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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
TitleBiomphalaria glabrata Acetylcholine-binding protein type 2 (BgAChBP2)
ComponentsACETYLCHOLINE-BINDING PROTEIN TYPE 2
KeywordsACETYLCHOLINE-BINDING PROTEIN / LIGAND GATED ION CHANNEL / LGIC / CYS-LOOP RECEPTOR / ACHBP / ACETYLCHOLINE / ACHR / ACETYLCHOLINE RECEPTOR / MYASTHENIA GRAVIS / PENTAGONAL DODECAHEDRON / NICOTINIC / SCHISTOSOMA MANSONI / BILHARZIOSIS
Function / homologyextracellular 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 / postsynapse / membrane / Acetylcholine-binding protein type 2
Function and homology information
Biological speciesBIOMPHALARIA GLABRATA (bloodfluke planorb)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6 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 26, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 26, 2012Group: Database references
Revision 1.2Oct 3, 2018Group: Data collection
Category: diffrn_radiation / diffrn_radiation_wavelength / em_software
Item: _em_software.image_processing_id
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_3d_fitting_list / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_oper_list / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _pdbx_entry_details.has_protein_modification / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _refine.ls_d_res_high
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

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Assembly

Deposited unit
A: ACETYLCHOLINE-BINDING PROTEIN TYPE 2
B: ACETYLCHOLINE-BINDING PROTEIN TYPE 2
C: ACETYLCHOLINE-BINDING PROTEIN TYPE 2
D: ACETYLCHOLINE-BINDING PROTEIN TYPE 2
E: ACETYLCHOLINE-BINDING PROTEIN TYPE 2


Theoretical massNumber of molelcules
Total (without water)117,6695
Polymers117,6695
Non-polymers00
Water00
1
A: ACETYLCHOLINE-BINDING PROTEIN TYPE 2
B: ACETYLCHOLINE-BINDING PROTEIN TYPE 2
C: ACETYLCHOLINE-BINDING PROTEIN TYPE 2
D: ACETYLCHOLINE-BINDING PROTEIN TYPE 2
E: ACETYLCHOLINE-BINDING PROTEIN TYPE 2
x 12


Theoretical massNumber of molelcules
Total (without water)1,412,02360
Polymers1,412,02360
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation11
2


  • Idetical with deposited unit
  • point asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: T (tetrahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-0.638235, 0.262556, 0.723685), (0.263276, -0.808923, 0.52567), (0.723424, 0.52603, 0.447158)93.2329, 145.85156, -99.61087
3generate(0.05354, -0.688324, 0.723425), (0.688513, -0.499271, -0.526002), (0.723245, 0.52625, 0.447189)130.33752, 191.18123, -99.61156
4generate(-0.138197, 0.951057, -0.27639), (-0.425326, -0.309014, -0.850652), (-0.894427, -2.0E-6, 0.447214)66.2839, 369.65385, 206.95127
5generate(0.361983, 0.262984, -0.89432), (-0.588201, 0.808715, -0.000268), (0.723179, 0.526137, 0.447428)181.51684, 111.52288, -99.64622
6generate(-0.44779, 0.850337, -0.276426), (-0.525647, -0.000262, 0.850703), (0.723312, 0.526239, 0.447094)124.96839, 96.54892, -99.6064
7generate(0.809328, -0.587357, 0.000117), (-0.587357, -0.809328, -4.6E-5), (0.000122, -3.1E-5, -1)111.22375, 342.75416, 285.98582
8generate(-0.671086, 0.687901, 0.27647), (0.162163, 0.500082, -0.850659), (-0.723427, -0.526032, -0.44715)101.05413, 169.9462, 385.60843
9generate(-0.361624, -0.263238, 0.89439), (-0.588261, 0.808671, 0.000161), (-0.72331, -0.526077, -0.447288)104.46807, 111.4548, 385.63868
10generate(0.447724, -0.850437, 0.276224), (-0.52593, -0.00063, 0.850528), (-0.723146, -0.526076, -0.447552)161.09678, 96.67429, 385.65377
11generate(0.638661, -0.262488, -0.723334), (0.263075, -0.808894, 0.525816), (-0.723121, -0.526109, -0.447555)192.634, 145.85092, 385.65465
12generate(-0.053475, 0.688102, -0.723641), (0.688529, -0.499455, -0.525807), (-0.723235, -0.526365, -0.44707)155.73938, 191.15112, 385.60831

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Components

#1: Protein
ACETYLCHOLINE-BINDING PROTEIN TYPE 2


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) BIOMPHALARIA GLABRATA (bloodfluke planorb)
Tissue: HEMOLYMPH / References: UniProt: J7JGR6*PLUS
Has protein modificationY
Sequence detailsGENBANK ACCESSION JQ814368

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: BIOMPHALARIA GLABRATA ACETYLCHOLINE-BINDING PROTEIN / Type: COMPLEX
Buffer solutionName: 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
SpecimenConc.: 1.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: 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
MicroscopyModel: FEI TECNAI F20 / Date: Jun 4, 2008
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 5000 nm / Nominal defocus min: 2000 nm / Cs: 2 mm
Specimen holderTemperature: 101 K / Tilt angle max: 0 °
Image recordingElectron dose: 30 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 151

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Processing

EM softwareName: EMAN / Version: 1.9 / Category: 3D reconstruction
CTF correctionDetails: PER MICROGRAPH
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: 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 buildingProtocol: OTHER / Space: RECIPROCAL / Details: REFINEMENT PROTOCOL--X-RAY
Atomic model buildingPDB-ID: 2BYN

2byn


Accession code: 2BYN / Source name: PDB / Type: experimental model
RefinementHighest resolution: 6 Å
Refinement stepCycle: LAST / Highest resolution: 5.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8295 0 0 0 8295

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