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- PDB-4aq5: Gating movement in acetylcholine receptor analysed by time-resolv... -

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Basic information

Entry
Database: PDB / ID: 4aq5
TitleGating movement in acetylcholine receptor analysed by time-resolved electron cryo-microscopy (closed class)
Components
  • ACETYLCHOLINE RECEPTOR BETA SUBUNIT
  • ACETYLCHOLINE RECEPTOR DELTA SUBUNIT
  • ACETYLCHOLINE RECEPTOR GAMMA SUBUNIT
  • ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA
KeywordsMEMBRANE PROTEIN / FREEZE-TRAPPING / ASYMMETRIC GATING / ALLOSTERIC MECHANISM
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
Nicotinic acetylcholine receptor / 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
Similarity search - Domain/homology
Acetylcholine receptor subunit alpha / Acetylcholine receptor delta subunit / Acetylcholine receptor gamma subunit / Acetylcholine receptor beta subunit
Similarity search - Component
Biological speciesTORPEDO MARMORATA (marbled electric ray)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 6.2 Å
AuthorsUnwin, N. / Fujiyoshi, Y.
CitationJournal: J Mol Biol / Year: 2012
Title: Gating movement of acetylcholine receptor caught by plunge-freezing.
Authors: Nigel Unwin / Yoshinori Fujiyoshi /
Abstract: The nicotinic acetylcholine (ACh) receptor converts transiently to an open-channel form when activated by ACh released into the synaptic cleft. We describe here the conformational change underlying ...The nicotinic acetylcholine (ACh) receptor converts transiently to an open-channel form when activated by ACh released into the synaptic cleft. We describe here the conformational change underlying this event, determined by electron microscopy of ACh-sprayed and freeze-trapped postsynaptic membranes. ACh binding to the α subunits triggers a concerted rearrangement in the ligand-binding domain, involving an ~1-Å outward displacement of the extracellular portion of the β subunit where it interacts with the juxtaposed ends of α-helices shaping the narrow membrane-spanning pore. The β-subunit helices tilt outward to accommodate this displacement, destabilising the arrangement of pore-lining helices, which in the closed channel bend inward symmetrically to form a central hydrophobic gate. Straightening and tangential motion of the pore-lining helices effect channel opening by widening the pore asymmetrically and increasing its polarity in the region of the gate. The pore-lining helices of the α(γ) and δ subunits, by flexing between alternative bent and straight conformations, undergo the greatest movements. This coupled allosteric transition shifts the structure from a tense (closed) state toward a more relaxed (open) state.
History
DepositionApr 12, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 12, 2012Group: Database references
Revision 1.2Sep 25, 2013Group: Other
Revision 1.3Aug 30, 2017Group: Data collection / Category: em_software
Item: _em_software.fitting_id / _em_software.image_processing_id / _em_software.name
Revision 1.4Oct 23, 2019Group: Data collection / Other / Category: cell / Item: _cell.Z_PDB
Revision 1.5Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / 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
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

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Assembly

Deposited unit
A: ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA
B: ACETYLCHOLINE RECEPTOR BETA SUBUNIT
C: ACETYLCHOLINE RECEPTOR DELTA SUBUNIT
D: ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA
E: ACETYLCHOLINE RECEPTOR GAMMA SUBUNIT


Theoretical massNumber of molelcules
Total (without water)278,0675
Polymers278,0675
Non-polymers00
Water00
1


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

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Components

#1: Protein ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA


Mass: 52845.523 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: STATION BIOLOGIQUE DE ROSCOFF / Source: (natural) TORPEDO MARMORATA (marbled electric ray) / Cell: ELECTROCYTE / Cell line: ELECTROCYTE CELLS / Organ: PLASMA MEMBRANE / Tissue: ELECTRIC ORGAN / References: UniProt: P02711
#2: Protein ACETYLCHOLINE RECEPTOR BETA SUBUNIT


Mass: 56123.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: STATION BIOLOGIQUE DE ROSCOFF / Source: (natural) TORPEDO MARMORATA (marbled electric ray) / Cell: ELECTROCYTE / Cell line: ELECTROCYTE CELLS / Organ: PLASMA MEMBRANE / Tissue: ELECTRIC ORGAN / References: UniProt: Q6S3I0
#3: Protein ACETYLCHOLINE RECEPTOR DELTA SUBUNIT


