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- PDB-2bg9: REFINED STRUCTURE OF THE NICOTINIC ACETYLCHOLINE RECEPTOR AT 4A R... -

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Basic information

Entry
Database: PDB / ID: 2bg9
TitleREFINED STRUCTURE OF THE NICOTINIC ACETYLCHOLINE RECEPTOR AT 4A RESOLUTION.
Components
  • ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA CHAIN
  • ACETYLCHOLINE RECEPTOR PROTEIN, BETA CHAIN
  • ACETYLCHOLINE RECEPTOR PROTEIN, DELTA CHAIN
  • ACETYLCHOLINE RECEPTOR PROTEIN, GAMMA CHAIN
KeywordsION CHANNEL/RECEPTOR / ACETYLCHOLINE RECEPTOR / ION CHANNEL / ION TRANSPORT / POSTSYNAPTIC MEMBRANE / ION CHANNEL-RECEPTOR complex
Function / homology
Function and homology information


acetylcholine-gated channel complex / acetylcholine-gated monoatomic cation-selective channel activity / acetylcholine receptor signaling pathway / transmembrane signaling receptor activity / postsynaptic membrane
Similarity search - Function
Neurotransmitter-gated ion-channel transmembrane domain / Nicotinic acetylcholine receptor / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor ...Neurotransmitter-gated ion-channel transmembrane domain / Nicotinic acetylcholine receptor / Acetylcholine Binding Protein; Chain: A, / Neurotransmitter-gated ion-channel ligand-binding domain / Neurotransmitter-gated ion-channel, conserved site / Neurotransmitter-gated ion-channels signature. / Neurotransmitter-gated ion-channel transmembrane domain / Neurotransmitter-gated ion-channel transmembrane region / Neurotransmitter-gated ion-channel transmembrane domain superfamily / Neuronal acetylcholine receptor / 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 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Distorted Sandwich / Up-down Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Acetylcholine receptor subunit alpha / Acetylcholine receptor subunit delta / Acetylcholine receptor gamma subunit / Acetylcholine receptor subunit beta
Similarity search - Component
Biological speciesTORPEDO MARMORATA (marbled electric ray)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4 Å
AuthorsUnwin, N.
Citation
Journal: J Mol Biol / Year: 2005
Title: Refined structure of the nicotinic acetylcholine receptor at 4A resolution.
Authors: Nigel Unwin /
Abstract: We present a refined model of the membrane-associated Torpedo acetylcholine (ACh) receptor at 4A resolution. An improved experimental density map was obtained from 342 electron images of helical ...We present a refined model of the membrane-associated Torpedo acetylcholine (ACh) receptor at 4A resolution. An improved experimental density map was obtained from 342 electron images of helical tubes, and the refined structure was derived to an R-factor of 36.7% (R(free) 37.9%) by standard crystallographic methods, after placing the densities corresponding to a single molecule into an artificial unit cell. The agreement between experimental and calculated phases along the helical layer-lines was used to monitor progress in the refinement and to give an independent measure of the accuracy. The atomic model allowed a detailed description of the whole receptor in the closed-channel form, including the ligand-binding and intracellular domains, which have not previously been interpreted at a chemical level. We confirm that the two ligand-binding alpha subunits have a different extended conformation from the three other subunits in the closed channel, and identify several interactions on both pairs of subunit interfaces, and within the alpha subunits, which may be responsible for their "distorted" structures. The ACh-coordinating amino acid side-chains of the alpha subunits are far apart in the closed channel, indicating that a localised rearrangement, involving closure of loops B and C around the bound ACh molecule, occurs upon activation. A comparison of the structure of the alpha subunit with that of AChBP having ligand present, suggests how the localised rearrangement overcomes the distortions and initiates the rotational movements associated with opening of the channel. Both vestibules of the channel are strongly electronegative, providing a cation-stabilising environment at either entrance of the membrane pore. Access to the pore on the intracellular side is further influenced by narrow lateral windows, which would be expected to screen out electrostatically ions of the wrong charge and size.
#1: Journal: Nature / Year: 2003
Title: Structure and gating mechanism of the acetylcholine receptor pore.
Authors: Atsuo Miyazawa / Yoshinori Fujiyoshi / Nigel Unwin /
Abstract: The nicotinic acetylcholine receptor controls electrical signalling between nerve and muscle cells by opening and closing a gated, membrane-spanning pore. Here we present an atomic model of the ...The nicotinic acetylcholine receptor controls electrical signalling between nerve and muscle cells by opening and closing a gated, membrane-spanning pore. Here we present an atomic model of the closed pore, obtained by electron microscopy of crystalline postsynaptic membranes. The pore is shaped by an inner ring of 5 alpha-helices, which curve radially to create a tapering path for the ions, and an outer ring of 15 alpha-helices, which coil around each other and shield the inner ring from the lipids. The gate is a constricting hydrophobic girdle at the middle of the lipid bilayer, formed by weak interactions between neighbouring inner helices. When acetylcholine enters the ligand-binding domain, it triggers rotations of the protein chains on opposite sides of the entrance to the pore. These rotations are communicated through the inner helices, and open the pore by breaking the girdle apart.
History
DepositionDec 17, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 2, 2019Group: Author supporting evidence / Data collection / Other / Category: atom_sites / cell / em_single_particle_entity
Item: _atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] ..._atom_sites.fract_transf_matrix[1][1] / _atom_sites.fract_transf_matrix[2][2] / _atom_sites.fract_transf_matrix[3][3] / _cell.length_a / _cell.length_b / _cell.length_c
Revision 1.4Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Remark 650 HELIX DETERMINATION METHOD: AUTHOR PROVIDED.
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Assembly

