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    Yorodumi
    - EMDB-1275: The pore structure of the closed RyR1 channel. -

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    Basic information

    Entry
    Database: EMDB / ID: 1275
    TitleThe pore structure of the closed RyR1 channel.
    Sampleryanodine receptor 1
    SourceOryctolagus cuniculus / mammal / rabbit /
    Map dataZ-axis of a 3D reconstruction coincides with the 4-fold axis of the channel complex
    Methodsingle particle reconstruction, at 9.6 A resolution
    AuthorsLudtke SJ / Serysheva II / Hamilton SL / Chiu W
    CitationStructure, 2005, 13, 1203-1211

    Structure, 2005, 13, 1203-1211 StrPapers
    The pore structure of the closed RyR1 channel.
    Steven J Ludtke / Irina I Serysheva / Susan L Hamilton / Wah Chiu

    DateDeposition: Jan 19, 2006 / Header (metadata) release: Oct 16, 2006 / Map release: Oct 16, 2007 / Last update: Jan 19, 2006

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 1
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 1
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_1275.map.gz (map file in CCP4 format, 65537 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    256 pix
    1.81 A/pix
    = 461.55 A
    256 pix
    1.81 A/pix
    = 461.55 A
    256 pix
    1.81 A/pix
    = 461.55 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.81 A
    Density
    Contour Level:0.631, 1 (movie #1):
    Minimum - Maximum-1.24222 - 2.25668
    Average (Standard dev.)0.0636951 (0.267637)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions256256256
    Origin-128-128-128
    Limit127127127
    Spacing256256256
    CellA=B=C: 461.55 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.811.811.81
    M x/y/z255255255
    origin x/y/z0.0000.0000.000
    length x/y/z461.550461.550461.550
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-184-184-183
    NX/NY/NZ368368368
    MAP C/R/S123
    start NC/NR/NS-128-128-128
    NC/NR/NS256256256
    D min/max/mean-1.2422.2570.064

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    Supplemental data

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    Sample components

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    Entire ryanodine receptor 1

    EntireName: ryanodine receptor 1
    Details: The sample was purified after solubilization with detergent from skeletal muscle cells
    Oligomeric State: homotetramer / Number of components: 1
    MassTheoretical: 565 kDa

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    Component #1: protein, Ryanodine receptor type 1

    ProteinName: Ryanodine receptor type 1 / a.k.a: Skeletal muscle calcium release channel / Oligomeric Details: homotetramer / Details: detergent solubilized membrane protein / Recombinant expression: No / Number of Copies: 4
    MassExperimental: 565 kDa
    SourceSpecies: Oryctolagus cuniculus / mammal / rabbit / / Strain: White New Zealand
    Source (natural)Organelle: sarcoplasmic reticulum / Location in cell: sarcoplasmic reticulum membrane / Cell: muscle cell / Organ or tissue: fast twitch skeletal muscle
    External referencesInterPro: InterPro: 000699 / Gene Ontology: GO: 0005219

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 2 mg/ml
    Buffer solution: 20 mM Mops, 300 mM KCl, 1 mM DTT,0.4% CHAPS,5%sucrose,1mM EGTA
    pH: 7.4
    Support filmholey carbon 400 mesh Cu grid
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 101 K / Method: Blot for 3 second before plunging
    Details: Vitrification instrument: Thin carbon film supported by holey carbon film

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 2010F
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 60000 X (nominal)
    Astigmatism: objective lens astigmatism was corrected at 400,000X
    Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1370 - 4550 nm
    Specimen HolderHolder: side entry / Model: GATAN LIQUID NITROGEN / Temperature: 96 K ( 96 - 97 K)
    CameraDetector: GENERIC GATAN (4k x 4k)

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    Image acquisition

    Image acquisitionNumber of digital images: 869 / Sampling size: 1.81 microns / Bit depth: 8

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of class averages: 2294 / Number of projections: 28036 / Applied symmetry: C4 (4 fold cyclic)
    3D reconstructionAlgorithm: Iterative projection matching and Direct Fourier inversion
    Software: EMAN / CTF correction: CTF correction of each micrograph / Resolution: 9.6 A / Resolution method: FSC 0.5

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