Mass: 60017.684 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: STATION BIOLOGIQUE DE ROSCOFF / Source: (natural) TORPEDO MARMORATA (marbled electric ray) / Cell: ELECTROCYTE / Cell line: ELECTROCYTE CELLS / Organ: PLASMA MEMBRANE / Tissue: ELECTRIC ORGAN / References: UniProt: Q6S3H8
#4: Protein ACETYLCHOLINE RECEPTOR GAMMA SUBUNIT


Mass: 56234.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: STATION BIOLOGIQUE DE ROSCOFF / Source: (natural) TORPEDO MARMORATA (marbled electric ray) / Cell: ELECTROCYTE / Cell line: ELECTROCYTE CELLS / Organ: PLASMA MEMBRANE / Tissue: ELECTRIC ORGAN / References: UniProt: Q6S3H9
Has protein modificationY

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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 NATIVE POSTSYNAPTIC MEMBRANE FROM TORPEDO MARMORATA
Type: COMPLEX
Details: PRELIMINARY SELECTION OF MICROGRAPHS BY OPTICAL DIFFRACTIO THEN EVALUATION USING COMPUTED FOURIER TRANSFORMS
Buffer solutionName: 100MM SODIUM CACODYLATE, 1MM CALCIUM CHLORIDE / pH: 7 / Details: 100MM SODIUM CACODYLATE, 1MM CALCIUM CHLORIDE
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: HOLEY CARBON
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE
Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 85 TEMPERATURE- 120 INSTRUMENT- HOMEMADE PLUNGER METHOD- BLOT UNTIL APPLIED DROPLET LOSES CONTACT WITH FILTER PAPER (INDICATED BY LOSS OF ...Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 85 TEMPERATURE- 120 INSTRUMENT- HOMEMADE PLUNGER METHOD- BLOT UNTIL APPLIED DROPLET LOSES CONTACT WITH FILTER PAPER (INDICATED BY LOSS OF TRANSPARENCY TYPICALLY 6S) TIMERESOLVEDSTATE- VITRIFIED WITHIN 10MS OF EXPOSURE TO ACETYLCHOLINE (APPLIED AS THE GRID IS BEING PLUNGED USING A FINE FOCUSSED SPRAY POSITIONED ABOUT 1CM ABOVE THE ETHANE SURFACE) DETAILS- VITRIFICATION CARRIED OUT AT AN AMBIENT TEMPERATURE OF 8 DEGREES

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Electron microscopy imaging

MicroscopyModel: JEOL 3000SFF / Date: Nov 1, 2005
Details: STANDARD LOW DOSE IMAGING OF SPECIMENS OVER HOLES IN THE CARBON SUPPORT FILM
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 40000 X / Calibrated magnification: 38500 X / Nominal defocus max: 2000 nm / Nominal defocus min: 900 nm / Cs: 1.6 mm
Specimen holderTemperature: 4 K
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 111
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1DireXmodel fitting
2Custom3D reconstruction
3MRC IMAGE PROCESSING PACKAGE3D reconstruction
CTF correctionDetails: EACH TUBE IMAGE
3D reconstructionMethod: STANDARD FOURIER-BESSEL SYNTHESIS / Resolution: 6.2 Å / Nominal pixel size: 1 Å / Actual pixel size: 1 Å / Magnification calibration: CALIBRATION GRID IN MICROSCOPE
Details: FOURIER-BESSEL SYNTHESIS AFTER APPLYING DISTORTION CORRECTIONS TO THE IMAGES. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2071.
Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Details: METHOD--MAXIMISATION OF CORRELATION BETWEEN EXPERIMENTAL DENSITIES AND ATOMIC MODEL, USING A DEFORMABLE ELASTIC NETWORK ALGORITHM (DIREX) REFINEMENT PROTOCOL--LOW RESOLUTION X-RAY
Atomic model buildingPDB-ID: 2BG9

2bg9


Accession code: 2BG9 / Source name: PDB / Type: experimental model
RefinementHighest resolution: 6.2 Å
Refinement stepCycle: LAST / Highest resolution: 6.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14924 0 0 0 14924

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