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

Entry
Summary
Database / ID	PORTEIN DATA BANK (PDB) / 4aq9
Title	Gating movement in acetylcholine receptor analysed by time- resolved electron cryo-microscopy (open class)
Descriptor	ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA ACETYLCHOLINE RECEPTOR BETA SUBUNIT ACETYLCHOLINE RECEPTOR DELTA SUBUNIT ACETYLCHOLINE RECEPTOR GAMMA SUBUNIT
Keywords	MEMBRANE PROTEIN, FREEZE-TRAPPING, ASYMMETRIC GATING, ALLOSTERIC MECHANISM
Authors	Unwin, N., Fujiyoshi, Y.
Date	Deposition: 2012-04-13, Release: 2012-08-01
PDBj Mine pages	Summary, Structural Details, Experimental Details, Functional Details
Other databases	RCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
Movies	Movie Page #1: Depositted structure unit, Made by Jmol #2: Superimposing with simplified surface model of EM map, EMDB-2072, Made by Jmol #3: Superimposing with EM 3D map: EMDB-2072, Made by UCSF CHIMERA
Structure viewers	Yorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
Related Entries	EMDB-2072 CiteFit EMDB-2071 Cite PDB-4aq5 Cite PDB-1l4w PDB-1ljz PDB-1oed PDB-2bg9 Cite: data citing same article Fit: target map of fitting
Similar strucutres (beta)	Diagram PDB-2bg9 PDB-4aq5 EMDB-1410 PDB-3j2p List of similar structure data about Omokage system

Article
Citation - primary
Article	J. Mol. Biol., Vol. 422, Issue 5, Page 617-34, Year 2012
Title	Gating movement of acetylcholine receptor caught by plunge-freezing.
Authors	Nigel Unwin, Yoshinori Fujiyoshi MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
Keywords	Acetylcholine (metabolism, 51-84-3), Allosteric Regulation, Animals, Cryoelectron Microscopy (methods), Ion Channel Gating, Models, Biological, Models, Molecular, Protein Conformation, Receptors, Cholinergic (chemistry), Torpedo
Links	PII: S0022-2836(12)00577-3, DOI: 10.1016/j.jmb.2012.07.010, PubMed: 22841691, PMC: PMC3443390

Components
ID 1 : ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA
Image
Description	ACETYLCHOLINE RECEPTOR SUBUNIT ALPHA
Type	polymer
Formula weight	52846.148 Da
Number of molecules	2
Details	PROTEIN IS EMBEDDED IN POSTSYNAPTIC MEMBRANE ISOLATED FROM TORPEDO MARMORATA ELECTRIC ORGAN
Source	Method: Isolated from a natural source Common name: MARBLED ELECTRIC RAY Details: STATION BIOLOGIQUE DE ROSCOFF Cell: ELECTROCYTE Cell line: ELECTROCYTE CELLS NCBI taxonomy: ID:7788 Organ: PLASMA MEMBRANE Organism scientific: TORPEDO MARMORATA Tissue: ELECTRIC ORGAN
Links	UniProt: P02711, Sequence view
ID 2 : ACETYLCHOLINE RECEPTOR BETA SUBUNIT
Image
Description	ACETYLCHOLINE RECEPTOR BETA SUBUNIT
Type	polymer
Formula weight	56124.336 Da
Number of molecules	1
Details	PROTEIN IS EMBEDDED IN POSTSYNAPTIC MEMBRANE ISOLATED FROM TORPEDO MARMORATA ELECTRIC ORGAN
Source	Method: Isolated from a natural source Common name: MARBLED ELECTRIC RAY Details: STATION BIOLOGIQUE DE ROSCOFF Cell: ELECTROCYTE Cell line: ELECTROCYTE CELLS NCBI taxonomy: ID:7788 Organ: PLASMA MEMBRANE Organism scientific: TORPEDO MARMORATA Tissue: ELECTRIC ORGAN
Links	UniProt: Q6S3I0, Sequence view
ID 3 : ACETYLCHOLINE RECEPTOR DELTA SUBUNIT
Image
Description	ACETYLCHOLINE RECEPTOR DELTA SUBUNIT
Type	polymer
Formula weight	60018.355 Da
Number of molecules	1
Details	PROTEIN IS EMBEDDED IN POSTSYNAPTIC MEMBRANE ISOLATED FROM TORPEDO MARMORATA ELECTRIC ORGAN
Source	Method: Isolated from a natural source Common name: MARBLED ELECTRIC RAY Details: STATION BIOLOGIQUE DE ROSCOFF Cell: ELECTROCYTE Cell line: ELECTROCYTE CELLS NCBI taxonomy: ID:7788 Organ: PLASMA MEMBRANE Organism scientific: TORPEDO MARMORATA Tissue: ELECTRIC ORGAN
Links	UniProt: Q6S3H8, Sequence view
ID 4 : ACETYLCHOLINE RECEPTOR GAMMA SUBUNIT
Image
Description	ACETYLCHOLINE RECEPTOR GAMMA SUBUNIT
Type	polymer
Formula weight	56235.281 Da
Number of molecules	1
Details	PROTEIN IS EMBEDDED IN POSTSYNAPTIC MEMBRANE ISOLATED FROM TORPEDO MARMORATA ELECTRIC ORGAN
Source	Method: Isolated from a natural source Common name: TORPEDO ELECTRIC RAY Details: STATION BIOLOGIQUE DE ROSCOFF Cell: ELECTROCYTE Cell line: ELECTROCYTE CELLS NCBI taxonomy: ID:7788 Organ: PLASMA MEMBRANE Organism scientific: TORPEDO MARMORATA Tissue: ELECTRIC ORGAN
Links	UniProt: Q6S3H9, Sequence view

