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    Yorodumi
    - EMDB-5258: Lidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state -

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    Basic information

    Entry
    Database: EMDB / ID: 5258
    TitleLidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state
    KeywordsMm-cpn / Chaperonin / ATP-bound
    SampleLidless D386A Mm-cpn variant
    SourceMethanococcus maripaludis / archaea
    Map dataThis is the density map of lidless D386A Mm-cpn in the pre-hydrolysis ATP-bound state.
    Methodsingle particle reconstruction, at 8 A resolution
    AuthorsZhang J / Ma B / DiMaio F / Douglas NR / Joachimiak L / Baker D / Frydman J / Levitt M / Chiu W
    CitationStructure, 2011, 19, 633-639

    Structure, 2011, 19, 633-639 StrPapers
    Cryo-EM structure of a group II chaperonin in the prehydrolysis ATP-bound state leading to lid closure.
    Junjie Zhang / Boxue Ma / Frank DiMaio / Nicholai R Douglas / Lukasz A Joachimiak / David Baker / Judith Frydman / Michael Levitt / Wah Chiu

    DateDeposition: Feb 10, 2011 / Header (metadata) release: May 11, 2011 / Map release: May 11, 2011 / Last update: Feb 10, 2011

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.075
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by cylindrical radius
    • Surface level: 0.075
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-3j02
    • Surface level: 0.075
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_5258.map.gz (map file in CCP4 format, 54001 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    240 pix
    1.42 A/pix
    = 340.8 A
    240 pix
    1.42 A/pix
    = 340.8 A
    240 pix
    1.42 A/pix
    = 340.8 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.42 A
    Density
    Contour Level:0.02 (by emdb), 0.075 (movie #1):
    Minimum - Maximum-0.12193819 - 0.23173273
    Average (Standard dev.)0.00300522 (0.01658083)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions240240240
    Origin-120-120-120
    Limit119119119
    Spacing240240240
    CellA=B=C: 340.8 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.421.421.42
    M x/y/z240240240
    origin x/y/z0.0000.0000.000
    length x/y/z340.800340.800340.800
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-62-62-62
    NX/NY/NZ125125125
    MAP C/R/S123
    start NC/NR/NS-120-120-120
    NC/NR/NS240240240
    D min/max/mean-0.1220.2320.003

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    Supplemental data

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    Sample components

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    Entire Lidless D386A Mm-cpn variant

    EntireName: Lidless D386A Mm-cpn variant / Number of components: 1
    MassTheoretical: 1000 kDa / Experimental: 1000 kDa

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    Component #1: protein, Methanococcus maripaludis chaperonin

    ProteinName: Methanococcus maripaludis chaperonin / a.k.a: Mm-cpn / Oligomeric Details: 16-mer / Details: incubated with 1mM ATP / Recombinant expression: Yes / Number of Copies: 1
    MassTheoretical: 1000 kDa / Experimental: 1000 kDa
    SourceSpecies: Methanococcus maripaludis / archaea
    Source (engineered)Expression System: Escherichia coli / bacteria /

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Humidity: 100 % / Details: Vitrification instrument: vitrobot

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 2200FS / Date: Sep 8, 2009
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 80000 X (nominal), 112000 X (calibrated) / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2500 nm / Energy filter: in-column omega energy filter / Energy window: 0-10 eV
    Specimen HolderHolder: Gatan side entry / Model: GATAN LIQUID NITROGEN
    CameraDetector: GENERIC GATAN (4k x 4k)

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    Image acquisition

    Image acquisitionNumber of digital images: 64

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 12761 / Applied symmetry: D8 (2*8 fold dihedral)
    3D reconstructionAlgorithm: projection matching / Software: EMAN / CTF correction: Each CCD image / Resolution: 8 A / Resolution method: FSC 0.5

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    Output model

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