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    - EMDB-5438: 3D reconstruction of a self-assembling designed oligomer with oct... -

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    Basic information

    Entry
    Database: EMDB / ID: 5438
    Title3D reconstruction of a self-assembling designed oligomer with octahedral symmetry
    Keywordsoctahedral symmetry / designed
    SampleDesigned protein oligomer with octahedral symmetry. The model for the design is PduT from Salmonella enterica with the following mutations: K15A, C38S, M67L, N148A, N149L, E156S, E160A, K161Y, R167A, V169L
    SourceSalmonella enterica / bacteria
    Map dataReconstruction of designed self-assembling protein oligomer with octahedral symmetry
    Methodsingle particle reconstruction, at 20 A resolution
    AuthorsVollmar BS / King NP / Baker D / Gonen T
    CitationScience, 2012, 336, 1171-1174

    Science, 2012, 336, 1171-1174 StrPapers
    Computational design of self-assembling protein nanomaterials with atomic level accuracy.
    Neil P King / William Sheffler / Michael R Sawaya / Breanna S Vollmar / John P Sumida / Ingemar André / Tamir Gonen / Todd O Yeates / David Baker

    DateDeposition: Jun 24, 2012 / Header (metadata) release: Jun 29, 2012 / Map release: Jun 29, 2012 / Last update: Jun 24, 2012

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 1.8
    • Imaged by UCSF CHIMERA
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    • Surface view colored by radius
    • Surface level: 1.8
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_5438.map.gz (map file in CCP4 format, 6751 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    120 pix
    1.47 A/pix
    = 176.88 A
    120 pix
    1.47 A/pix
    = 176.88 A
    120 pix
    1.47 A/pix
    = 176.88 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 1.474 A
    Density
    Contour Level:1.8 (by author), 1.8 (movie #1):
    Minimum - Maximum-2.47524214 - 4.30226564
    Average (Standard dev.)-2E-8 (1)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions120120120
    Origin000
    Limit119119119
    Spacing120120120
    CellA=B=C: 176.88 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z1.4741.4741.474
    M x/y/z120120120
    origin x/y/z0.0000.0000.000
    length x/y/z176.880176.880176.880
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-150-1500
    NX/NY/NZ301301151
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS120120120
    D min/max/mean-2.4754.302-0.000

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    Supplemental data

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    Sample components

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    Entire Designed protein oligomer with octahedral symmetry. The model for...

    EntireName: Designed protein oligomer with octahedral symmetry. The model for the design is PduT from Salmonella enterica with the following mutations: K15A, C38S, M67L, N148A, N149L, E156S, E160A, K161Y, R167A, V169L
    Details: Monodisperse sample / Number of components: 1 / Oligomeric State: 24
    MassTheoretical: 480 kDa

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    Component #1: protein, Propanediol utilization polyhedral body protein PduT

    ProteinName: Propanediol utilization polyhedral body protein PduT
    Details: Mutations: K15A, C38S, M67L, N148A, N149L, E156S, E160A, K161Y, R167A, V169L
    Recombinant expression: Yes / Number of Copies: 24
    SourceSpecies: Salmonella enterica / bacteria
    Source (engineered)Expression System: Escherichia coli / bacteria / / Vector: pET29b

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 0.3 mg/ml / Buffer solution: 25 mM Tris, pH 8.0, 150 mM NaCl, 1 mM DTT / pH: 8
    Support filmQuantifoil R1.2/1.3 holey carbon 400 mesh copper grids
    VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 100 %
    Method: Blotted with filter paper and plunged into liquid ethane.

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20 / Date: Jul 12, 2011
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
    LensMagnification: 100000 X (nominal), 217096 X (calibrated) / Cs: 2.12 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 2000 nm
    Specimen HolderModel: GATAN LIQUID NITROGEN
    CameraDetector: TVIPS TEMCAM-F816 (8k x 8k)

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    Image acquisition

    Image acquisitionNumber of digital images: 565

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 42025
    Details: Particles were selected using the automatic selection program Electron Micrograph Utility (cryoem.ucsf.edu).
    Applied symmetry: O (octahedral)
    3D reconstructionSoftware: FREALIGN / CTF correction: CTFFIND3
    Details: Reconstruction was calculated based on 2x binned images yielding a pixel size of 1.474 A/pixel.
    Resolution: 20 A / Resolution method: FSC 0.5

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