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    Yorodumi
    - EMDB-5140: Lidless Mm-cpn in the open state -

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    Open data

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    Basic information

    Entry
    Database: EMDB / ID: 5140
    TitleLidless Mm-cpn in the open state
    KeywordsGroup II chaperonin / Protein Folding / Mm-cpn / Single Particle Reconstruction / Methanococcus maripaludis / Chaperone
    SampleLidless Mm-cpn
    SourceMethanococcus maripaludis / archaea
    Map dataThis is a map of the lidless Mm-cpn in the nucleotide-free open state.
    Methodsingle particle reconstruction, at 8 A resolution
    AuthorsZhang J / Baker ML / Schroeder G / Douglas NR / Reissmann S / Jakana J / Dougherty M / Fu CJ / Levitt M / Ludtke SJ / Frydman J / Chiu W
    CitationNature, 2010, 463, 379-383

    Nature, 2010, 463, 379-383 StrPapers
    Mechanism of folding chamber closure in a group II chaperonin.
    Junjie Zhang / Matthew L Baker / Gunnar F Schröder / Nicholai R Douglas / Stefanie Reissmann / Joanita Jakana / Matthew Dougherty / Caroline J Fu / Michael Levitt / Steven J Ludtke / Judith Frydman / Wah Chiu

    DateDeposition: Oct 23, 2009 / Header (metadata) release: Feb 4, 2010 / Map release: Feb 4, 2010 / Last update: Oct 23, 2009

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    Structure visualization

    Movie
    • Colored surface
    • Surface level: 1.05
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by cylindrical radius
    • Surface level: 1.05
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-3iyf
    • Surface level: 1.05
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view with fitted model
    • Atomic models: : PDB-3iyf
    • Surface level: 1.05
    • Imaged by UCSF CHIMERA
    • Download
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_5140.map.gz (map file in CCP4 format, 54001 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    240 pix
    1.33 A/pix
    = 319.2 A
    240 pix
    1.33 A/pix
    = 319.2 A
    240 pix
    1.33 A/pix
    = 319.2 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.33 A
    Density
    Contour Level:0.95 (by author), 1.05 (movie #1):
    Minimum - Maximum-1.7838 - 2.47715
    Average (Standard dev.)0.0335325 (0.191107)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions240240240
    Origin-120-120-120
    Limit119119119
    Spacing240240240
    CellA=B=C: 319.2 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.331.331.33
    M x/y/z240240240
    origin x/y/z0.0000.0000.000
    length x/y/z319.200319.200319.200
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-34-26-72
    NX/NY/NZ6953145
    MAP C/R/S123
    start NC/NR/NS-120-120-120
    NC/NR/NS240240240
    D min/max/mean-1.7842.4770.034

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    Supplemental data

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    Sample components

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    Entire Lidless Mm-cpn

    EntireName: Lidless Mm-cpn / Number of components: 1 / Oligomeric State: 16-mer
    MassTheoretical: 960 kDa / Experimental: 960 kDa

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    Component #1: protein, Lidless Methanococcus maripaludis chaperonin

    ProteinName: Lidless Methanococcus maripaludis chaperonin / a.k.a: Lidless Mm-cpn / Oligomeric Details: 16-mer / Recombinant expression: Yes / Number of Copies: 16
    MassTheoretical: 960 kDa / Experimental: 960 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 % / Method: 1 blot 3 seconds / Details: Vitrification instrument: Vitrobot

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    Electron microscopy imaging

    ImagingMicroscope: JEOL 3200FSC
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 80000 X (nominal), 112000 X (calibrated)
    Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
    Cs: 4.1 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3000 nm / Energy filter: in column omega filter / Energy window: 0-10 eV
    Specimen HolderHolder: side-entry / Model: JEOL 3200FSC CRYOHOLDER / Temperature: 100 K
    CameraDetector: GENERIC GATAN (4k x 4k)

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    Image processing

    ProcessingMethod: single particle reconstruction / Applied symmetry: D8 (2*8 fold dihedral)
    3D reconstructionAlgorithm: Projection-match / Software: EMAN / CTF correction: Each micrograph / Resolution: 8 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Output model

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