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

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Basic information

Entry
Database: EMDB / ID: 5405
TitleIcosahedral reconstruction of bacteriophage P4 procapsid
Keywordsbacteriophage / P2 / P4 / capsid / procapsid / assembly / size determination / scaffolding protein / triangulation numbers / T=7 dextro / Sid / gpN
SampleSatellite bacteriophage P4 procapsid
SourceEscherichia coli / bacteria / Escherichia coli, E. coli / エシェリキア・コリ, 大腸菌 /
Map dataReconstruction of P4 procapsid
Methodsingle particle (icosahedral) reconstruction, at 8 A resolution
AuthorsDearborn AD / Laurinmaki P / Chandramouli P / Rodenburg CM / Wang S / Butcher SJ / Dokland T
CitationJ. Struct. Biol., 2012, 178, 215-224

J. Struct. Biol., 2012, 178, 215-224 StrPapers
Structure and size determination of bacteriophage P2 and P4 procapsids: function of size responsiveness mutations.
Altaira D Dearborn / Pasi Laurinmaki / Preethi Chandramouli / Cynthia M Rodenburg / Sifang Wang / Sarah J Butcher / Terje Dokland

DateDeposition: Feb 20, 2012 / Header (metadata) release: Feb 22, 2012 / Map release: May 29, 2012 / Last update: Feb 20, 2012

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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
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_5405.map.gz (map file in CCP4 format, 39917 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
217 pix
2.73 A/pix
= 592.41 A
217 pix
2.73 A/pix
= 592.41 A
217 pix
2.73 A/pix
= 592.41 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.73 A
Density
Contour Level:2 (by author), 2 (movie #1):
Minimum - Maximum-6.67676449 - 11.10193157
Average (Standard dev.)-2E-8 (1)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions217217217
Origin-108-108-108
Limit108108108
Spacing217217217
CellA=B=C: 592.41003 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
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 / Number of components: 2 / Oligomeric State: 240 copies of gpN and 60 copies of Sid
MassTheoretical: 11.268 MDa

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Component #1: protein, gpN

ProteinName: gpN / a.k.a: N*, major capsid protein / Oligomeric Details: icosahedral / Recombinant expression: Yes
MassTheoretical: 9.648 MDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: BL21(DE3)
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pET21

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Component #2: protein, Sid

ProteinName: Sid / a.k.a: external scaffolding protein / Oligomeric Details: icosahedral / Recombinant expression: Yes
MassTheoretical: 1.62 MDa
SourceSpecies: Escherichia coli / bacteria / E. coli / エシェリキア・コリ, 大腸菌 /
Strain: BL21(DE3)
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Vector: pET21

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml
Buffer solution: 10 mM Tris-HCl, pH 8.0, 20 mM NaCl, 1 mM MgCl2
pH: 8
Support film200 mesh Quantifoil R2/2
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 110 K / Method: Blot for 2 sec before plunging

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20 / Date: Jan 1, 1999
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 50000 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 900 - 3000 nm
Specimen HolderModel: GATAN LIQUID NITROGEN / Temperature: 97 K ( 95 - 99 K)
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionScanner: OTHER / Sampling size: 4.545 microns / Bit depth: 8

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction / Number of projections: 2286 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: projection matching, polar Fourier transform / Software: EMAN,AUTO3DEM / CTF correction: Each micrograph / Resolution: 8 A / Resolution method: FSC at 0.25 cutoff

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Atomic model buiding

Modeling #1Software: Chimera / Refinement protocol: rigid body / Refinement space: REAL
Details: Protocol: Rigid body fitting of individual subsegments
Input PDB model: 3E8K
Chain ID: B

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