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- EMDB-5406: Icosahedral reconstruction of bacteriophage P2 procapsid -

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Basic information

Entry
Database: EMDB / ID: EMD-5406
TitleIcosahedral reconstruction of bacteriophage P2 procapsid
Map dataReconstruction of bacteriophage P2 procapsid
Sample
  • Sample: Bacteriophage P2 procapsid
  • Protein or peptide: gpN
Keywordsbacteriophage / P2 / P4 / capsid / procapsid / assembly / size determination / scaffolding protein / triangulation numbers / T=7 dextro / Sid / gpN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.0 Å
AuthorsDearborn AD / Laurinmaki P / Chandramouli P / Rodenburg CM / Wang S / Butcher SJ / Dokland T
CitationJournal: J Struct Biol / Year: 2012
Title: Structure and size determination of bacteriophage P2 and P4 procapsids: function of size responsiveness mutations.
Authors: Altaira D Dearborn / Pasi Laurinmaki / Preethi Chandramouli / Cynthia M Rodenburg / Sifang Wang / Sarah J Butcher / Terje Dokland /
Abstract: Bacteriophage P4 is dependent on structural proteins supplied by a helper phage, P2, to assemble infectious virions. Bacteriophage P2 normally forms an icosahedral capsid with T=7 symmetry from the ...Bacteriophage P4 is dependent on structural proteins supplied by a helper phage, P2, to assemble infectious virions. Bacteriophage P2 normally forms an icosahedral capsid with T=7 symmetry from the gpN capsid protein, the gpO scaffolding protein and the gpQ portal protein. In the presence of P4, however, the same structural proteins are assembled into a smaller capsid with T=4 symmetry. This size determination is effected by the P4-encoded protein Sid, which forms an external scaffold around the small P4 procapsids. Size responsiveness (sir) mutants in gpN fail to assemble small capsids even in the presence of Sid. We have produced large and small procapsids by co-expression of gpN with gpO and Sid, respectively, and applied cryo-electron microscopy and three-dimensional reconstruction methods to visualize these procapsids. gpN has an HK97-like fold and interacts with Sid in an exposed loop where the sir mutations are clustered. The T=7 lattice of P2 has dextro handedness, unlike the laevo lattices of other phages with this fold observed so far.
History
DepositionFeb 20, 2012-
Header (metadata) releaseFeb 22, 2012-
Map releaseMay 29, 2012-
UpdateMay 29, 2012-
Current statusMay 29, 2012Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5406_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5406.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of bacteriophage P2 procapsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 320 pix.
= 655.36 Å		2.05 Å/pix.
x 320 pix.
= 655.36 Å		2.05 Å/pix.
x 320 pix.
= 655.36 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: 2.0 / Movie #1: 2
Minimum - Maximum-6.91172457 - 10.358766559999999
Average (Standard dev.)0.07234638 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 655.36005 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.0482.0482.048
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z655.360655.360655.360
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-160-160-160
NC/NR/NS320320320
D min/max/mean-6.91210.3590.072

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Supplemental data

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Sample components

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Entire : Bacteriophage P2 procapsid

EntireName: Bacteriophage P2 procapsid
Components
  • Sample: Bacteriophage P2 procapsid
  • Protein or peptide: gpN

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Supramolecule #1000: Bacteriophage P2 procapsid

SupramoleculeName: Bacteriophage P2 procapsid / type: sample / ID: 1000 / Details: gpO is disordered and not visible in the map
Oligomeric state: 420 copies of gpN and 100-150 copies of gpO
Number unique components: 2
Molecular weightTheoretical: 16.884 MDa

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Macromolecule #1: gpN

MacromoleculeName: gpN / type: protein_or_peptide / ID: 1 / Name.synonym: N*, major capsid protein / Oligomeric state: icosahedral / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3) / synonym: Escherichia coli
Molecular weightTheoretical: 16.884 MDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET21

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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: 8 / Details: 10 mM Tris-HCl, pH 8.0, 20 mM NaCl, 1 mM MgCl2
GridDetails: 200 mesh Quantifoil R2/2 or Lacey carbon
VitrificationCryogen name: ETHANE / Chamber temperature: 110 K / Instrument: HOMEMADE PLUNGER / Method: Blot for 2 sec before plunging

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 95 K / Max: 99 K / Average: 97 K
DateApr 22, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 12.7 µm / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 50000
Sample stageSpecimen 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 reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 8.0 Å / Resolution method: OTHER / Software - Name: EMAN,AUTO3DEM / Number images used: 7582

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Atomic model buiding 1

Initial modelPDB ID:

3e8k


Chain - Chain ID: B
SoftwareName: Chimera
DetailsProtocol: Rigid body fitting of individual subsegments
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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