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    Yorodumi
    - EMDB-2026: Structure of the proteasome subunit Rpn1 -

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    Basic information

    Entry
    Database: EMDB / ID: 2026
    TitleStructure of the proteasome subunit Rpn1
    Keywordsproteasome / rpn1 / 19S subunit
    SampleRpn1
    SourceSaccharomyces cerevisiae / yeast / Baker's yeast /
    Map dataMap of the proteasome subunit Rpn1 from S. cerevisiae
    Methodsingle particle reconstruction, at 25 A resolution
    AuthorsHe J / Kulkarni K / daFonseca P / Krutauz D / Glickman M / Barford D / Morris E
    CitationStructure, 2012, 20, 513-521

    Structure, 2012, 20, 513-521 StrPapers
    The structure of the 26S proteasome subunit Rpn2 reveals its PC repeat domain as a closed toroid of two concentric α-helical rings.
    Jun He / Kiran Kulkarni / Paula C A da Fonseca / Dasha Krutauz / Michael H Glickman / David Barford / Edward P Morris

    DateDeposition: Jan 9, 2012 / Header (metadata) release: Jan 20, 2012 / Map release: Apr 13, 2012 / Last update: Jan 9, 2012

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 5.5
    • Imaged by UCSF CHIMERA
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    • Surface view colored by height
    • Surface level: 5.5
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_2026.map.gz (map file in CCP4 format, 8193 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    128 pix
    2.17 A/pix
    = 278.144 A
    128 pix
    2.17 A/pix
    = 278.144 A
    128 pix
    2.17 A/pix
    = 278.144 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.173 A
    Density
    Contour Level:5.5 (by author), 5.5 (movie #1):
    Minimum - Maximum-11.30645084 - 36.75227737
    Average (Standard dev.)0E-8 (1.00000012)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions128128128
    Origin-64-64-64
    Limit636363
    Spacing128128128
    CellA=B=C: 278.144 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.1732.1732.173
    M x/y/z128128128
    origin x/y/z0.0000.0000.000
    length x/y/z278.144278.144278.144
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ
    NX/NY/NZ
    MAP C/R/S123
    start NC/NR/NS-64-64-64
    NC/NR/NS128128128
    D min/max/mean-11.30636.752-0.000

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    Supplemental data

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    Sample components

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    Entire Rpn1

    EntireName: Rpn1 / Number of components: 1
    MassTheoretical: 109.492 kDa

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    Component #1: protein, Rpn1

    ProteinName: Rpn1 / a.k.a: Rpn1 / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 1
    MassTheoretical: 109.492 kDa
    SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast /
    Source (engineered)Expression System: Escherichia coli / bacteria /

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.1 mg/ml
    Support filmCarbon film on quantifoil
    Staining2% uranyl acetate
    VitrificationInstrument: NONE / Cryogen name: NONE

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 100 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 80000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 800 - 900 nm
    Specimen HolderHolder: Eucentric / Model: SIDE ENTRY, EUCENTRIC
    CameraDetector: TVIPS TEMCAM-F415 (4k x 4k)

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    Image acquisition

    Image acquisitionNumber of digital images: 71 / Bit depth: 16

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    Image processing

    ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric)
    3D reconstructionSoftware: Imagic / Resolution: 25 A / Resolution method: FSC 0.5

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