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- PDB-4aoe: Biomphalaria glabrata Acetylcholine-binding protein type 2 (BgAChBP2) -
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Basic information
Entry | Database: PDB / ID: 4aoe | ||||||
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Title | Biomphalaria glabrata Acetylcholine-binding protein type 2 (BgAChBP2) | ||||||
![]() | ACETYLCHOLINE-BINDING PROTEIN TYPE 2 | ||||||
![]() | ACETYLCHOLINE-BINDING PROTEIN / LIGAND GATED ION CHANNEL / LGIC / CYS-LOOP RECEPTOR / ACHBP / ACETYLCHOLINE / ACHR / ACETYLCHOLINE RECEPTOR / MYASTHENIA GRAVIS / PENTAGONAL DODECAHEDRON / NICOTINIC / SCHISTOSOMA MANSONI / BILHARZIOSIS | ||||||
Function / homology | extracellular ligand-gated monoatomic ion channel activity / 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 / transmembrane signaling receptor activity / membrane => GO:0016020 / Acetylcholine-binding protein type 2![]() | ||||||
Biological species | ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 Å | ||||||
![]() | Saur, M. / Moeller, V. / Kapetanopoulos, K. / Braukmann, S. / Gebauer, W. / Tenzer, S. / Markl, J. | ||||||
![]() | ![]() 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 |
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Remark 650 | HELIX DETERMINATION METHOD: AUTHOR PROVIDED. | ||||||
Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 185 KB | Display | ![]() |
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PDB format | ![]() | 155.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2055MC ![]() 4aodC C: citing same article ( M: map data used to model this data |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Symmetry | Point symmetry: (Schoenflies symbol: T (tetrahedral)) | ||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 23533.713 Da / Num. of mol.: 5 / Source method: isolated from a natural source Details: TWELVE PENTAMERS CONSTITUTE THE BGACHBP PENTAGONAL DODECAHEDRON Source: (natural) ![]() Tissue: HEMOLYMPH / References: UniProt: J7JGR6*PLUS Sequence details | GENBANK ACCESSION JQ814368 | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: BIOMPHALARIA GLABRATA ACETYLCHOLINE-BINDING PROTEIN / Type: COMPLEX |
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Buffer solution | Name: 50 MM TRIS-HCL, 5 MM MGCL2 5MM CACL2, 300MM NACL / pH: 7.4 / Details: 50 MM TRIS-HCL, 5 MM MGCL2 5MM CACL2, 300MM NACL |
Specimen | Conc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 97, TEMPERATURE- 97, INSTRUMENT- GATAN CRYOPLUNGE 3, METHOD- 2 X3.5 MICROLITRES, 2 X 3S BLOTTING |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Jun 4, 2008 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm |
Specimen holder | Temperature: 101 K / Tilt angle max: 0 ° |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 151 |
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Processing
EM software | Name: EMAN / Version: 1.9 / Category: 3D reconstruction | ||||||||||||
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CTF correction | Details: PER MICROGRAPH | ||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Method: PROJECTION MATCHING / Resolution: 6 Å / Num. of particles: 8183 / Nominal pixel size: 1 Å / Actual pixel size: 1 Å Details: A NEGATIVE TEMPERATURE FACTOR OF 278.9 WAS APPLIED TO THE FINAL CRYO-EM RECONSTRUCTION. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2055 (DEPOSITION ID: 10661). Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: OTHER / Space: RECIPROCAL / Details: REFINEMENT PROTOCOL--X-RAY | ||||||||||||
Atomic model building | PDB-ID: 2BYN | ||||||||||||
Refinement | Highest resolution: 5.8 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 5.8 Å
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