Sample
Assembly
Aggregation state	FILAMENT
Details	PRELIMINARY SELECTION BY OPTICAL DIFFRACTION THEN EVALUATION OF FOURIER TRANSFORMS
Name	NICOTINIC ACETYLCHOLINE RECEPTOR IN NATIVE POSTSYNAPTIC MEMBRANE FROM TORPEDO MARMORATA
Buffer
Name	100MM SODIUM CACODYLATE, 1MM CALCIUM CHLORIDE
Experiment
Reconstruction method	HELICAL
Specimen type	VITREOUS ICE
Sample preparation
pH	7.0
Sample support
Details	HOLEY CARBON
Vitrification
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
Microscope	model: JEOL 3000FS
Date	2005-11-01
Details	STANDARD LOW DOSE IMAGING OF SPECIMENS OVER HOLES IN THE CARBON SUPPORT FILM
Electron gun
Electron source	FIELD EMISSION GUN
Accelerating voltage	300 kV
Electron dose	25 e/A**2
Illumination mode	FLOOD BEAM
Lens
Mode	BRIGHT FIELD
Magnification	calibrated: 38500 X, nominal: 40000 X
Cs	nominal: 1.6 mm
Nominal defocus	max: 2000 nm, min: 900 nm
Specimen holder
Temperature	4 Kelvin
Detector
Type	KODAK SO163 FILM
Image scans
Number digital images	123

Processing
2D projection selection
Software name	MRC AND OWN PROGRAMS
3D reconstruction
Actual pixel size	1.0 A/pix
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.
Magnification calibration	CALIBRATION GRID IN MICROSCOPE
Method	STANDARD FOURIER-BESSEL SYNTHESIS
Nominal pixel size	1.0 A/pix
Resolution	6.2 A
3D fitting
Method	MAXIMISATION OF CORRELATION BETWEEN EXPERIMENTAL DENSITIES AND ATOMIC MODEL, USING A DEFORMABLE ELASTIC NETWORK ALGORITHM (DIREX)
Refinement Protocol	LOW RESOLUTION X-RAY
Refinement Space	REAL
3D fitting list
PDB entry ID	2BG9 PDB-2bg9
Refine
Ls d res high	6.20 A
ID	1
Refine hist
D res high	6.20
Total atoms	14924
Protein atoms	14924