 2.048 Å
Density
Contour LevelBy AUTHOR: 0.66 / Movie #1: 0.66
Minimum - Maximum-1.07676 - 2.84138
Average (Standard dev.)-0.0336995 (±0.450525)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-94-94-94
Dimensions384384384
Spacing384384384
CellA=B=C: 786.432 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.0482.0482.048
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z786.432786.432786.432
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-94-94-94
NC/NR/NS384384384
D min/max/mean-1.0772.841-0.034

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Supplemental data

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Sample components

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Entire : Staphylococcus aureus RN10616 (Bacteriophage 80alpha)

EntireName: Staphylococcus aureus RN10616 (Bacteriophage 80alpha)
Components
  • Sample: Staphylococcus aureus RN10616 (Bacteriophage 80alpha)
  • Virus: bacteriophage 80alpha (virus)

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Supramolecule #1000: Staphylococcus aureus RN10616 (Bacteriophage 80alpha)

SupramoleculeName: Staphylococcus aureus RN10616 (Bacteriophage 80alpha) / type: sample / ID: 1000 / Details: Purified by CsCl centrifugation / Number unique components: 1
Molecular weightTheoretical: 14.7 MDa

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Supramolecule #1: bacteriophage 80alpha

SupramoleculeName: bacteriophage 80alpha / type: virus / ID: 1 / Name.synonym: bacteriophage 80alpha / Sci species name: bacteriophage 80alpha / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No / Syn species name: bacteriophage 80alpha
Host (natural)Organism: Staphylococcus aureus (bacteria) / synonym: BACTERIA(EUBACTERIA)
Molecular weightExperimental: 14.7 MDa / Theoretical: 14.7 MDa
Virus shellShell ID: 1 / Name: capsid / Diameter: 630.0 Å / T number (triangulation number): 7

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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

Concentration1.0 mg/mL
BufferpH: 7.8 / Details: 20 mM Tris-HCl, 50 mM NaCl, 1 mM MgCl2, 2 mM CaCl2
GridDetails: 400 mesh holey film C-flat R 2/1
VitrificationCryogen name: ETHANE / Chamber temperature: 108 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: manual / Method: blotted for 2 sec before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 62000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 2.8 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 62000
Sample stageSpecimen holder: eucentric / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 97 K
DateJun 15, 2007
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.3 µm / Number real images: 174 / Average electron dose: 20 e/Å2
Details: scanned images were binned to 12.6 microns per pixel
Od range: 2 / Bits/pixel: 16
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN
Details: Final maps were calculated to 8A and filtered at 6A resolution
Number images used: 8080

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