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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)
Descriptor(ACETYLCHOLINE RECEPTOR ...) x 4
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 Å resolution / Helical array / Helical)
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

Validation Report
SummaryFull reportAbout validation report
DateDeposition: Apr 13, 2012 / Release: Aug 1, 2012
RevisionDateData content typeGroupProviderType
1.0Aug 1, 2012Structure modelrepositoryInitial release
1.1Sep 12, 2012Structure modelDatabase references
1.2Sep 25, 2013Structure modelOther

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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
Polyers278,0675
Non-polymers00
Water0
#1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Polypeptide(L)ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA


Mass: 52845.523 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-gated cation-selective channel activity (GO: 0022848)
#2: Polypeptide(L)ACETYLCHOLINE RECEPTOR BETA SUBUNIT


Mass: 56123.594 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-gated cation-selective channel activity (GO: 0022848)
#3: Polypeptide(L)ACETYLCHOLINE RECEPTOR DELTA SUBUNIT


Mass: 60017.684 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-gated cation-selective channel activity (GO: 0022848)
#4: Polypeptide(L)ACETYLCHOLINE RECEPTOR GAMMA SUBUNIT


Mass: 56234.578 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-gated cation-selective channel activity (GO: 0022848)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: HELICAL ARRAY / Reconstruction method: HELICAL

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Sample preparation

ComponentName: NICOTINIC ACETYLCHOLINE RECEPTOR IN NATIVE POSTSYNAPTIC MEMBRANE FROM TORPEDO MARMORATA
Type: COMPLEX
Details: PRELIMINARY SELECTION BY OPTICAL DIFFRACTION THEN EVALUATION OF FOURIER TRANSFORMS
Buffer solutionName: 100MM SODIUM CACODYLATE, 1MM CALCIUM CHLORIDE / Details: 100MM SODIUM CACODYLATE, 1MM CALCIUM CHLORIDE / pH: 7
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 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 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 / Calibrated magnification: 38500 / Nominal defocus max: 2000 nm / Nominal defocus min: 900 nm / Cs: 1.6 mm
Specimen holderTemperature: 4 kelvins
Image recordingElectron dose: 25 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 123
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameCategory
1DireXMODEL FITTING
2CustomRECONSTRUCTION
3MRCRECONSTRUCTION
CTF correctionDetails: EACH TUBE IMAGE
3D reconstructionMethod: STANDARD FOURIER-BESSEL SYNTHESIS / Resolution: 6.2 Å / Nominal pixel size: 1 / Actual pixel size: 1 / 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-2072.
Symmetry type: HELICAL
Atomic model buildingDetails: METHOD--MAXIMISATION OF CORRELATION BETWEEN EXPERIMENTAL DENSITIES AND ATOMIC MODEL, USING A DEFORMABLE ELASTIC NETWORK ALGORITHM (DIREX) REFINEMENT PROTOCOL--LOW RESOLUTION X-RAY
Ref protocol: FLEXIBLE FIT / Ref space: REAL
Atomic model buildingPDB-ID: 2BG9
Least-squares processHighest resolution: 6.2 Å
Refine hist #LASTHighest resolution: 6.2 Å
Number of atoms included #LASTProtein: 14924 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 14924

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