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    Yorodumi
    - EMDB-1143: Structure of the E. coli protein-conducting channel bound to a tr... -

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    Basic information

    Entry
    Database: EMDB / ID: 1143
    TitleStructure of the E. coli protein-conducting channel bound to a translating ribosome.
    Sampleco-translational E. coli 70S ribosome-nascent chain complexed with SecYEG
    SourceEscherichia coli / bacteria / translocon /
    Unidentified / translocon
    Map dataEM map of the E.coli proten-conducting channel bound to a translating ribosome
    Methodsingle particle reconstruction, at 14.9 A resolution
    AuthorsMitra K / Schaffitzel C / Shaikh T / Tama F / Jenni S / Brooks III CL / Ban N / Frank J
    CitationNature, 2005, 438, 318-324

    Nature, 2005, 438, 318-324 StrPapers
    Structure of the E. coli protein-conducting channel bound to a translating ribosome.
    Kakoli Mitra / Christiane Schaffitzel / Tanvir Shaikh / Florence Tama / Simon Jenni / Charles L Brooks / Nenad Ban / Joachim Frank

    DateDeposition: Aug 3, 2005 / Header (metadata) release: Aug 3, 2005 / Map release: Jun 13, 2006 / Last update: Aug 3, 2005

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 50
    • Imaged by UCSF CHIMERA
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    • Surface view colored by height
    • Surface level: 50
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_1143.map.gz (map file in CCP4 format, 6922 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    121 pix
    2.82 A/pix
    = 341.22 A
    121 pix
    2.82 A/pix
    = 341.22 A
    121 pix
    2.82 A/pix
    = 341.22 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel size
    XYZ
    EMDB info.2.822.822.82
    CCP4 map header2.822.822.82
    EM Navigator Movie #13.593.593.59
    Density
    Contour Level:46.1, 50 (movie #1):
    Minimum - Maximum-299.714 - 454.815
    Average (Standard dev.)5.83623 (33.8063)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions121121121
    Origin-60-60-60
    Limit606060
    Spacing121121121
    CellA=B=C: 341.22 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.822.822.82
    M x/y/z121121121
    origin x/y/z0.0000.0000.000
    length x/y/z341.220341.220341.220
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-90-90-190
    NX/NY/NZ180180380
    MAP C/R/S123
    start NC/NR/NS-60-60-60
    NC/NR/NS121121121
    D min/max/mean-299.714454.8155.836

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    Supplemental data

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    Sample components

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    Entire co-translational E. coli 70S ribosome-nascent chain complexed wit...

    EntireName: co-translational E. coli 70S ribosome-nascent chain complexed with SecYEG
    Number of components: 8

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    Component #1: ribosome-prokaryote, 30S

    Ribosome-prokaryoteName: 30S / a.k.a: small subunit / Prokaryote: SSU 30S / Recombinant expression: No
    SourceSpecies: Escherichia coli / bacteria /

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    Component #2: ribosome-prokaryote, 50S

    Ribosome-prokaryoteName: 50S / a.k.a: large subunit / Prokaryote: LSU 50S / Recombinant expression: No
    SourceSpecies: Escherichia coli / bacteria /

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    Component #3: nucleic-acid, A-site tRNA

    Nucleic-acidName: A-site tRNA / Class: RNA / Structure: DOUBLE HELIX / Synthetic: No
    SourceSpecies: Escherichia coli / bacteria /

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    Component #4: nucleic-acid, P-site tRNA

    Nucleic-acidName: P-site tRNA / Class: RNA / Structure: DOUBLE HELIX / Synthetic: No
    SourceSpecies: Escherichia coli / bacteria /

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    Component #5: nucleic-acid, E-site tRNA

    Nucleic-acidName: E-site tRNA / Class: RNA / Structure: DOUBLE HELIX / Synthetic: No
    SourceSpecies: Escherichia coli / bacteria /

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    Component #6: nucleic-acid, mRNA

    Nucleic-acidName: mRNA / Class: RNA / Structure: SINGLE STRANDED / Synthetic: Yes
    SourceSpecies: Escherichia coli / bacteria /

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    Component #7: protein, protein-conducting channel

    ProteinName: protein-conducting channel / a.k.a: translocon, SecYEG / Oligomeric Details: dimer of heterotrimer / Recombinant expression: Yes / Number of Copies: 2
    SourceSpecies: Escherichia coli / bacteria / translocon /
    Source (engineered)Expression System: Escherichia coli / bacteria /
    Source (natural)Location in cell: inner membrane

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    Component #8: protein, nascent chain

    ProteinName: nascent chain / Details: Strep-II-FtsQ-SecM construct / Recombinant expression: Yes
    SourceSpecies: Unidentified / translocon

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 93 K / Humidity: 90 % / Method: Blot for 2 seconds before plunging
    Details: Vitrification instrument: two sided blotting plunger

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F30 / Date: Mar 9, 2004
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 11 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 39000 X (nominal), 39000 X (calibrated) / Cs: 2.26 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 4300 nm
    Specimen HolderHolder: Cryo stage / Model: OTHER / Temperature: 93 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 385 / Scanner: ZEISS SCAI / Sampling size: 14 microns / Bit depth: 12 / OD range: 1.2

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 53325 / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: reference projection / Software: SPIDER package / CTF correction: defocus groups / Resolution: 14.9 A / Resolution method: FSC 0.5 / Euler angles: SPIDER: theta 15 degrees, phi 15 degrees
    Details: The falloff of Fourier amplitudes toward higher spatial frequencies was corrected using the x-ray solution scattering intensity distribution of 70S ribosomes from E. coli during each round of refinement

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    Atomic model buiding

    Modeling #1Refinement protocol: flexible / Target criteria: correlation coefficient / Refinement space: REAL
    Details: Protocol: normal mode-based flexible fitting. Fitting of SecYEG atomic model into isolated EM density of protein-conducting channels
    Modeling #2Refinement protocol: flexible / Target criteria: correlation coefficient / Refinement space: REAL
    Details: Protocol: normal mode-based flexible fitting. Fitting of SecYEG atomic model into isolated EM density of protein-conducting channels
    Modeling #3Software: RSR2000 / Refinement protocol: rigid body / Target criteria: R-factor / Refinement space: REAL / Details: Protocol: real space refinement
    Modeling #4Software: RSR2000 / Refinement protocol: rigid body / Target criteria: R-factor / Refinement space: REAL / Details: Protocol: real space refinement
    Output model

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