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- EMDB-5405: Icosahedral reconstruction of bacteriophage P4 procapsid -

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Basic information

Entry
Database: EMDB / ID: EMD-5405
TitleIcosahedral reconstruction of bacteriophage P4 procapsid
Map dataReconstruction of P4 procapsid
Sample
  • Sample: Satellite bacteriophage P4 procapsid
  • Protein or peptide: gpN
  • Protein or peptide: Sid
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_5405_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5405.map.gz / Format: CCP4 / Size: 38.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of P4 procapsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.73 Å/pix.
x 217 pix.
= 592.41 Å		2.73 Å/pix.
x 217 pix.
= 592.41 Å		2.73 Å/pix.
x 217 pix.
= 592.41 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.73 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 2
Minimum - Maximum-6.67676449 - 11.10193157
Average (Standard dev.)-0.00000002 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-108-108-108
Dimensions217217217
Spacing217217217
CellA=B=C: 592.41003 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.732.732.73
M x/y/z217217217
origin x/y/z0.0000.0000.000
length x/y/z592.410592.410592.410
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-108-108-108
NC/NR/NS217217217
D min/max/mean-6.67711.102-0.000

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Supplemental data

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Sample components

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Entire : Satellite bacteriophage P4 procapsid

EntireName: Satellite bacteriophage P4 procapsid
Components
  • Sample: Satellite bacteriophage P4 procapsid
  • Protein or peptide: gpN
  • Protein or peptide: Sid

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Supramolecule #1000: Satellite bacteriophage P4 procapsid

SupramoleculeName: Satellite bacteriophage P4 procapsid / type: sample / ID: 1000 / Oligomeric state: 240 copies of gpN and 60 copies of Sid / Number unique components: 2
Molecular weightTheoretical: 11.268 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: 9.648 MDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET21

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Macromolecule #2: Sid

MacromoleculeName: Sid / type: protein_or_peptide / ID: 2 / Name.synonym: external scaffolding protein / Oligomeric state: icosahedral / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli) / Strain: BL21(DE3) / synonym: E. coli
Molecular weightTheoretical: 1.62 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
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
DateJan 1, 1999
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 4.545 µm / Average electron dose: 20 e/Å2 / Bits/pixel: 8
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: 2286

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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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