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    ID:- Chain:- Residue:- Atom:-
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    - PDB-3eq3: Model of tRNA(Trp)-EF-Tu in the ribosomal pre-accommodated state ... -

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    Basic information

    Entry
    Database: PDB / ID: 3eq3
    TitleModel of tRNA(Trp)-EF-Tu in the ribosomal pre-accommodated state revealed by cryo-EM
    DescriptorElongation factor Tu
    30S ribosomal protein S12
    50S ribosomal protein L11/RNA complex
    KeywordsRIBOSOMAL PROTEIN/RNA / protein translation / ternary complex / A/T-tRNA / automated data collection / Antibiotic resistance / Elongation factor / GTP-binding / Membrane / Methylation / Nucleotide-binding / Phosphoprotein / Protein biosynthesis / Ribonucleoprotein / Ribosomal protein / RNA-binding / rRNA-binding / tRNA-binding / RIBOSOMAL PROTEIN-RNA COMPLEX
    Specimen sourceEscherichia coli k12 / bacteria / image: Escherichia coli
    MethodElectron microscopy (9 A resolution)
    AuthorsFrank, J. / Li, W. / Agirrezabala, X.
    CitationEMBO J., 2008, 27, 3322-3331

    EMBO J., 2008, 27, 3322-3331 StrPapers
    Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM.
    Wen Li / Xabier Agirrezabala / Jianlin Lei / Lamine Bouakaz / Julie L Brunelle / Rodrigo F Ortiz-Meoz / Rachel Green / Suparna Sanyal / Måns Ehrenberg / Joachim Frank

    DateDeposition: Sep 30, 2008 / Release: Dec 16, 2008 / Last modification: May 30, 2012

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    Assembly

    Deposited unit
    X: Elongation factor Tu
    L: 30S ribosomal protein S12
    I: 50S ribosomal protein L11
    Y: tRNA
    A: Fragment h18 of the 16S rRNA
    C: Fragment h44 of the 16S rRNA
    B: Fragment H43-44 of the 23S rRNA
    D: Fragment H95 of the 23S rRNA
    E: Fragment H69 of the 23S rRNA

    132 kDa, 9 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    131,9799
    Polyers131,9799
    Non-polymers00
    Water0

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

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    RNA chain , 6 types, 6 molecules YACBDE

    #4RNA chain / tRNA / Source: Escherichia coli K12 (gene. exp.)
    #5RNA chain / Fragment h18 of the 16S rRNA / Source: Escherichia coli K12 (gene. exp.)
    #6RNA chain / Fragment h44 of the 16S rRNA / Source: Escherichia coli K12 (gene. exp.)
    #7RNA chain / Fragment H43-44 of the 23S rRNA / Source: Escherichia coli K12 (gene. exp.)
    #8RNA chain / Fragment H95 of the 23S rRNA / Source: Escherichia coli K12 (gene. exp.)
    #9RNA chain / Fragment H69 of the 23S rRNA / Source: Escherichia coli K12 (gene. exp.)

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    polypeptide(L) / 30S ribosomal protein ... / 50S ribosomal protein ... , 3 types, 3 molecules XLI

    #1polypeptide(L) / Elongation factor Tu / EF-Tu, P-43 / Source: Escherichia coli K12 (gene. exp.) / References: UniProt: P0A6N1
    #2polypeptide(L) / 30S ribosomal protein S12 / Source: Escherichia coli K12 (gene. exp.) / References: UniProt: P0A7S3
    #3polypeptide(L) / 50S ribosomal protein L11 / Source: Escherichia coli K12 (gene. exp.) / References: UniProt: P0A7J7

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    Experimental details

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    Experiment

    ExperimentMethod: ELECTRON MICROSCOPY

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    Sample preparation

    Assembly of specimenAggregation state: PARTICLE
    Composition: A/T-tRNA(Trp), EF-Tu, L11, S12, fragments h44 and h18 from the 16S rRNA, fragments H43-H44, H69, and H95 from the 23S rRNA

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    Electron microscopy imaging

    MicroscopyDate: Jan 1, 2007
    CameraType: AMT
    RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionSoftware name: RSRef
    3D reconstructionMethod: SINGLE PARTICLE / Resolution: 9 A
    Atomic model buildingMethod: See Method in the citation / Software name: RSRef / Ref protocol: auto / Ref space: REAL / Target criteria: cross-correlation coefficient
    Number of atoms included #LASTProtein: 657 / Nucleic acid: 187 / Ligand: 0 / Solvent: 0 / Total: 844

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