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- EMDB-1123: Membrane proteins modulate the bilayer curvature in the bacterial... -

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Basic information

Entry
Database: EMDB / ID: EMD-1123
TitleMembrane proteins modulate the bilayer curvature in the bacterial virus Bam35.
Map dataBam35 virion
Sample
  • Sample: Bam35c virion
  • Virus: Bacillus phage Bam35 (virus)
Biological speciesBacillus phage Bam35 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsLaurinmaki PA / Huiskonen JT / Bamford DH / Butcher SJ
CitationJournal: Structure / Year: 2005
Title: Membrane proteins modulate the bilayer curvature in the bacterial virus Bam35.
Authors: Pasi Antero Laurinmäki / Juha Tapio Huiskonen / Dennis Henry Bamford / Sarah Jane Butcher /
Abstract: Biological membranes control the flow of molecules into and out of cells, and they transmit information about the milieu. Structural studies of membrane-containing viruses provide one way to study ...Biological membranes control the flow of molecules into and out of cells, and they transmit information about the milieu. Structural studies of membrane-containing viruses provide one way to study these membranes in situ. Cryo-electron microscopy and image reconstruction of bacteriophage Bam35 to 7.3 A resolution revealed a membrane bilayer constrained within an icosahedrally symmetric pseudo T = 25 capsid. A total of 60 large transmembrane protein complexes affect the curvature and thickness of the membrane. Here, we describe these membrane parameters quantitatively. Furthermore, we show that Bam35 differs from bacteriophage PRD1 in these parameters, even though the two viruses share the same principles of capsid architecture. Most notably, each virus possesses a tape measure protein suggesting a general mechanism for capsid size determination in icosahedral viruses.
History
DepositionApr 27, 2005-
Header (metadata) releaseApr 27, 2005-
Map releaseDec 21, 2005-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1590
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1590
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1123.gif

Downloads & links

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Map

FileDownload / File: emd_1123.map.gz / Format: CCP4 / Size: 392.4 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationBam35 virion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.42 Å/pix.
x 595 pix.
= 844.9 Å		1.42 Å/pix.
x 595 pix.
= 844.9 Å		1.42 Å/pix.
x 595 pix.
= 844.9 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.42 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 1430.0 / Movie #1: 1590
Minimum - Maximum-2798.0 - 4683.0
Average (Standard dev.)0.0980345 (±679.715000000000032)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions595595595
Spacing595595595
CellA=B=C: 844.9 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z1.421.421.42
M x/y/z595595595
origin x/y/z0.0000.0000.000
length x/y/z844.900844.900844.900
α/β/γ90.00090.00090.000
start NX/NY/NZ-220-220-220
NX/NY/NZ441441441
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS595595595
D min/max/mean-2798.0004683.0000.098

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Supplemental data

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Sample components

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Entire : Bam35c virion

EntireName: Bam35c virion
Components
  • Sample: Bam35c virion
  • Virus: Bacillus phage Bam35 (virus)

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Supramolecule #1000: Bam35c virion

SupramoleculeName: Bam35c virion / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Bacillus phage Bam35

SupramoleculeName: Bacillus phage Bam35 / type: virus / ID: 1 / Name.synonym: Bam35c / NCBI-ID: 341938 / Sci species name: Bacillus phage Bam35 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: Bam35c
Host (natural)Organism: Bacillus thuringiensis (bacteria) / synonym: BACTERIA(EUBACTERIA)
Virus shellShell ID: 1 / Name: Outer layer / Diameter: 650 Å / T number (triangulation number): 25

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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

Concentration3.0 mg/mL
BufferpH: 7.2 / Details: 10mM KPO4
GridDetails: 400 mesh copper grid, Quantifoil R2/2 holey
VitrificationCryogen name: ETHANE / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: EMBL design
Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding 3 microliters of the sample is held in place at the bottom of a plunger by the means of fine ...Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding 3 microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot off excess buffer, sufficient to leave a thin layer on the grid. The filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed in liquid nitrogen for later use in the microscope.

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 90 K / Max: 94 K / Average: 93 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 50,000
DetailsLow Dose Conditions
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7.0 µm / Number real images: 69 / Bits/pixel: 12
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49300 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 1.9 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsParticles selected using program ETHAN and windowed manually in EMAN. Only particles with DNA were selected.
CTF correctionDetails: Each particle, wiener factor 0.1
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EM3DR2, P3DR / Number images used: 4474

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