Deposited unit
A: ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA CHAIN
B: ACETYLCHOLINE RECEPTOR PROTEIN, BETA CHAIN
C: ACETYLCHOLINE RECEPTOR PROTEIN, DELTA CHAIN
D: ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA CHAIN
E: ACETYLCHOLINE RECEPTOR PROTEIN, GAMMA CHAIN


Theoretical massNumber of molelcules
Total (without water)211,7505
Polymers211,7505
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS

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Components

#1: Protein ACETYLCHOLINE RECEPTOR PROTEIN, ALPHA CHAIN / / NICOTINIC ACETYLCHOLINE RECEPTOR


Mass: 42501.316 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) TORPEDO MARMORATA (marbled electric ray) / Organ: ELECTRIC ORGAN / Tissue: DERIVED FROM MUSCLE / References: UniProt: P02711
#2: Protein ACETYLCHOLINE RECEPTOR PROTEIN, BETA CHAIN / / NICOTINIC ACETYLCHOLINE RECEPTOR


Mass: 42167.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TORPEDO MARMORATA (marbled electric ray) / Organ: ELECTRIC ORGAN / Tissue: DERIVED FROM MUSCLE / References: UniProt: Q6S3I0
#3: Protein ACETYLCHOLINE RECEPTOR PROTEIN, DELTA CHAIN / / NICOTINIC ACETYLCHOLINE RECEPTOR


Mass: 42280.695 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) TORPEDO MARMORATA (marbled electric ray) / Organ: ELECTRIC ORGAN / Tissue: DERIVED FROM MUSCLE / References: UniProt: Q6S3H8
#4: Protein ACETYLCHOLINE RECEPTOR PROTEIN, GAMMA CHAIN / / NICOTINIC ACETYLCHOLINE RECEPTOR


Mass: 42299.496 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: INHABITS THE EUROPEAN COAST / Source: (natural) TORPEDO MARMORATA (marbled electric ray) / Organ: ELECTRIC ORGAN / Tissue: DERIVED FROM MUSCLE / References: UniProt: Q6S3H9

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: NICOTINIC ACETYLCHOLINE RECEPTOR in postsynaptic membrane
Type: COMPLEX
Buffer solutionName: 100MM SODIUM CACODYLATE / pH: 6.8 / Details: 100MM SODIUM CACODYLATE
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationDetails: LIQUID ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL 3000SFF / Date: Oct 1, 2000
Details: THE SPECIMENS WERE TUBULAR CRYSTALS GROWN IN LOW SALT BUFFER FROM ISOLATED TORPEDO POSTSYNAPTIC MEMBRANES. THEY WERE APPLIED TO THE MICROSCOPE GRIDS AND FROZEN IN THE SAME SOLUTION. THESE ...Details: THE SPECIMENS WERE TUBULAR CRYSTALS GROWN IN LOW SALT BUFFER FROM ISOLATED TORPEDO POSTSYNAPTIC MEMBRANES. THEY WERE APPLIED TO THE MICROSCOPE GRIDS AND FROZEN IN THE SAME SOLUTION. THESE CRYSTALS WERE TOO SMALL AND DISTORTED TO YIELD MEANINGFUL ELECTRON DIFFRACTION PATTERNS, SO BOTH THE AMPLITUDE AND THE PHASE TERMS HAD TO BE MEASURED FROM FOURIER TRANSFORMS OF THE IMAGES. THE IMAGES WERE RECORDED USING A DOSE OF 2000 ELECTRONS/NM2 DURING THE PERIOD: JAN-1996 TO OCT-2002. THE DATASETS INVOLVED 4 HELICAL FAMILIES OF TUBES. STRUCTURES WERE SYNTHESISED FROM THE AMPLITUDE AND PHASE TERMS DERIVED FROM EACH FAMILY. THE FINAL DATASET WAS OBTAINED BY AVERAGING THESE 4 STRUCTURES IN REAL SPACE.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 40000 X / Calibrated magnification: 36800 X / Nominal defocus max: 1800 nm / Nominal defocus min: 800 nm / Cs: 1.3 mm
Specimen holderTemperature: 4.2 K
Image recordingFilm or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 342
Radiation wavelengthRelative weight: 1

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Processing

3D reconstructionSymmetry type: HELICAL
RefinementHighest resolution: 4 Å
Refinement stepCycle: LAST / Highest resolution: 4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14924 0 0 0 14924

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