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- EMDB-2486: Electron microscopy of negatively-stained p9 tail protein from ba... -

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Basic information

Entry
Database: EMDB / ID: EMD-2486
TitleElectron microscopy of negatively-stained p9 tail protein from bacillus phi29 bacteriophage
Map dataReconstruction of bacteriophage phi29 tail protein
Sample
  • Sample: p9 protein from phi29 bacteriophage
  • Protein or peptide: p9
KeywordsBacteriophage / Tail protein
Function / homologyDistal tube protein, N-terminal / Caudoviral major tail protein N-terminus / virus tail, tube / symbiont genome ejection through host cell envelope, short tail mechanism / virus tail / symbiont genome entry into host cell via pore formation in plasma membrane / Tail knob protein gp9
Function and homology information
Biological speciesBacillus phage phi29 (virus)
Methodsingle particle reconstruction / negative staining / Resolution: 20.0 Å
AuthorsCuervo A / Chagoyen M / Pulido-Cid M / Camacho A / Carrascosa JL
CitationJournal: To Be Published
Title: Structural characterization of T7 tail machinery reveals a conserved tubular structure among other members of the Podoviridae family suggesting a common mechanism for DNA delivery
Authors: Cuervo A / Chagoyen M / Pulido-Cid M / Camacho A / Carrascosa JL
History
DepositionOct 15, 2013-
Header (metadata) releaseOct 30, 2013-
Map releaseOct 29, 2014-
UpdateOct 29, 2014-
Current statusOct 29, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018061
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.018061
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2486.png

Downloads & links

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Map

FileDownload / File: emd_2486.map.gz / Format: CCP4 / Size: 825.2 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of bacteriophage phi29 tail protein
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.14 Å/pix.
x 60 pix.
= 248.4 Å		4.14 Å/pix.
x 60 pix.
= 248.4 Å		4.14 Å/pix.
x 60 pix.
= 248.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.14 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018061 / Movie #1: 0.018061
Minimum - Maximum-0.00461828 - 0.09322559
Average (Standard dev.)0.00154414 (±0.00842365)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions606060
Spacing606060
CellA=B=C: 248.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.144.144.14
M x/y/z606060
origin x/y/z0.0000.0000.000
length x/y/z248.400248.400248.400
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS606060
D min/max/mean-0.0050.0930.002

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Supplemental data

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Sample components

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Entire : p9 protein from phi29 bacteriophage

EntireName: p9 protein from phi29 bacteriophage
Components
  • Sample: p9 protein from phi29 bacteriophage
  • Protein or peptide: p9

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Supramolecule #1000: p9 protein from phi29 bacteriophage

SupramoleculeName: p9 protein from phi29 bacteriophage / type: sample / ID: 1000 / Oligomeric state: hexamer / Number unique components: 1
Molecular weightTheoretical: 402 KDa

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Macromolecule #1: p9

MacromoleculeName: p9 / type: protein_or_peptide / ID: 1 / Details: The protein was cloned with an His-tag / Number of copies: 6 / Oligomeric state: hexamer / Recombinant expression: Yes
Source (natural)Organism: Bacillus phage phi29 (virus)
Molecular weightExperimental: 67 KDa / Theoretical: 67 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant strain: Top10 / Recombinant plasmid: pBAD/His B
SequenceUniProtKB: Tail knob protein gp9

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.8 / Details: 50 mM Tris-HCl, 100mM NaCl and 10 mM MgCl2
StainingType: NEGATIVE
Details: GraFix-fixated proteins stained on 2% w/v uranyl acetate for 1 min.
GridDetails: 400 mesh cupper grid coated with a carbon layer, glow discharged
VitrificationCryogen name: NONE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
DateJan 25, 2012
Image recordingCategory: CCD / Film or detector model: FEI EAGLE (4k x 4k) / Number real images: 100 / Average electron dose: 10 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 108696
Sample stageSpecimen holder model: PHILIPS ROTATION HOLDER
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each micrograph
Final reconstructionApplied symmetry - Point group: C6 (6 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN, Xmipp / Number images used: 4362

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