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    Yorodumi
    - EMDB-1858: Structure of the ribosome-SecYE complex in the membrane environment -

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    Basic information

    Entry
    Database: EMDB / ID: 1858
    TitleStructure of the ribosome-SecYE complex in the membrane environment
    SampleAn active E.coli SecYEG complex embedded in a lipid bilayer (Nanodisc), bound to a translating E.coli ribosome
    SourceEscherichia coli / bacteria /
    Map dataThis map represents an E.coli 70S ribosome carrying an elongation arrested nascent chain of 118 amino acid residues, with the first 102 residues representing the N-terminus of the membrane protein FtsQ with the signal anchor, a tRNA in the P-site and the E.coli SecYEG complex embedded in a E.coli lipid bilayer (Nanodisc).
    Methodsingle particle reconstruction, at 7.1 A resolution
    AuthorsFrauenfeld J / Gumbart J / Sluis EO / Funes S / Gartmann M / Beatrix B / Mielke T / Berninghausen O / Becker T / Schulten K / Beckmann R
    CitationNat. Struct. Mol. Biol., 2011, 18, 614-621

    Nat. Struct. Mol. Biol., 2011, 18, 614-621 StrPapers
    Cryo-EM structure of the ribosome-SecYE complex in the membrane environment.
    Jens Frauenfeld / James Gumbart / Eli O van der Sluis / Soledad Funes / Marco Gartmann / Birgitta Beatrix / Thorsten Mielke / Otto Berninghausen / Thomas Becker / Klaus Schulten / Roland Beckmann

    DateDeposition: Jan 17, 2011 / Header (metadata) release: Apr 21, 2011 / Map release: Apr 21, 2011 / Last update: Jan 17, 2011

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.7
    • Imaged by UCSF CHIMERA
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    • Surface view colored by height
    • Surface level: 0.7
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-4v6m
    • Surface level: 0.8
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_1858.map.gz (map file in CCP4 format, 128001 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)X (Row.)Y (Col.)
    320 pix
    1.24 A/pix
    = 396. A
    320 pix
    1.24 A/pix
    = 396. A
    320 pix
    1.24 A/pix
    = 396. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.2375 A
    Density
    Contour Level:0.5 (by author), 0.7 (movie #1):
    Minimum - Maximum-3.53351 - 6.82334
    Average (Standard dev.)0.0507365 (0.456442)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderYXZ
    Dimensions320320320
    Origin-160-160-159
    Limit159159160
    Spacing320320320
    CellA=B=C: 396 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.23751.23751.2375
    M x/y/z320320320
    origin x/y/z0.0000.0000.000
    length x/y/z396.000396.000396.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-160-160-159
    NX/NY/NZ320320320
    MAP C/R/S213
    start NC/NR/NS-160-160-159
    NC/NR/NS320320320
    D min/max/mean-3.5346.8230.051

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    Supplemental data

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    Sample components

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    Entire An active E.coli SecYEG complex embedded in a lipid bilayer (Nano...

    EntireName: An active E.coli SecYEG complex embedded in a lipid bilayer (Nanodisc), bound to a translating E.coli ribosome
    Details: The heterotrimeric SecYEG complex was embedded in a lipid bilayer (nascent HDL, Nanodisc)
    Number of components: 2
    Oligomeric State: 70S ribosome bound to one copy of the E.coli SecYEG complex in a lipid bilayer
    MassTheoretical: 2.7 MDa

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    Component #1: ribosome-prokaryote, 70S ribosome nascent chain complex

    Ribosome-prokaryoteName: 70S ribosome nascent chain complex / a.k.a: 70S RNC / Prokaryote: ALL / Recombinant expression: No
    MassTheoretical: 2.7 MDa
    SourceSpecies: Escherichia coli / bacteria /

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    Component #2: ligand, Nd-SecYEG

    LigandName: Nd-SecYEG / a.k.a: SecYEG embedded in a Nanodisc / Oligomeric Details: Heterotrimeric / Recombinant expression: Yes / Number of Copies: 1
    SourceSpecies: Escherichia coli / bacteria /
    Source (engineered)Expression System: Escherichia coli / bacteria /
    Source (natural)Location in cell: Plasma membrane

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionBuffer solution: 20 mM Hepes (pH 7.2), 100 mM KOAc, 10 mM Mg(OAc)2, 1 mM DTT, 250 microg/ml chloramphenicol
    pH: 7.2
    VitrificationInstrument: NONE / Cryogen name: ETHANE

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    Electron microscopy imaging

    ImagingMicroscope: FEI POLARA 300
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 22 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 39000 X (nominal), 38000 X (calibrated) / Cs: 2.26 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 4500 nm
    Specimen HolderHolder: FEI Polara cartridge system / Model: OTHER
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionScanner: PRIMESCAN / Sampling size: 4.76 microns / Details: Scanned at 5334 dpi

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 85664 / Applied symmetry: C1 (asymmetric)
    3D reconstructionSoftware: SPIDER / CTF correction: Defocus group volumes / Resolution: 7.1 A / Resolution method: FSC 0.5

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    Output model

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