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- EMDB-2377: The structure and super-organization of acetylcholine receptor-ra... -

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Basic information

Entry
Database: EMDB / ID: 2377
TitleThe structure and super-organization of acetylcholine receptor-rapsyn complexes; class A
Keywordsneurotransmitter receptor / clustering / synapse / neuromuscular junction / nicotinic / acetylcholine receptor / rapsyn / 43K / electric organ
SamplePostsynaptic membrane isolated from Torpedo marmorata electric organ
SourceTorpedo marmorata / fish / Marble electric ray / image: Torpedo californica
Map dataAcetylcholine receptor with one rapsyn bound
Methodsubtomogram averaging
AuthorsZuber B / Unwin N
CitationProc. Natl. Acad. Sci. U.S.A., 2013, 110, 10622-10627

Proc. Natl. Acad. Sci. U.S.A., 2013, 110, 10622-10627 StrPapers
Structure and superorganization of acetylcholine receptor-rapsyn complexes.
Benoît Zuber / Nigel Unwin

Validation ReportPDB-ID: 4boi

SummaryFull reportAbout validation report
DateDeposition: May 20, 2013 / Header (metadata) release: May 29, 2013 / Map release: Jun 26, 2013 / Last update: Aug 12, 2015

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.413
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by height
  • Surface level: 0.413
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-4boi
  • Surface level: 0.413
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

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Map

Fileemd_2377.map.gz (map file in CCP4 format, 845 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
60 pix
7.48 Å/pix.
= 448.8 Å
60 pix
7.48 Å/pix.
= 448.8 Å
60 pix
7.48 Å/pix.
= 448.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 7.48 Å
Density
Contour Level:0.413 (by author), 0.413 (movie #1):
Minimum - Maximum-0.68770933 - 1.22997284
Average (Standard dev.)0E-8 (0.07752144)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions606060
Origin000
Limit595959
Spacing606060
CellA=B=C: 448.8 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z7.487.487.48
M x/y/z606060
origin x/y/z0.0000.0000.000
length x/y/z448.800448.800448.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS606060
D min/max/mean-0.6881.2300.000

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Supplemental data

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Sample components

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Entire Postsynaptic membrane isolated from Torpedo marmorata electric organ

EntireName: Postsynaptic membrane isolated from Torpedo marmorata electric organ
Details: class average / Number of components: 2
Oligomeric State: acetylcholine receptors bound to one rapsyn
MassTheoretical: 336 kDa

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Component #1: protein, nicotinic acetylcholine receptor

ProteinName: nicotinic acetylcholine receptor / a.k.a: AChR / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 280 kDa / Experimental: 290 kDa
SourceSpecies: Torpedo marmorata / fish / Marble electric ray / image: Torpedo californica
Source (natural)Location in cell: Postsynaptic plasma membrane / Cell: Electrocyte / Organ or tissue: Electric organ
External referencesInterPro: InterPro: 002394

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Component #2: protein, Rapsyn

ProteinName: Rapsyn / a.k.a: 43 kDa receptor-associated protein of the synapse
Details: the number of copies is suggested by the volume of the rapsyn density
Recombinant expression: No / Number of Copies: 1
MassTheoretical: 46 kDa / Experimental: 43 kDa
SourceSpecies: Torpedo marmorata / fish / Marble electric ray / image: Torpedo californica
Source (natural)Location in cell: Postsynaptic plasma membrane / Cell: Electrocyte / Organ or tissue: Electric organ
External referencesInterPro: InterPro: 001237, InterPro: 019568, InterPro: 011990, InterPro: 013026, InterPro: 013083, InterPro: 001841, InterPro: 019734, InterPro: 001440, InterPro: 018293
Gene Ontology: GO: 0007268, GO: 0005515, GO: 0008270, GO: 0033130, GO: 0005856, GO: 0030054, GO: 0045202, GO: 0045211

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 400 mM NaCl, 20 mM phosphate buffer, leupeptin 0.3 mg/l, pepstatin 1 mg/l
pH: 7.4
Support film300 mesh copper grid with lacy carbon support, glow discharge in amylamine atmosphere
Stainingunstained
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 78 K / Humidity: 90 % / Method: blot from the carbon side

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300 / Date: Jul 25, 2008 / Details: dual tilt axis tomography
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 50 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 69000 X (nominal), 80213 X (calibrated)
Astigmatism: objective lens astigmatism was corrected at 69,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 3000 - 6000 nm / Energy filter: Gatan / Energy window: 0-20 eV
Specimen HolderModel: GATAN LIQUID NITROGEN / Tilt Angle: -70 - 70 deg. / Temperature: 85 K ( 80 - 95 K)
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 142 / Sampling size: 15 microns / Bit depth: 16 / Details: dual axis tilt series

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Image processing

ProcessingMethod: subtomogram averaging / Number of subtomograms: 3564 / Applied symmetry: C1 (asymmetric) / Number of class averages: 5
3D reconstruction #1Software: IMOD, PRIISM/IVE
Algorithm: Simultaneous Iterative Reconstruction Technique (SIRT)
3D reconstruction #2Resolution: 41 Å / Algorithm: Maximum-likelihood subtomogram averaging / Resolution method: FSC 0.5 / Software: XMIPP, ML, TOMO

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Atomic model buiding

Modeling #1Software: Chimera / Refinement protocol: rigid body / Refinement space: REAL
Input PDB model: 2BG9
Chain ID: A, B, C, D, E
Output model

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