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    - EMDB-1046: ATP-bound states of GroEL captured by cryo-electron microscopy. -

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    Basic information

    Entry
    Database: EMDB / ID: 1046
    TitleATP-bound states of GroEL captured by cryo-electron microscopy.
    SampleGroES-ADP7-GroEL-ATP7 from E.coli
    SourceEscherichia coli / bacteria /
    Map dataGroEL with GroES and ADP bound to one ring, and ATP bound to the other ring
    Methodsingle particle reconstruction, at 23.5 A resolution
    AuthorsSaibil HR
    CitationCell, 2001, 107, 869-879

    Cell, 2001, 107, 869-879 StrPapers
    ATP-bound states of GroEL captured by cryo-electron microscopy.
    N A Ranson / G W Farr / A M Roseman / B Gowen / W A Fenton / A L Horwich / H R Saibil

    DateDeposition: Mar 13, 2003 / Header (metadata) release: May 16, 2003 / Map release: May 16, 2003 / Last update: Mar 13, 2003

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.08
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 0.08
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-1gru
    • Surface level: 0.08
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_1046.map.gz (map file in CCP4 format, 8193 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    128 pix
    2.8 A/pix
    = 358.4 A
    128 pix
    2.8 A/pix
    = 358.4 A
    128 pix
    2.8 A/pix
    = 358.4 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.8 A
    Density
    Contour Level:0.029 (by author), 0.08 (movie #1):
    Minimum - Maximum-0.04720771 - 0.27609465
    Average (Standard dev.)0.00606513 (0.02973022)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions128128128
    Origin000
    Limit127127127
    Spacing128128128
    CellA=B=C: 358.4 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.82.82.8
    M x/y/z128128128
    origin x/y/z0.0000.0000.000
    length x/y/z358.400358.400358.400
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ0052
    NX/NY/NZ12812855
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS128128128
    D min/max/mean-0.0470.2760.006

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    Supplemental data

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    Sample components

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    Entire GroES-ADP7-GroEL-ATP7 from E.coli

    EntireName: GroES-ADP7-GroEL-ATP7 from E.coli
    Details: The complexes were prepared by pre-forming a GroEL-GroES-ADP complex, with 100 uM ADP, then adding an excess of single ring GroEL (SR1) to trap any released GroES; then 1 mM ATP was added. Any GroEL-GroES complexes remaining have ADP in the GroES-bound ring and ATP in the other ring, modelling the in vivo ATP-binding reaction.
    Oligomeric State: 14-mer / Number of components: 2
    MassTheoretical: 1000 kDa / Experimental: 1000 kDa

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    Component #1: protein, GroEL

    ProteinName: GroEL / a.k.a: Chaperonin 60 / Oligomeric Details: 14-mer / Number of Copies: 1 / Recombinant expression: Yes
    MassTheoretical: 800 kDa / Experimental: 800 kDa
    SourceSpecies: Escherichia coli / bacteria /
    Source (engineered)Expression System: Escherichia coli / bacteria /
    Source (natural)Cell: E. coli

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    Component #2: protein, GroES

    ProteinName: GroES / a.k.a: Chaperonin 10 / Oligomeric Details: 7-mer / Recombinant expression: Yes / Number of Copies: 1
    MassTheoretical: 70 kDa / Experimental: 70 kDa
    SourceSpecies: Escherichia coli / bacteria /
    Source (engineered)Expression System: Escherichia coli / bacteria /

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.8 mg/ml
    Buffer solution: 12.5 mM HEPES, 5 mM KCl, 5 mM MgCl2, 100 uM ADP, then 2x molar excess of single ring mutant of GroEL (SR1), then 1 mM ATP just before vitrification. See sample details for an explanation of the experimental design.
    pH: 7.5
    Support filmholey carbon film
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 100 K / Method: Blot for 1 second before plunging
    Time resolved state: The sample was vitrified within a few seconds of manually mixing in ATP.
    Details: Vitrification instrument: self made

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 900 - 3000 nm
    Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN / Temperature: 105 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 71 / Scanner: ZEISS SCAI / Sampling size: 14 microns / Bit depth: 8 / OD range: 1

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 1448 / Applied symmetry: C7 (7 fold cyclic)
    3D reconstructionAlgorithm: Projection matching / Software: Spider
    CTF correction: CTF multiplication and merging of 2D averages
    Resolution: 23.5 A / Resolution method: FSC 0.5
    Euler angles: Full coverage around a single axis, using mainly side views
    Details: Filtered back projection

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    Atomic model buiding

    Modeling #1Software: Manual fitting in O / Refinement protocol: rigid body / Refinement space: REAL
    Details: Protocol: Rigid body. The only movement relative to the crystal structure of GroEL-ES-ADP seen at this resolution is a twist of the free apical domains.
    Input PDB model: 1AON
    Output model

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