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- EMDB-2055: Acetylcholine-binding protein in the hemolymph of the planorbid s... -

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Basic information

Entry
Database: EMDB / ID: 2055
TitleAcetylcholine-binding protein in the hemolymph of the planorbid snail Biomphalaria glabrata is a pentagonal dodecahedron (60 subunits)
Keywordsligand gated ion channel / LGIC / Cys-loop receptor / AChBP / acetylcholine binding protein / acetylcholine / AChR / acetylcholine receptor / Myasthenia gravis / pentagonal dodecahedron / nicotinic / dodecahedron / Schistosoma mansoni / bilharziosis / Biomphalaria glabrata / snail
SampleAcetylcholine Binding Protein (AChBP) from Biomphalaria glabrata
SourceBiomphalaria glabrata / invertebrata
Map dataA negative temperature factor of 278.9 A^2 was applied to the map.
Methodsingle particle (icosahedral) reconstruction, at 6 A resolution
AuthorsSaur M / Moeller V / Kapetanopoulos K / Braukmann S / Gebauer W / Tenzer S / Markl J
CitationPLoS ONE, 2012, 7, e43685-e43685

PLoS ONE, 2012, 7, e43685-e43685 StrPapers
Acetylcholine-binding protein in the hemolymph of the planorbid snail Biomphalaria glabrata is a pentagonal dodecahedron (60 subunits).
Michael Saur / Vanessa Moeller / Katharina Kapetanopoulos / Sandra Braukmann / Wolfgang Gebauer / Stefan Tenzer / Jürgen Markl

DateDeposition: Mar 19, 2012 / Header (metadata) release: Apr 5, 2012 / Map release: Aug 29, 2012 / Last update: Mar 19, 2012

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF CHIMERA
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-4aod
  • Surface level: 1
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-4aoe
  • Surface level: 1
  • Imaged by UCSF CHIMERA
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Supplemental images

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Map

Fileemd_2055.map.gz (map file in CCP4 format, 91383 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
286 pix
1 A/pix
= 286. A
286 pix
1 A/pix
= 286. A
286 pix
1 A/pix
= 286. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1 A
Density
Contour Level:1 (by author), 1 (movie #1):
Minimum - Maximum-0.59094787 - 3.62690711
Average (Standard dev.)0.14051077 (0.43470621)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions286286286
Origin000
Limit285285285
Spacing286286286
CellA=B=C: 286 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z111
M x/y/z286286286
origin x/y/z0.0000.0000.000
length x/y/z286.000286.000286.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS286286286
D min/max/mean-0.5913.6270.141

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Supplemental data

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Sample components

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Entire Acetylcholine Binding Protein (AChBP) from Biomphalaria glabrata

EntireName: Acetylcholine Binding Protein (AChBP) from Biomphalaria glabrata
Number of components: 1
MassTheoretical: 1.86 MDa / Experimental: 1.86 MDa / Measured by: SDS-PAGE

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Component #1: protein, Biomphalaria glabrata Acetylcholine Binding Protein

ProteinName: Biomphalaria glabrata Acetylcholine Binding Protein / a.k.a: BgAChBP / Oligomeric Details: Dodecapentamer
Details: As yet, it is not entirely clear whether the dodecahedron is a homomeric assembly of either type one and/or two, or a heteromeric assembly of types one and two.
Recombinant expression: No / Number of Copies: 60
MassTheoretical: 1.86 MDa / Experimental: 1.86 MDa
SourceSpecies: Biomphalaria glabrata / invertebrata
Source (natural)Organ or tissue: Hemolymph

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1.2 mg/ml
Buffer solution: 50 mM Tris-HCl, 5 mM MgCl2, 5mM CaCl2, 300mM NaCl
pH: 7.4
Support filmC-flat holey carbon grids CF-2/2-3C-T, 30s glow discharge at 25 mA
VitrificationInstrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Temperature: 97 K / Humidity: 97 % / Method: 2 x3.5 microlitres with 2 x 3s blotting

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Electron microscopy imaging #1

ImagingMicroscope: FEI TECNAI F20 / Date: Jun 4, 2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 30 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal)
Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 5000 nm
Specimen HolderModel: GATAN LIQUID NITROGEN / Temperature: 101 K
CameraDetector: KODAK SO-163 FILM

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Electron microscopy imaging #2

ImagingMicroscope: FEI TECNAI F20 / Date: May 25, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 30 e/A2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal)
Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 5000 nm
Specimen HolderModel: GATAN LIQUID NITROGEN / Temperature: 101 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 151 / Scanner: PRIMESCAN / Sampling size: 5 microns / Bit depth: 8

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Image processing

ProcessingMethod: single particle (icosahedral) reconstruction
Details: manual selection with boxer, ctf-correction with FindCTF2d, refinement: EMAN1.9 (15 iterative cycles), final reconstruction using 1-degree references
Number of projections: 8374 / Number of class averages: 608 / Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Projection matching / Software: EMAN1.9 / CTF correction: per micrograph / Resolution: 6 A / Resolution method: FSC 0.5

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Output model

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