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    Yorodumi
    - EMDB-1283: Molecular architecture and conformational flexibility of human RN... -

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    Basic information

    Entry
    Database: EMDB / ID: 1283
    TitleMolecular architecture and conformational flexibility of human RNA polymerase II.
    Samplehuman RNA Polymerase II
    SourceHomo sapiens / human
    Map dataConformation 1
    Methodsingle particle reconstruction, at 20 A resolution
    AuthorsKostek SA / Grob P / De Carlo S / Lipscomb JS / Garczarek F / Nogales E
    CitationStructure, 2006, 14, 1691-1700

    Structure, 2006, 14, 1691-1700 StrPapers
    Molecular architecture and conformational flexibility of human RNA polymerase II.
    Seth A Kostek / Patricia Grob / Sacha De Carlo / J Slaton Lipscomb / Florian Garczarek / Eva Nogales

    DateDeposition: Oct 28, 2006 / Header (metadata) release: Oct 28, 2006 / Map release: Oct 28, 2006 / Last update: Oct 28, 2006

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.32
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by radius
    • Surface level: 0.32
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_1283.map.gz (map file in CCP4 format, 6751 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    120 pix
    2.5 A/pix
    = 300. A
    120 pix
    2.5 A/pix
    = 300. A
    120 pix
    2.5 A/pix
    = 300. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.5 A
    Density
    Contour Level:0.126, 0.32 (movie #1):
    Minimum - Maximum-0.158582 - 0.587113
    Average (Standard dev.)0.0115372 (0.0722153)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions120120120
    Origin-60-60-60
    Limit595959
    Spacing120120120
    CellA=B=C: 300 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.52.52.5
    M x/y/z120120120
    origin x/y/z0.0000.0000.000
    length x/y/z300.000300.000300.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-184-184-183
    NX/NY/NZ368368368
    MAP C/R/S123
    start NC/NR/NS-60-60-60
    NC/NR/NS120120120
    D min/max/mean-0.1590.5870.012

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    Supplemental data

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    Sample components

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    Entire human RNA Polymerase II

    EntireName: human RNA Polymerase II / Oligomeric State: 12 subunit complex / Number of components: 12
    MassTheoretical: 520 kDa / Experimental: 500 kDa

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    Component #1: protein, Rpb1

    ProteinName: Rpb1 / Number of Copies: 1 / Recombinant expression: No
    MassExperimental: 220 kDa
    SourceSpecies: Homo sapiens / human
    Source (natural)Organelle: Nucleus / Cell: HeLa

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    Component #2: protein, Rpb2

    ProteinName: Rpb2 / Number of Copies: 1 / Recombinant expression: No
    MassExperimental: 130 kDa
    SourceSpecies: Homo sapiens / human
    Source (natural)Organelle: Nucleus / Cell: HeLa

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    Component #3: protein, Rpb3

    ProteinName: Rpb3 / Recombinant expression: No / Number of Copies: 1
    MassExperimental: 30 kDa
    SourceSpecies: Homo sapiens / human
    Source (natural)Organelle: Nucleus / Cell: HeLa

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    Component #4: protein, Rpb4

    ProteinName: Rpb4 / Number of Copies: 1 / Recombinant expression: No
    MassExperimental: 20 kDa
    SourceSpecies: Homo sapiens / human
    Source (natural)Organelle: Nucleus / Cell: HeLa

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    Component #5: protein, Rpb5

    ProteinName: Rpb5 / Number of Copies: 1 / Recombinant expression: No
    MassExperimental: 20 kDa
    SourceSpecies: Homo sapiens / human
    Source (natural)Organelle: Nucleus / Cell: HeLa

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    Component #6: protein, Rpb6

    ProteinName: Rpb6 / Recombinant expression: No / Number of Copies: 1
    MassExperimental: 10 kDa
    SourceSpecies: Homo sapiens / human
    Source (natural)Organelle: Nucleus / Cell: HeLa

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    Component #7: protein, Rpb7

    ProteinName: Rpb7 / Recombinant expression: No / Number of Copies: 1
    MassExperimental: 20 kDa
    SourceSpecies: Homo sapiens / human
    Source (natural)Organelle: Nucleus / Cell: HeLa

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    Component #8: protein, Rpb8

    ProteinName: Rpb8 / Recombinant expression: No / Number of Copies: 1
    MassExperimental: 20 kDa
    SourceSpecies: Homo sapiens / human
    Source (natural)Organelle: Nucleus / Cell: HeLa

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    Component #9: protein, Rpb9

    ProteinName: Rpb9 / Number of Copies: 1 / Recombinant expression: No
    MassExperimental: 10 kDa
    SourceSpecies: Homo sapiens / human
    Source (natural)Organelle: Nucleus / Cell: HeLa

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    Component #10: protein, Rpb10

    ProteinName: Rpb10 / Number of Copies: 1 / Recombinant expression: No
    MassExperimental: 10 kDa
    SourceSpecies: Homo sapiens / human
    Source (natural)Organelle: Nucleus / Cell: HeLa

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    Component #11: protein, Rpb11

    ProteinName: Rpb11 / Number of Copies: 1 / Recombinant expression: No
    MassExperimental: 10 kDa
    SourceSpecies: Homo sapiens / human
    Source (natural)Organelle: Nucleus / Cell: HeLa

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    Component #12: protein, Rpb12

    ProteinName: Rpb12 / Number of Copies: 1 / Recombinant expression: No
    MassExperimental: 10 kDa
    SourceSpecies: Homo sapiens / human
    Source (natural)Organelle: Nucleus / Cell: HeLa

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.01 mg/ml
    Buffer solution: 200mM (NH4)2SO4, 25mM Hepes, 0.2M EDTA, 0.05% NP-40
    pH: 7.9
    Support film400 mesh copper grid
    Stainingcryo-negative staining in a saturated solution of ammonium molybdate neutralized to a pH of 7.2. with 10 N NaOH
    VitrificationCryogen name: ETHANE / Temperature: 90 K / Method: stained with ammonium molybdate before plunging

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    Electron microscopy imaging

    ImagingMicroscope: FEI/PHILIPS CM200FEG
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 17 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal), 50280 X (calibrated) / Cs: 2.2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200 - 3600 nm
    Specimen HolderHolder: side entry / Model: GATAN LIQUID NITROGEN / Temperature: 90 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 19 / Scanner: OTHER / Sampling size: 6.3 microns / Bit depth: 14 / OD range: 1

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 3406 / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: Fourier method / Software: FREALIGN / CTF correction: each micrograph / Resolution: 20 A / Resolution method: FSC 0.143

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