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Gating movement in acetylcholine receptor analysed by time- resolved electron cryo-microscopy (open class)

by helical reconstruction, at 6.2 A resolution

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#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-2072, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-2072, Image by UCSF CHIMERA

Entry
Summary
Database / IDPORTEIN DATA BANK (PDB) / 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
AuthorsUnwin, N., Fujiyoshi, Y.
DateDeposition: 2012-04-13, Release: 2012-08-01
PDBj Mine pagesSummary, Structural Details, Experimental Details, Functional Details
Other databasesRCSB-PDB, PDBe, CATH, CE, FSSP, SCOP, VAST
Structure Visualization
MoviesMovie Page

#1: Depositted structure unit, Image by Jmol

#2: Superimposing with simplified surface model of EM map, EMDB-2072, Image by Jmol

#3: Superimposing with EM 3D map: EMDB-2072, Image by UCSF CHIMERA

Structure viewersYorodumi, jV4, Jmol, Biological unit (Images, jV)
Related Structure Data
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EMDB-2072

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Article
Citation - primary
ArticleJ. Mol. Biol., Vol. 422, Issue 5, Page 617-34, Year 2012
TitleGating movement of acetylcholine receptor caught by plunge-freezing.
AuthorsNigel Unwin, Yoshinori Fujiyoshi
MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.
KeywordsAcetylcholine (metabolism), Allosteric Regulation, Animals, Cryoelectron Microscopy (methods), Ion Channel Gating, Models, Biological, Models, Molecular, Protein Conformation, Receptors, Cholinergic (chemistry), Torpedo
LinksPII: 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
DescriptionACETYLCHOLINE RECEPTOR SUBUNIT ALPHA
Typepolypeptide(L)
Formula weight52846.148 Da
Number of molecules2
ID1
DetailsPROTEIN IS EMBEDDED IN POSTSYNAPTIC MEMBRANE ISOLATED FROM TORPEDO MARMORATA ELECTRIC ORGAN
SourceMethod: 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
LinksUniProt: P02711, Sequence view
ID 2 : ACETYLCHOLINE RECEPTOR BETA SUBUNIT
Image
DescriptionACETYLCHOLINE RECEPTOR BETA SUBUNIT
Typepolypeptide(L)
Formula weight56124.336 Da
Number of molecules1
ID2
DetailsPROTEIN IS EMBEDDED IN POSTSYNAPTIC MEMBRANE ISOLATED FROM TORPEDO MARMORATA ELECTRIC ORGAN
SourceMethod: 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
LinksUniProt: Q6S3I0, Sequence view
ID 3 : ACETYLCHOLINE RECEPTOR DELTA SUBUNIT
Image
DescriptionACETYLCHOLINE RECEPTOR DELTA SUBUNIT
Typepolypeptide(L)
Formula weight60018.355 Da
Number of molecules1
ID3
DetailsPROTEIN IS EMBEDDED IN POSTSYNAPTIC MEMBRANE ISOLATED FROM TORPEDO MARMORATA ELECTRIC ORGAN
SourceMethod: 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
LinksUniProt: Q6S3H8, Sequence view
ID 4 : ACETYLCHOLINE RECEPTOR GAMMA SUBUNIT
Image
DescriptionACETYLCHOLINE RECEPTOR GAMMA SUBUNIT
Typepolypeptide(L)
Formula weight56235.281 Da
Number of molecules1
ID4
DetailsPROTEIN IS EMBEDDED IN POSTSYNAPTIC MEMBRANE ISOLATED FROM TORPEDO MARMORATA ELECTRIC ORGAN
SourceMethod: 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
LinksUniProt: Q6S3H9, Sequence view
Sample
Assembly
Aggregation stateFILAMENT
DetailsPRELIMINARY SELECTION BY OPTICAL DIFFRACTION THEN EVALUATION OF FOURIER TRANSFORMS
NameNICOTINIC ACETYLCHOLINE RECEPTOR IN NATIVE POSTSYNAPTIC MEMBRANE FROM TORPEDO MARMORATA
Buffer
Name100MM SODIUM CACODYLATE, 1MM CALCIUM CHLORIDE
Experiment
Reconstruction methodHELICAL
Specimen typeVITREOUS ICE
Sample preparation
pH7.0
Sample support
DetailsHOLEY CARBON
Vitrification
DetailsVITRIFICATION 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
Experiment
MethodELECTRON MICROSCOPY
Electron Microscopy
Imaging
MicroscopeModel: JEOL 3000FS
Date2005-11-01
DetailsSTANDARD LOW DOSE IMAGING OF SPECIMENS OVER HOLES IN THE CARBON SUPPORT FILM
Electron gun
Electron sourceFIELD EMISSION GUN
Accelerating voltage300 kV
Electron dose25 e/A**2
Illumination modeFLOOD BEAM
Lens
ModeBRIGHT FIELD
MagnificationCalibrated: 38500 X, Nominal: 40000 X
CsNominal: 1.6 mm
Nominal defocusMax: 2000 nm, Min: 900 nm
Specimen holder
Temperature4 Kelvin
Detector
TypeKODAK SO163 FILM
Image scans
Number digital images123
Processing
2D projection selection
Software nameMRC AND OWN PROGRAMS
3D reconstruction
Actual pixel size1.0 A/pix
CTF correction methodEACH TUBE IMAGE
DetailsFOURIER-BESSEL SYNTHESIS AFTER APPLYING DISTORTION CORRECTIONS TO THE IMAGES SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2072.
Magnification calibrationCALIBRATION GRID IN MICROSCOPE
MethodSTANDARD FOURIER-BESSEL SYNTHESIS
Nominal pixel size1.0 A/pix
Resolution6.2 A
3D fitting
MethodMAXIMISATION OF CORRELATION BETWEEN EXPERIMENTAL DENSITIES AND ATOMIC MODEL, USING A DEFORMABLE ELASTIC NETWORK ALGORITHM (DIREX)
Refinement ProtocolLOW RESOLUTION X-RAY
Refinement SpaceREAL
3D fitting list
3D Fitting ID1
PDB entry ID2BG9
Refine
Refine idELECTRON MICROSCOPY
Ls d res high6.20 A
Refine hist
Cycle idLAST
Refine idELECTRON MICROSCOPY
D res high6.20
Total atoms14924
Protein atoms14924
Download
PDB format
Allpdb4aq9.ent.gz
pdb4aq9.ent (uncompressed file)
Header onlypdb4aq9.ent.gz
mmCIF format
mmCIF4aq9.cif.gz
XML format
All4aq9.xml.gz
No-atom4aq9-noatom.xml.gz
Ext-atom4aq9-extatom.xml.gz
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 2.6 MB
.webm (WebM/VP8 format), 3.5 MB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.7 MB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 5 MB