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    Yorodumi
    - EMDB-1985: Structure of the full human RXR-VDR nuclear receptor heterodimer ... -

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    Basic information

    Entry
    Database: EMDB / ID: 1985
    TitleStructure of the full human RXR-VDR nuclear receptor heterodimer complex with its DR3 target DNA
    KeywordsNuclear receptor / retinoic acid / vitamin D / DNA response element
    Samplefull human RXR-VDR nuclear receptor heterodimer complex with its DR3 target DNA response element
    SourceHomo sapiens / human
    Map dataVDR-RXR DR3 DNA complex
    Methodsingle particle reconstruction, at 12 A resolution
    AuthorsOrlov I / Rochel N / Moras D / Klaholz BP
    CitationEMBO J., 2012, 31, 291-300

    EMBO J., 2012, 31, 291-300 StrPapers
    Structure of the full human RXR/VDR nuclear receptor heterodimer complex with its DR3 target DNA.
    Igor Orlov / Natacha Rochel / Dino Moras / Bruno P Klaholz

    DateDeposition: Nov 8, 2011 / Header (metadata) release: Aug 1, 2012 / Map release: Aug 1, 2012 / Last update: Nov 8, 2011

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.2
    • Imaged by UCSF CHIMERA
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    • Surface view colored by height
    • Surface level: 0.2
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_1985.map.gz (map file in CCP4 format, 8193 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    128 pix
    2 A/pix
    = 256. A
    128 pix
    2 A/pix
    = 256. A
    128 pix
    2 A/pix
    = 256. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2 A
    Density
    Contour Level:0.5 (by author), 0.2 (movie #1):
    Minimum - Maximum-2.59364676 - 16.3394928
    Average (Standard dev.)0.01883154 (0.34013131)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions128128128
    Origin-63-64-64
    Limit646363
    Spacing128128128
    CellA=B=C: 256 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z222
    M x/y/z128128128
    origin x/y/z0.0000.0000.000
    length x/y/z256.000256.000256.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-56-56-55
    NX/NY/NZ112112112
    MAP C/R/S123
    start NC/NR/NS-64-63-64
    NC/NR/NS128128128
    D min/max/mean-2.59416.3390.019

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    Supplemental data

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    Sample components

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    Entire full human RXR-VDR nuclear receptor heterodimer complex with its ...

    EntireName: full human RXR-VDR nuclear receptor heterodimer complex with its DR3 target DNA response element
    Number of components: 3
    MassTheoretical: 100 kDa / Experimental: 100 kDa

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    Component #1: protein, VDR-RXR

    ProteinName: VDR-RXR / a.k.a: VDR-RXR / Oligomeric Details: hetero dimer / Recombinant expression: Yes / Number of Copies: 1
    SourceSpecies: Homo sapiens / human
    Source (engineered)Expression System: Escherichia coli / bacteria / / Vector: pACYC

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.15 mg/ml
    Buffer solution: Tris 20 mM pH7.5, NaCl 50 mM, KCl 50 mM, MgCl2 4mM, DTT 5mM
    pH: 7.5
    Support film300 mesh Cu/Rh
    Stainingno staining, cryo on holey carbon film
    VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Humidity: 100 % / Method: 2 seconds / Details: Vitrification instrument: Vitrobot

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2000 - 4000 nm
    Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 20 / Scanner: PRIMESCAN / Sampling size: 5.8 microns / Bit depth: 16

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 19938
    Details: EMAN-1 boxer semi-automatic selection and visual control of each boxed particle
    Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: cross-common lines / Software: IMAGIC / CTF correction: each particle
    Details: resolution 12.3A or 9.1 according to FSC at 0.5 or 0.143 cut-off
    Resolution: 12 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Software: IMAGIC, pyMOL / Refinement protocol: rigid body / Refinement space: REAL
    Details: Protocol: rigid body. The domains were separately fitted by manual docking using the program Pymol
    Input PDB model: 1DKF
    Chain ID: 1DKF_A
    Modeling #2Software: IMAGIC, pyMOL / Refinement protocol: rigid body / Refinement space: REAL
    Details: Protocol: rigid body. The domains were separately fitted by manual docking using the program Pymol
    Input PDB model: 1DB1
    Chain ID: 1DB1_A
    Modeling #3Software: IMAGIC, pyMOL / Refinement protocol: rigid body / Refinement space: REAL
    Details: Protocol: rigid body. The domains were separately fitted by manual docking using the program Pymol
    Input PDB model: 1YNW
    Chain ID: 1YNW_A
    Modeling #4Software: IMAGIC, pyMOL / Refinement protocol: rigid body / Refinement space: REAL
    Details: Protocol: rigid body. The domains were separately fitted by manual docking using the program Pymol
    Input PDB model: 2NLL
    Chain ID: 2NLL_A

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