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    - PDB-1ry1: Structure of the signal recognition particle interacting with the... -

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    Basic information

    Entry
    Database: PDB / ID: 1ry1
    TitleStructure of the signal recognition particle interacting with the elongation-arrested ribosome
    Descriptorsignal receptor proteins/RNA Complex
    KeywordsTRANSLATION / signal recognition particle / RNA binding
    Specimen sourceHomo sapiens / human
    Thermus aquaticus / bacteria / thermophilic
    Mus musculus / mammal / house mouse /
    Tursiops truncatus / mammal / bottlenosed dolphin /
    MethodElectron microscopy (12 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsHalic, M. / Becker, T. / Pool, M.R. / Spahn, C.M. / Grassucci, R.A. / Frank, J. / Beckmann, R.
    CitationNature, 2004, 427, 808-814

    Nature, 2004, 427, 808-814 StrPapers
    Structure of the signal recognition particle interacting with the elongation-arrested ribosome.
    Mario Halic / Thomas Becker / Martin R Pool / Christian M T Spahn / Robert A Grassucci / Joachim Frank / Roland Beckmann

    DateDeposition: Dec 19, 2003 / Release: Apr 20, 2004 / Last modification: Feb 24, 2009

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    Assembly

    Deposited unit
    E: ALU DOMAIN (RNA FRAGMENTS)
    A: ALU DOMAIN (SRP9, SRP14 + RNA)
    M: fragment of 7S RNA
    N: RNA (31-MER)
    O: RNA (5'-R(P*GP*UP*UP*CP*UP*GP*GP*GP*CP*UP*GP*UP*AP*GP*UP*GP*CP*GP*CP*UP*AP*UP*GP*C)-3')
    P: RNA (5'-R(*CP*AP*AP*UP*AP*GP*CP*CP*AP*CP*UP*GP*CP*AP*CP*UP*CP*CP*AP*G)-3')
    Q: RNA (5'-R(P*CP*GP*AP*UP*CP*GP*GP*GP*UP*GP*UP*C)-3')
    R: RNA (5'-R(P*AP*UP*CP*GP*CP*GP*CP*CP*UP*GP*UP*G)-3')
    C: PROTEIN (Signal recognition particle 9 kDa protein)
    D: PROTEIN (Signal recognition particle 14 kDa protein)
    B: PROTEIN (Signal recognition particle 19 kDa protein)
    U: Signal recognition particle protein
    W: Signal recognition particle 54 kDa protein
    S: Rhodopsin

    180 kDa, 14 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    179,84814
    Polyers179,84814
    Non-polymers00
    Water0

    Omokage search
    #1idetical with deposited unit / defined by author / Symmetry operations: (identity)x1
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    Components

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    RNA chain , 8 types, 8 molecules EAMNOPQR

    #1RNA chain / ALU DOMAIN (RNA FRAGMENTS)
    #2RNA chain / ALU DOMAIN (SRP9, SRP14 + RNA)
    #3RNA chain / fragment of 7S RNA
    #4RNA chain / RNA (31-MER)
    #5RNA chain / RNA (5'-R(P*GP*UP*UP*CP*UP*GP*GP*GP*CP*UP*GP*UP*AP*GP*UP*GP*CP*GP*CP*UP*AP*UP*GP*C)-3')
    #6RNA chain / RNA (5'-R(*CP*AP*AP*UP*AP*GP*CP*CP*AP*CP*UP*GP*CP*AP*CP*UP*CP*CP*AP*G)-3')
    #7RNA chain / RNA (5'-R(P*CP*GP*AP*UP*CP*GP*GP*GP*UP*GP*UP*C)-3')
    #8RNA chain / RNA (5'-R(P*AP*UP*CP*GP*CP*GP*CP*CP*UP*GP*UP*G)-3')

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    Polypeptide(L) , 6 types, 6 molecules CDBUWS

    #9polypeptide(L) / PROTEIN (Signal recognition particle 9 kDa protein) / SRP9 / Source: Homo sapiens (gene. exp.) / References: UniProt: P49458
    #10polypeptide(L) / PROTEIN (Signal recognition particle 14 kDa protein) / SRP14, 18 kDa ALU RNA binding protein / Source: Homo sapiens (gene. exp.) / References: UniProt: P37108
    #11polypeptide(L) / PROTEIN (Signal recognition particle 19 kDa protein) / SRP19 / Source: Homo sapiens (gene. exp.) / References: UniProt: P09132
    #12polypeptide(L) / Signal recognition particle protein / Fifty-four homolog / Source: Thermus aquaticus (gene. exp.) / References: UniProt: O07347
    #13polypeptide(L) / Signal recognition particle 54 kDa protein / SRP54 / Source: Mus musculus (gene. exp.) / References: UniProt: P14576
    #14polypeptide(L) / Rhodopsin / Source: Tursiops truncatus (gene. exp.) / References: UniProt: O62798

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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: COMPLEX SAMPLE CONCENTRATION (MG ML-1) : / Aggregation state: PARTICLE
    Sample preparationpH: 7.4
    Specimen supportDetails: HOLEY CARBON
    VitrificationDetails: PLUNGED INTO ETHANE

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    Electron microscopy imaging

    MicroscopyMicroscope model: FEI TECNAI F20 / Date: Jan 1, 2000
    Details: SAMPLES WERE MAINTAINED AT LIQUID NITROGEN TEMPERATURES IN THE ELECTRON MICROSCOPE.
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 160 kV / Electron dose: 1000 e/A2 / Illumination mode: FLOOD BEAM LOW DOSE
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 51000 X / Calibrated magnification: 52000 X / Nominal defocus max: 45000 nm / Nominal defocus min: 10000 nm / Cs: 2 mm
    Specimen holderTemperature: 95 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
    CameraType: KODAK SO163 FILM
    EM image scansNumber digital images: 75

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    Processing

    Image selectionSoftware name: SPIDER
    EM single particle entitySymmetry type: ASYMMETRIC
    3D reconstructionDetails: The chains M, N, O, P, Q and R are fragments of a double helical strand of RNA. The author maintains that some of the residues could not be modeled correctly due to limited resolution in this region.
    Atomic model buildingSoftware name: SPIDER
    Least-squares processHighest resolution: 12 A
    Refine hist #LASTHighest resolution: 12 A
    Number of atoms included #LASTProtein: 5335 / Nucleic acid: 6459 / Ligand: 0 / Solvent: 0 / Total: 11794

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