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    - PDB-2wwb: CRYO-EM STRUCTURE OF THE MAMMALIAN SEC61 COMPLEX BOUND TO THE ACT... -

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    Entry
    Database: PDB / ID: 2wwb
    TitleCRYO-EM STRUCTURE OF THE MAMMALIAN SEC61 COMPLEX BOUND TO THE ACTIVELY TRANSLATING WHEAT GERM 80S RIBOSOME
    DescriptorPROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 1
    PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT GAMMA
    PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT BETA
    (60S ribosomal protein ...) x 8
    KeywordsRIBOSOME / PROTEIN EXIT TUNNEL / COTRANSLATIONAL PROTEIN TRANSLOCATION / PROTEIN CONDUCTING CHANNEL / SIGNAL SEQUENCE
    Specimen sourceCanis lupus familiaris / mammal / DOG /
    Triticum aestivum / plant / BREAD WHEAT /
    MethodElectron microscopy (6.48 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsBecker, T. / Mandon, E. / Bhushan, S. / Jarasch, A. / Armache, J.P. / Funes, S. / Jossinet, F. / Gumbart, J. / Mielke, T. / Berninghausen, O. / Schulten, K. / Westhof, E. / Gilmore, R. / Beckmann, R.
    CitationScience, 2009, 326, 1369-1373

    Science, 2009, 326, 1369-1373 StrPapers
    Structure of monomeric yeast and mammalian Sec61 complexes interacting with the translating ribosome.
    Thomas Becker / Shashi Bhushan / Alexander Jarasch / Jean-Paul Armache / Soledad Funes / Fabrice Jossinet / James Gumbart / Thorsten Mielke / Otto Berninghausen / Klaus Schulten / Eric Westhof / Reid Gilmore / Elisabet C Mandon / Roland Beckmann

    DateDeposition: Oct 22, 2009 / Release: Dec 8, 2009 / Last modification: Jul 20, 2011

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    Assembly

    Deposited unit
    A: PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 1
    B: PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT GAMMA
    C: PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT BETA
    D: 5.8S RRNA
    E: 25S RRNA
    F: 25S RRNA
    G: 25S RRNA
    H: 60S RIBOSOMAL PROTEIN L4-B
    I: 60S RIBOSOMAL PROTEIN L17-A
    J: 60S RIBOSOMAL PROTEIN L19
    K: 60S RIBOSOMAL PROTEIN L25
    L: 60S RIBOSOMAL PROTEIN L26-A
    M: 60S RIBOSOMAL PROTEIN L31-A
    N: 60S RIBOSOMAL PROTEIN L35
    O: 60S RIBOSOMAL PROTEIN L39

    259 kDa, 15 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    258,76015
    Polyers258,76015
    Non-polymers00
    Water0

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    #1idetical with deposited unit / defined by author&software (PISA) / Symmetry operations: (identity)x1
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    Components

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    Polypeptide(L) , 3 types, 3 molecules ABC

    #1polypeptide(L) / PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 1 / SEC61ALPHA, SEC61 ALPHA-1 / Source: CANIS LUPUS FAMILIARIS (gene. exp.) / References: UniProt: P38377
    #2polypeptide(L) / PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT GAMMA / SEC61GAMMA / Source: CANIS LUPUS FAMILIARIS (gene. exp.) / References: UniProt: P60058
    #3polypeptide(L) / PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT BETA / SEC61BETA / Source: CANIS LUPUS FAMILIARIS (gene. exp.) / References: UniProt: P60467

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    RNA chain , 4 types, 4 molecules DEFG

    #4RNA chain / 5.8S RRNA / H5_H6_H7 FRAGMENT / Source: TRITICUM AESTIVUM (gene. exp.)
    #5RNA chain / 25S RRNA / H24 FRAGMENT / Source: TRITICUM AESTIVUM (gene. exp.)
    #6RNA chain / 25S RRNA / H50 FRAGMENT / Source: TRITICUM AESTIVUM (gene. exp.)
    #7RNA chain / 25S RRNA / H59 FRAGMENT / Source: TRITICUM AESTIVUM (gene. exp.)

