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Yorodumi- PDB-4aq5: Gating movement in acetylcholine receptor analysed by time-resolv... -
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-Basic information
Entry | Database: PDB / ID: 4aq5 | ||||||
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Title | Gating movement in acetylcholine receptor analysed by time-resolved electron cryo-microscopy (closed class) | ||||||
Components |
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Keywords | MEMBRANE 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 / neuron projection Similarity search - Function | ||||||
Biological species | TORPEDO MARMORATA (marbled electric ray) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 6.2 Å | ||||||
Authors | Unwin, N. / Fujiyoshi, Y. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4aq5.cif.gz | 363.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4aq5.ent.gz | 270 KB | Display | PDB format |
PDBx/mmJSON format | 4aq5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4aq5_validation.pdf.gz | 875.5 KB | Display | wwPDB validaton report |
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Full document | 4aq5_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 4aq5_validation.xml.gz | 132 KB | Display | |
Data in CIF | 4aq5_validation.cif.gz | 175.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aq/4aq5 ftp://data.pdbj.org/pub/pdb/validation_reports/aq/4aq5 | HTTPS FTP |
-Related structure data
Related structure data | 2071MC 2072C 4aq9C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
#1: Protein | 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 | | 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 | | 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 | | 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 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: 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 |
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Buffer solution | Name: 100MM SODIUM CACODYLATE, 1MM CALCIUM CHLORIDE / pH: 7 / Details: 100MM SODIUM CACODYLATE, 1MM CALCIUM CHLORIDE |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: 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 |
-Electron microscopy imaging
Microscopy | Model: JEOL 3000SFF / Date: Nov 1, 2005 Details: STANDARD LOW DOSE IMAGING OF SPECIMENS OVER HOLES IN THE CARBON SUPPORT FILM |
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Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: 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 holder | Temperature: 4 K |
Image recording | Electron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 111 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
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CTF correction | Details: EACH TUBE IMAGE | ||||||||||||
3D reconstruction | Method: 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 building | Protocol: 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 building | PDB-ID: 2BG9 | ||||||||||||
Refinement | Highest resolution: 6.2 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 6.2 Å
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