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- PDB-4aq9: Gating movement in acetylcholine receptor analysed by time- resol... -

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Basic information

Entry
Database: PDB / ID: 4aq9
TitleGating movement in acetylcholine receptor analysed by time- resolved electron cryo-microscopy (open class)
DescriptorACETYLCHOLINE RECEPTOR SUBUNIT ALPHA
ACETYLCHOLINE RECEPTOR BETA SUBUNIT
ACETYLCHOLINE RECEPTOR DELTA SUBUNIT
ACETYLCHOLINE RECEPTOR GAMMA SUBUNIT
KeywordsMEMBRANE PROTEIN / FREEZE-TRAPPING / ASYMMETRIC GATING / ALLOSTERIC MECHANISM
Specimen sourceTorpedo marmorata / fish / MARBLED ELECTRIC RAY / TORPEDO ELECTRIC RAY / image: Torpedo californica
MethodElectron microscopy (6.2 A resolution / Helical / Vitreous ice)
AuthorsUnwin, N. / Fujiyoshi, Y.
CitationJ. Mol. Biol., 2012, 422, 617-634

J. Mol. Biol., 2012, 422, 617-634 StrPapers
Gating movement of acetylcholine receptor caught by plunge-freezing.
Nigel Unwin / Yoshinori Fujiyoshi

DateDeposition: Apr 13, 2012 / Release: Aug 1, 2012 / Last modification: Sep 25, 2013

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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)278,0705
Polyers278,0705
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Polypeptide(L)ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA


Mass: 52846.148 Da / Num. of mol.: 2
Details: PROTEIN IS EMBEDDED IN POSTSYNAPTIC MEMBRANE ISOLATED FROM TORPEDO MARMORATA ELECTRIC ORGAN
Source: (natural) Torpedo marmorata / fish / image: Torpedo californica
References: UniProt: P02711

Cellular component

Molecular function

  • acetylcholine-activated cation-selective channel activity (GO: 0004889)
#2: Polypeptide(L)ACETYLCHOLINE RECEPTOR BETA SUBUNIT


Mass: 56124.336 Da / Num. of mol.: 1
Details: PROTEIN IS EMBEDDED IN POSTSYNAPTIC MEMBRANE ISOLATED FROM TORPEDO MARMORATA ELECTRIC ORGAN
Source: (natural) Torpedo marmorata / fish / image: Torpedo californica
References: UniProt: Q6S3I0

Cellular component

Molecular function

  • acetylcholine-activated cation-selective channel activity (GO: 0004889)
#3: Polypeptide(L)ACETYLCHOLINE RECEPTOR DELTA SUBUNIT


Mass: 60018.355 Da / Num. of mol.: 1
Details: PROTEIN IS EMBEDDED IN POSTSYNAPTIC MEMBRANE ISOLATED FROM TORPEDO MARMORATA ELECTRIC ORGAN
Source: (natural) Torpedo marmorata / fish / image: Torpedo californica
References: UniProt: Q6S3H8

Cellular component

Molecular function

  • acetylcholine-activated cation-selective channel activity (GO: 0004889)
#4: Polypeptide(L)ACETYLCHOLINE RECEPTOR GAMMA SUBUNIT


Mass: 56235.281 Da / Num. of mol.: 1
Details: PROTEIN IS EMBEDDED IN POSTSYNAPTIC MEMBRANE ISOLATED FROM TORPEDO MARMORATA ELECTRIC ORGAN
Source: (natural) Torpedo marmorata / fish / image: Torpedo californica
References: UniProt: Q6S3H9

Cellular component

Molecular function

  • acetylcholine-activated cation-selective channel activity (GO: 0004889)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: HELICAL / Specimen type: VITREOUS ICE

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Sample preparation

Assembly of specimenName: NICOTINIC ACETYLCHOLINE RECEPTOR IN NATIVE POSTSYNAPTIC MEMBRANE FROM TORPEDO MARMORATA
Aggregation state: FILAMENT
Details: PRELIMINARY SELECTION BY OPTICAL DIFFRACTION THEN EVALUATION OF FOURIER TRANSFORMS
Buffer solutionName: 100MM SODIUM CACODYLATE, 1MM CALCIUM CHLORIDE
Sample preparationpH: 7
Specimen supportDetails: HOLEY CARBON
VitrificationDetails: 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

MicroscopyMicroscope model: JEOL 3000FS / 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 / Electron dose: 25 e/A2 / 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
CameraType: KODAK SO163 FILM
EM image scansNumber digital images: 123
Radiation wavelengthRelative weight: 1

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Processing

Image selectionSoftware name: MRC AND OWN PROGRAMS
3D reconstructionMethod: STANDARD FOURIER-BESSEL SYNTHESIS / Resolution: 6.2 A / Nominal pixel size: 1 A/pix / Actual pixel size: 1 A/pix / Magnification calibration: CALIBRATION GRID IN MICROSCOPE / CTF correction method: EACH TUBE IMAGE
Details: FOURIER-BESSEL SYNTHESIS AFTER APPLYING DISTORTION CORRECTIONS TO THE IMAGES SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2072.
Atomic model buildingMethod: MAXIMISATION OF CORRELATION BETWEEN EXPERIMENTAL DENSITIES AND ATOMIC MODEL, USING A DEFORMABLE ELASTIC NETWORK ALGORITHM (DIREX)
Ref protocol: LOW RESOLUTION X-RAY / Ref space: REAL
Atomic model buildingPDB-ID: 2BG9
Least-squares processHighest resolution: 6.2 A
Refine hist #LASTHighest resolution: 6.2 A
Number of atoms included #LASTProtein: 14924 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 14924

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