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- EMDB-1869: Procapsid of Staphylococcus aureus Pathogenicity Island 1 -

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Basic information

Entry
Database: EMDB / ID: EMD-1869
TitleProcapsid of Staphylococcus aureus Pathogenicity Island 1
Map dataTwofold (222) view of isosurface representation of Staphylococcus aureus Pathogenicity Island 1 (SaPI1) procapsid icosahedral reconstruction.
Sample
  • Sample: Staphylococcus aureus ST63 (Bacteriophage 80alpha delta(terS) SaPI1 delta(terS))
  • Virus: Staphylococcus aureus Pathogenicity Island 1 procapsid
KeywordsStaphylococcus aureus / bacteriophage / capsid / procapsid / size determination / pathogenicity island
Biological speciesStaphylococcus aureus Pathogenicity Island 1 procapsid
Methodsingle particle reconstruction / cryo EM / Resolution: 9.99 Å
AuthorsDearborn AD / Spilman MS / Damle PK / Chang JR / Monroe EB / Saad JS / Christie GE / Dokland T
CitationJournal: J Mol Biol / Year: 2011
Title: The Staphylococcus aureus pathogenicity island 1 protein gp6 functions as an internal scaffold during capsid size determination.
Authors: Altaira D Dearborn / Michael S Spilman / Priyadarshan K Damle / Jenny R Chang / Eric B Monroe / Jamil S Saad / Gail E Christie / Terje Dokland /
Abstract: Staphylococcus aureus pathogenicity island 1 (SaPI1) is a mobile genetic element that carries genes for several superantigen toxins. SaPI1 is normally stably integrated into the host genome but can ...Staphylococcus aureus pathogenicity island 1 (SaPI1) is a mobile genetic element that carries genes for several superantigen toxins. SaPI1 is normally stably integrated into the host genome but can become mobilized by "helper" bacteriophage 80α, leading to the packaging of SaPI1 genomes into phage-like transducing particles that are composed of structural proteins supplied by the helper phage but having smaller capsids. We show that the SaPI1-encoded protein gp6 is necessary for efficient formation of small capsids. The NMR structure of gp6 reveals a dimeric protein with a helix-loop-helix motif similar to that of bacteriophage scaffolding proteins. The gp6 dimer matches internal densities that bridge capsid subunits in cryo-electron microscopy reconstructions of SaPI1 procapsids, suggesting that gp6 acts as an internal scaffolding protein in capsid size determination.
History
DepositionJan 27, 2011-
Header (metadata) releaseMar 15, 2012-
Map releaseMar 15, 2012-
UpdateMar 15, 2012-
Current statusMar 15, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3.1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_1869.png

Downloads & links

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Map

FileDownload / File: emd_1869.map.gz / Format: CCP4 / Size: 89 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTwofold (222) view of isosurface representation of Staphylococcus aureus Pathogenicity Island 1 (SaPI1) procapsid icosahedral reconstruction.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 288 pix.
= 589.824 Å		2.05 Å/pix.
x 288 pix.
= 589.824 Å		2.05 Å/pix.
x 288 pix.
= 589.824 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.048 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.1 / Movie #1: 3.1
Minimum - Maximum-2.80164194 - 7.15723228
Average (Standard dev.)-0.70188761 (±1.50645566)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-70-70-70
Dimensions288288288
Spacing288288288
CellA=B=C: 589.82404 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.0482.0482.048
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z589.824589.824589.824
α/β/γ90.00090.00090.000
start NX/NY/NZ-160-160-159
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS-70-70-70
NC/NR/NS288288288
D min/max/mean-2.8027.157-0.702

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Supplemental data

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Sample components

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Entire : Staphylococcus aureus ST63 (Bacteriophage 80alpha delta(terS) SaP...

EntireName: Staphylococcus aureus ST63 (Bacteriophage 80alpha delta(terS) SaPI1 delta(terS))
Components
  • Sample: Staphylococcus aureus ST63 (Bacteriophage 80alpha delta(terS) SaPI1 delta(terS))
  • Virus: Staphylococcus aureus Pathogenicity Island 1 procapsid

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Supramolecule #1000: Staphylococcus aureus ST63 (Bacteriophage 80alpha delta(terS) SaP...

SupramoleculeName: Staphylococcus aureus ST63 (Bacteriophage 80alpha delta(terS) SaPI1 delta(terS))
type: sample / ID: 1000
Details: Purified by CsCl and sucrose gradient centrifugation
Number unique components: 1
Molecular weightTheoretical: 8.4 MDa

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Supramolecule #1: Staphylococcus aureus Pathogenicity Island 1 procapsid

SupramoleculeName: Staphylococcus aureus Pathogenicity Island 1 procapsid
type: virus / ID: 1 / Name.synonym: SaPI1 procapsid
Sci species name: Staphylococcus aureus Pathogenicity Island 1 procapsid
Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes / Syn species name: SaPI1 procapsid
Host (natural)Organism: Staphylococcus aureus (bacteria) / synonym: BACTERIA(EUBACTERIA)
Molecular weightExperimental: 8.4 MDa / Theoretical: 8.4 MDa
Virus shellShell ID: 1 / Name: procapsid / Diameter: 370 Å / T number (triangulation number): 4

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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 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureAverage: 97 K
DateNov 18, 2008
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: 83 / Average electron dose: 20 e/Å2
Details: Scanned images were binned to 12.6 microns per pixel
Od range: 2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 62000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 62000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each micrograph
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.99 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN
Details: Final maps were calculated to 8A and filtered at 5A resolution
Number images used: 3944

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