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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: EMD-2055
TitleAcetylcholine-binding protein in the hemolymph of the planorbid snail Biomphalaria glabrata is a pentagonal dodecahedron (60 subunits)
Map dataA negative temperature factor of 278.9 A^2 was applied to the map.
Sample
  • Sample: Acetylcholine Binding Protein (AChBP) from Biomphalaria glabrata
  • Protein or peptide: Biomphalaria glabrata Acetylcholine Binding Protein
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
Function / homology
Function and homology information


excitatory extracellular ligand-gated monoatomic ion channel activity / transmitter-gated monoatomic ion channel activity involved in regulation of postsynaptic membrane potential / transmembrane signaling receptor activity / postsynapse / neuron projection / membrane
Similarity search - Function
Neurotransmitter-gated ion-channel / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel ligand-binding domain superfamily / Neurotransmitter-gated ion-channel ligand binding domain
Similarity search - Domain/homology
Acetylcholine-binding protein type 2 / Acetylcholine-binding protein type 1
Similarity search - Component
Biological speciesBiomphalaria glabrata (bloodfluke planorb)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.0 Å
AuthorsSaur M / Moeller V / Kapetanopoulos K / Braukmann S / Gebauer W / Tenzer S / Markl J
CitationJournal: PLoS One / Year: 2012
Title: Acetylcholine-binding protein in the hemolymph of the planorbid snail Biomphalaria glabrata is a pentagonal dodecahedron (60 subunits).
Authors: Michael Saur / Vanessa Moeller / Katharina Kapetanopoulos / Sandra Braukmann / Wolfgang Gebauer / Stefan Tenzer / Jürgen Markl /
Abstract: Nicotinic acetylcholine receptors (nAChR) play important neurophysiological roles and are of considerable medical relevance. They have been studied extensively, greatly facilitated by the gastropod ...Nicotinic acetylcholine receptors (nAChR) play important neurophysiological roles and are of considerable medical relevance. They have been studied extensively, greatly facilitated by the gastropod acetylcholine-binding proteins (AChBP) which represent soluble structural and functional homologues of the ligand-binding domain of nAChR. All these proteins are ring-like pentamers. Here we report that AChBP exists in the hemolymph of the planorbid snail Biomphalaria glabrata (vector of the schistosomiasis parasite) as a regular pentagonal dodecahedron, 22 nm in diameter (12 pentamers, 60 active sites). We sequenced and recombinantly expressed two ∼25 kDa polypeptides (BgAChBP1 and BgAChBP2) with a specific active site, N-glycan site and disulfide bridge variation. We also provide the exon/intron structures. Recombinant BgAChBP1 formed pentamers and dodecahedra, recombinant BgAChBP2 formed pentamers and probably disulfide-bridged di-pentamers, but not dodecahedra. Three-dimensional electron cryo-microscopy (3D-EM) yielded a 3D reconstruction of the dodecahedron with a resolution of 6 Å. Homology models of the pentamers docked to the 6 Å structure revealed opportunities for chemical bonding at the inter-pentamer interfaces. Definition of the ligand-binding pocket and the gating C-loop in the 6 Å structure suggests that 3D-EM might lead to the identification of functional states in the BgAChBP dodecahedron.
History
DepositionMar 19, 2012-
Header (metadata) releaseApr 5, 2012-
Map releaseAug 29, 2012-
UpdateSep 26, 2012-
Current statusSep 26, 2012Processing site: PDBe / Status: Released

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Structure visualization

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  • Surface view with fitted model
  • Atomic models: PDB-4aod
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  • Surface view with fitted model
  • Atomic models: PDB-4aoe
  • Surface level: 1
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4aoe
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2055_gal...

Downloads & links

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Map

FileDownload / File: emd_2055.map.gz / Format: CCP4 / Size: 87.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA negative temperature factor of 278.9 A^2 was applied to the map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 286 pix.
= 286. Å		1 Å/pix.
x 286 pix.
= 286. Å		1 Å/pix.
x 286 pix.
= 286. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-0.59094787 - 3.62690711
Average (Standard dev.)0.14051077 (±0.43470621)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions286286286
Spacing286286286
CellA=B=C: 286.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z286286286
origin x/y/z0.0000.0000.000
length x/y/z286.000286.000286.000
α/β/γ90.00090.00090.000
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
Components
  • Sample: Acetylcholine Binding Protein (AChBP) from Biomphalaria glabrata
  • Protein or peptide: Biomphalaria glabrata Acetylcholine Binding Protein

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Supramolecule #1000: Acetylcholine Binding Protein (AChBP) from Biomphalaria glabrata

SupramoleculeName: Acetylcholine Binding Protein (AChBP) from Biomphalaria glabrata
type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 1.86 MDa / Theoretical: 1.86 MDa / Method: SDS-PAGE

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Macromolecule #1: Biomphalaria glabrata Acetylcholine Binding Protein

MacromoleculeName: Biomphalaria glabrata Acetylcholine Binding Protein / type: protein_or_peptide / ID: 1 / Name.synonym: BgAChBP
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.
Number of copies: 60 / Oligomeric state: Dodecapentamer / Recombinant expression: No
Source (natural)Organism: Biomphalaria glabrata (bloodfluke planorb) / Tissue: Hemolymph
Molecular weightExperimental: 1.86 MDa / Theoretical: 1.86 MDa

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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

Concentration1.2 mg/mL
BufferpH: 7.4 / Details: 50 mM Tris-HCl, 5 mM MgCl2, 5mM CaCl2, 300mM NaCl
GridDetails: C-flat holey carbon grids CF-2/2-3C-T, 30s glow discharge at 25 mA
VitrificationCryogen name: ETHANE / Chamber humidity: 97 % / Chamber temperature: 97 K / Instrument: GATAN CRYOPLUNGE 3 / Method: 2 x3.5 microlitres with 2 x 3s blotting

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Electron microscopy #1

Microscopy ID1
MicroscopeFEI TECNAI F20
TemperatureAverage: 101 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification
DateJun 4, 2008
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 5 µm / Number real images: 151 / Average electron dose: 30 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Electron microscopy #2

Microscopy ID2
MicroscopeFEI TECNAI F20
TemperatureAverage: 101 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 120,000 times magnification
DateMay 25, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 5 µm / Number real images: 151 / Average electron dose: 30 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 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

Detailsmanual selection with boxer, ctf-correction with FindCTF2d, refinement: EMAN1.9 (15 iterative cycles), final reconstruction using 1-degree references
CTF correctionDetails: per micrograph
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN1.9 / Number images used: 8374
Final two d classificationNumber classes: 608

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