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    Yorodumi
    - EMDB-5421: Archaeoglobus fulgidus methylation-guide sRNP -

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    Basic information

    Entry
    Database: EMDB / ID: 5421
    TitleArchaeoglobus fulgidus methylation-guide sRNP
    Keywordsarchaea / box C/D sRNP / single particle EM / rRNA modification / RNA-protein complex / non-coding RNA
    SampleArchaeoglobus fulgidus methylation-guide sRNP
    SourceArchaeoglobus fulgidus / archaea / thermophilic
    Map dataProjection matching single particle reconstruction of Archaeoglobus fulgidus box C/D sRNP, 26 Angstrom resolution
    Methodsingle particle reconstruction, at 26 A resolution
    AuthorsBower-Phipps KR / Taylor DW / Wang HW / Baserga SJ
    CitationRNA, 2012, 18, 1527-1540

    RNA, 2012, 18, 1527-1540 StrPapers
    The box C/D sRNP dimeric architecture is conserved across domain Archaea.
    Kathleen R Bower-Phipps / David W Taylor / Hong-Wei Wang / Susan J Baserga

    DateDeposition: May 8, 2012 / Header (metadata) release: Jun 5, 2012 / Map release: Jul 9, 2012 / Last update: May 8, 2012

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 3
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 3
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_5421.map.gz (map file in CCP4 format, 8193 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    128 pix
    2.7 A/pix
    = 345.6 A
    128 pix
    2.7 A/pix
    = 345.6 A
    128 pix
    2.7 A/pix
    = 345.6 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.7 A
    Density
    Contour Level:3 (by author), 3 (movie #1):
    Minimum - Maximum-5.50738192 - 17.90023232
    Average (Standard dev.)0.0008348 (0.99800557)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions128128128
    Origin000
    Limit127127127
    Spacing128128128
    CellA=B=C: 345.6 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.72.72.7
    M x/y/z128128128
    origin x/y/z0.0000.0000.000
    length x/y/z345.600345.600345.600
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-62-62-62
    NX/NY/NZ125125125
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS128128128
    D min/max/mean-5.50717.9000.001

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    Supplemental data

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    Sample components

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    Entire Archaeoglobus fulgidus methylation-guide sRNP

    EntireName: Archaeoglobus fulgidus methylation-guide sRNP / Number of components: 1
    Oligomeric State: Four copies of each box C/D core protein could be docked in this map.
    MassTheoretical: 308 kDa

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    Component #1: protein, ribonucleoprotein

    ProteinName: ribonucleoprotein / a.k.a: box C/D sRNP / Recombinant expression: Yes
    MassTheoretical: 308 kDa
    SourceSpecies: Archaeoglobus fulgidus / archaea / thermophilic

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionBuffer solution: 20mM HEPES, 500mM NaCl, 1.5mM MgCl2 / pH: 7.5
    Staining2% uranyl formate
    VitrificationInstrument: NONE / Cryogen name: NONE

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI 12 / Date: Sep 9, 2011 / Details: low-dose conditions
    Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 42000 X (nominal) / Imaging mode: BRIGHT FIELD
    Specimen HolderModel: SIDE ENTRY, EUCENTRIC
    CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 6336 / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: Projection matching / Software: SPIDER / Resolution: 26 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Software: Chimera, Situs / Refinement space: REAL
    Input PDB model: 1RLG
    Modeling #2Software: Chimera, Situs / Refinement space: REAL
    Input PDB model: 1NT2

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