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    - PDB-2xql: Fitting of the H2A-H2B histones in the electron microscopy map of... -

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    Basic information

    Entry
    Database: PDB / ID: 2xql
    TitleFitting of the H2A-H2B histones in the electron microscopy map of the complex Nucleoplasmin:H2A-H2B histones (1:5).
    DescriptorHISTONE H2A-IV
    HISTONE H2B 5
    KeywordsNUCLEAR PROTEIN / CHAPERONE / CHROMATIN / NUCLEAR-CHAPERONE / HISTONE-CHAPERONE
    Specimen sourceGallus gallus / bird / CHICKEN /
    MethodElectron microscopy (19.5 A resolution / Single particle / Negative stain uranyl acetate)
    AuthorsRamos, I. / Martin-Benito, J. / Finn, R. / Bretana, L. / Aloria, K. / Arizmendi, J.M. / Ausio, J. / Muga, A. / Valpuesta, J.M. / Prado, A.
    CitationJ. Biol. Chem., 2010, 285, 33771-33778

    J. Biol. Chem., 2010, 285, 33771-33778 StrPapers
    Nucleoplasmin binds histone H2A-H2B dimers through its distal face.
    Isbaal Ramos / Jaime Martín-Benito / Ron Finn / Laura Bretaña / Kerman Aloria / Jesús M Arizmendi / Juan Ausió / Arturo Muga / José M Valpuesta / Adelina Prado

    DateDeposition: Sep 2, 2010 / Release: Nov 3, 2010 / Last modification: Mar 20, 2013

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    Assembly

    Deposited unit
    A: HISTONE H2A-IV
    B: HISTONE H2B 5
    C: HISTONE H2A-IV
    D: HISTONE H2B 5
    E: HISTONE H2A-IV
    F: HISTONE H2B 5
    G: HISTONE H2A-IV
    H: HISTONE H2B 5
    I: HISTONE H2A-IV
    J: HISTONE H2B 5

    100 kDa, 10 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    100,06110
    Polyers100,06110
    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

    #1polypeptide(L) / HISTONE H2A-IV / H2A HISTONE / Fragment: RESIDUES 16-106 / Source: GALLUS GALLUS (gene. exp.) / References: UniProt: P02263
    #2polypeptide(L) / HISTONE H2B 5 / H2B HISTONE, H2B V / Fragment: RESIDUES 37-126 / Source: GALLUS GALLUS (gene. exp.) / References: UniProt: P0C1H4

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    Experimental details

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    Experiment

    ExperimentMethod: ELECTRON MICROSCOPY
    EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: NEGATIVE STAIN URANYL ACETATE

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    Sample preparation

    Assembly of specimenName: NUCLEOPLASMIN H2A-H2B HISTONES COMPLEX. / Aggregation state: PARTICLE
    Buffer solutionName: 2MM MGCL2, 240MM NACL, 25MM TRIS-HCL
    Sample preparationpH: 7.5
    Specimen supportDetails: CARBON

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    Electron microscopy imaging

    MicroscopyMicroscope model: OTHER
    Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 100 kV / Illumination mode: LOW DOSE
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 60000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 5.6 mm
    Specimen holderTemperature: 293 K
    CameraType: KODAK SO163 FILM
    EM image scansNumber digital images: 14
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionSoftware name: EMAN XMIPP SPIDER / Number of particles: 5557
    3D reconstructionMethod: PROJECTION MATCHING / Resolution: 19.5 A / Nominal pixel size: 2.3 A/pix / CTF correction method: EACH PLATE
    Details: DOCKING OF FIVE DIMERS OF H2A-H2B HISTONES IN THE NUCLEOPLASMIN H2A-H2B COMPLEX (1 5-5). THE EXTENDED REGION OF THE H2A HISTONE WAS REMOVED. THE FINAL DOCKING INCLUDES THE FRAGMENTS FROM AMINOACID 15 TO 105 OF H2A HISTONE AND 36 TO 125 OF H2B HISTONE. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1777. (DEPOSITION ID: 7474).
    Atomic model buildingMethod: VOLUMETRIC CORRELATION / Ref protocol: PROJECTION MATCHING / Ref space: REAL
    Least-squares processHighest resolution: 19.5 A
    Refine hist #LASTHighest resolution: 19.5 A
    Number of atoms included #LASTProtein: 7030 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 7030

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