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    - PDB-2c7c: FITTED COORDINATES FOR GROEL-ATP7-GROES CRYO-EM COMPLEX (EMD-1180) -

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    Basic information

    Entry
    Database: PDB / ID: 2c7c
    TitleFITTED COORDINATES FOR GROEL-ATP7-GROES CRYO-EM COMPLEX (EMD-1180)
    Descriptor60 KDA CHAPERONIN
    10 KDA CHAPERONIN MOLECULE: GROES
    PROTEIN CPN10
    GROES PROTEIN
    KeywordsCHAPERONE / ATP-BINDING / ATOMIC STRUCTURE FITTING / CELL CYCLE / CELL DIVISION / CHAPERONIN / NUCLEOTIDE-BINDING / PHOSPHORYLATION
    Specimen sourceEscherichia coli / bacteria /
    MethodElectron microscopy (7.7 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsRanson, N.A. / Clare, D.K. / Farr, G.W. / Houldershaw, D. / Horwich, A.L. / Saibil, H.R.
    CitationNat. Struct. Mol. Biol., 2006, 13, 147-152

    Nat. Struct. Mol. Biol., 2006, 13, 147-152 StrPapers
    Allosteric signaling of ATP hydrolysis in GroEL-GroES complexes.
    Neil A Ranson / Daniel K Clare / George W Farr / David Houldershaw / Arthur L Horwich / Helen R Saibil

    DateDeposition: Nov 22, 2005 / Release: Jan 25, 2006 / Last modification: Jan 12, 2010

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    Assembly

    Deposited unit
    A: 60 KDA CHAPERONIN
    B: 60 KDA CHAPERONIN
    C: 60 KDA CHAPERONIN
    D: 60 KDA CHAPERONIN
    E: 60 KDA CHAPERONIN
    F: 60 KDA CHAPERONIN
    G: 60 KDA CHAPERONIN
    H: 60 KDA CHAPERONIN
    I: 60 KDA CHAPERONIN
    J: 60 KDA CHAPERONIN
    K: 60 KDA CHAPERONIN
    L: 60 KDA CHAPERONIN
    M: 60 KDA CHAPERONIN
    N: 60 KDA CHAPERONIN
    O: 10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN
    P: 10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN
    Q: 10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN
    R: 10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN
    S: 10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN
    T: 10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN
    U: 10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN

    874 kDa, 21 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    874,46221
    Polyers874,46221
    Non-polymers00
    Water0

    Omokage search
    #1idetical with deposited unit / defined by software (PISA)
    Buried area (A2)62390
    Surface area (A2)321960
    ΔGint (kcal/M)-390.12
    / Symmetry operations: (identity)x1
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    Components

    #1polypeptide(L) / 60 KDA CHAPERONIN / GROEL, PROTEIN CPN60, GROEL PROTEIN / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0A6F5
    #2polypeptide(L) / 10 KDA CHAPERONIN MOLECULE: GROES, PROTEIN CPN10, GROES PROTEIN / Source: ESCHERICHIA COLI (gene. exp.) / References: UniProt: P0A6F9

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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: GROEL-ATP7-GROES / Aggregation state: PARTICLE
    Buffer solutionName: 12.5MM HEPES, 5MM KCL, 5MM MGCL2
    Sample preparationpH: 7.5 / Sample conc.: 1 mg/ml
    Specimen supportDetails: HOLEY CARBON
    VitrificationDetails: LIQUID ETHANE

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    Electron microscopy imaging

    MicroscopyMicroscope model: FEI TECNAI F20
    Electron gunAccelerating voltage: 200 kV / Illumination mode: LOW DOSE
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 3200 nm / Nominal defocus min: 1100 nm / Cs: 2 mm
    Specimen holderTemperature: 100 K
    CameraType: KODAK SO-163 FILM
    EM image scansNumber digital images: 189
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionSoftware name: SPIDER, IMAGIC / Number of particles: 16281
    EM single particle entitySymmetry type: CYCLIC
    3D reconstructionMethod: PROJECTION MATCHING-BASED ANGULAR REFINEMENT OF MSA GENERATED CLASSES. ITERATIVE ALGEBRAIC RECONSTRUCTION IN SPIDER.
    Resolution: 7.7 A / Nominal pixel size: 1.4 A/pix / CTF correction method: FULL CORRECTION ON 2D CLASS AVERAGES
    Details: RECIPROCAL SPACE FITTING OF SEVEN INDEPENDENT RIGID BODIES WITH URO. FITTED ENTITIES WERE GROEL EQUATORIAL (RESIDUES 3-136 AND 410-524), INTERMEDIATE (RESIDUES 137-192 AND 374-409) AND APICAL (RESIDUES 192-373) DOMAINS, PLUS A GROES SUBUNIT. THE MAP INTO WHICH THESE COORDINATES WERE FITTED IS AVAILABLE AT THE EMD (EMD-1180)
    Atomic model buildingMethod: RECIPROCAL SPACE FITTING IN URO
    Least-squares processHighest resolution: 7.7 A
    Refine hist #LASTHighest resolution: 7.7 A
    Number of atoms included #LASTProtein: 57946 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 57946

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