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    60S ribosomal protein ... , 8 types, 8 molecules HIJKLMNO

    #8polypeptide(L) / 60S RIBOSOMAL PROTEIN L4-B / 60S RIBOSOMAL PROTEIN L4, L2, YL2, RP2 / Source: TRITICUM AESTIVUM (gene. exp.)
    #9polypeptide(L) / 60S RIBOSOMAL PROTEIN L17-A / 60S RIBOSOMAL PROTEIN L17, L20A, YL17 / Source: TRITICUM AESTIVUM (gene. exp.)
    #10polypeptide(L) / 60S RIBOSOMAL PROTEIN L19 / L23, YL14, RP15L, RP33 / Source: TRITICUM AESTIVUM (gene. exp.)
    #11polypeptide(L) / 60S RIBOSOMAL PROTEIN L25 / YL25, RP16L, YP42' / Source: TRITICUM AESTIVUM (gene. exp.)
    #12polypeptide(L) / 60S RIBOSOMAL PROTEIN L26-A / 60S RIBOSOMAL PROTEIN L26, L33, YL33 / Source: TRITICUM AESTIVUM (gene. exp.)
    #13polypeptide(L) / 60S RIBOSOMAL PROTEIN L31-A / 60S RIBOSOMAL PROTEIN L31, L34, YL28 / Source: TRITICUM AESTIVUM (gene. exp.)
    #14polypeptide(L) / 60S RIBOSOMAL PROTEIN L35 / Source: TRITICUM AESTIVUM (gene. exp.)
    #15polypeptide(L) / 60S RIBOSOMAL PROTEIN L39 / L46, YL40 / Source: TRITICUM AESTIVUM (gene. exp.)

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    Experimental details

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    Experiment

    ExperimentMethod: ELECTRON MICROSCOPY
    EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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    Sample preparation

    Assembly of specimenName: ACTIVELY TRANSLATING WHEAT GERM (O. SATIVA) 80S RIBOSOME PROGRAMMED WITH A NASCENT POLYPEPTIDE CHAIN CONTAINING A P- SITE TRNA AND THE TYPE I SIGNAL ANCHOR SEQUENCE OF DPAP-B ( DIPEPTIDYLAMINOPEPTIDASE B) BOUND TO THE MAMMALIAN (CANIS FAMILIARIS) SEC61 COMPLEX.
    Aggregation state: PARTICLE
    Buffer solutionName: 30 MM HEPES/KOH, PH 7.5 180 MM KOAC, 10 MM MG(OAC)2, 1 MM DTT, 3.5 % (W/V) GLYCEROL 0.3 % (W/V) DIGITONIN
    Sample preparationpH: 7.5 / Sample conc.: 0.02 mg/ml
    Specimen supportDetails: OTHER
    VitrificationDetails: CRYOGEN- ETHANE, HUMIDITY- 95, INSTRUMENT- VITROBOT, METHOD- BLOT FOR 10 SECONDS BEFORE PLUNGING, USE 2 LAYERS OF FILTER PAPER

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    Electron microscopy imaging

    MicroscopyMicroscope model: OTHER
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/A2 / Illumination mode: FLOOD BEAM
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 39000 X / Calibrated magnification: 38000 X / Nominal defocus max: 4700 nm / Nominal defocus min: 1250 nm / Cs: 2.26 mm
    Specimen holderTemperature: 84 K / Tilt angle max: 0 deg.
    CameraType: KODAK SO163
    EM image scansNumber digital images: 155
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionSoftware name: SPIDER / Number of particles: 221445
    EM single particle entitySymmetry type: MIXED SYMMETRY
    3D reconstructionMethod: PROJECTION MATCHING / Resolution: 6.48 A / Nominal pixel size: 1.2375 A/pix / Actual pixel size: 1.2375 A/pix / CTF correction method: DEFOCUS GROUP VOLUMES
    Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1652.
    Atomic model buildingMethod: MANUAL FOLLOWED BY MDFF
    Least-squares processHighest resolution: 6.48 A
    Refine hist #LASTHighest resolution: 6.48 A
    Number of atoms included #LASTProtein: 11394 / Nucleic acid: 2919 / Ligand: 0 / Solvent: 0 / Total: 14313

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