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    Yorodumi
    - EMDB-5391: 8-fold symmetric rATcpn-alpha in apo state -

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    Basic information

    Entry
    Database: EMDB / ID: 5391
    Title8-fold symmetric rATcpn-alpha in apo state
    KeywordsGroup II chaperonin / thermosome
    SamplerATcpn-alpha in apo state
    SourceAcidianus tengchongensis / archaea
    Map dataReconstruction of the 8-fold symmetric class of apo rATcpn-alpha
    Methodsingle particle reconstruction, at 4.9 A resolution
    AuthorsZhang K / Wang L / Liu YX / Wang X / Gao B / Hu ZJ / Ji G / Chan KY / Schulten K / Dong ZY / Sun F
    CitationProtein Cell, 2013, 4, 432-444

    Protein Cell, 2013, 4, 432-444 StrPapers
    Flexible interwoven termini determine the thermal stability of thermosomes.
    Kai Zhang / Li Wang / Yanxin Liu / Kwok-Yan Chan / Xiaoyun Pang / Klaus Schulten / Zhiyang Dong / Fei Sun

    DateDeposition: Feb 7, 2012 / Header (metadata) release: Feb 16, 2012 / Map release: Aug 7, 2013 / Last update: Feb 7, 2012

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 3.3
    • Imaged by UCSF CHIMERA
    • Download
    • Surface view colored by cylindrical radius
    • Surface level: 3.3
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-3j1b
    • Surface level: 3.3
    • Imaged by UCSF CHIMERA
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    Supplemental images

    Downloads & links

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    Map

    Fileemd_5391.map.gz (map file in CCP4 format, 93313 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    288 pix
    0.93 A/pix
    = 268.704 A
    288 pix
    0.93 A/pix
    = 268.704 A
    288 pix
    0.93 A/pix
    = 268.704 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 0.933 A
    Density
    Contour Level:3.3 (by author), 3.3 (movie #1):
    Minimum - Maximum-7.62247181 - 13.75225735
    Average (Standard dev.)0E-8 (1.2475096)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions288288288
    Origin-144-144-144
    Limit143143143
    Spacing288288288
    CellA=B=C: 268.704 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z0.9330.9330.933
    M x/y/z288288288
    origin x/y/z0.0000.0000.000
    length x/y/z268.704268.704268.704
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-62-62-62
    NX/NY/NZ125125125
    MAP C/R/S123
    start NC/NR/NS-144-144-144
    NC/NR/NS288288288
    D min/max/mean-7.62213.752-0.000

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    Supplemental data

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    Sample components

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    Entire rATcpn-alpha in apo state

    EntireName: rATcpn-alpha in apo state
    Details: This sample contains about 90% 8-fold symmetric particles and about 10% 9-fold symmetric particles
    Number of components: 1 / Oligomeric State: hexadecamer
    MassTheoretical: 960 kDa / Experimental: 960 kDa

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    Component #1: protein, Group II chaperonin alpha

    ProteinName: Group II chaperonin alpha / a.k.a: rATcpn-alpha / Oligomeric Details: hexadecamer / Recombinant expression: Yes / Number of Copies: 1
    MassTheoretical: 960 kDa / Experimental: 960 kDa
    SourceSpecies: Acidianus tengchongensis / archaea / Strain: S5T
    Source (engineered)Expression System: Escherichia coli / bacteria / / Vector: PET-23b

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 3 mg/ml
    Buffer solution: 25 mM Tris-HCl, pH 7.5, 12 mM MgCl2, 50 mM KCl
    pH: 7.5
    Support film400-mesh GiGTM grid with holes of 2 um diameter and 2 um spacing
    VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 100 K / Humidity: 100 % / Method: Blot for 4 seconds before plunging

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    Electron microscopy imaging

    ImagingMicroscope: FEI TITAN KRIOS / Date: Jul 23, 2010
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 96000 X (nominal), 96000 X (calibrated)
    Astigmatism: Objective lens astigmatism was corrected at 96,000 times magnification
    Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 3500 nm
    Specimen HolderModel: GATAN LIQUID NITROGEN
    CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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    Image acquisition

    Image acquisitionNumber of digital images: 3424 / Bit depth: 32

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 55460 / Applied symmetry: D8 (2*8 fold dihedral)
    3D reconstructionSoftware: Spider,EMAN1.9 / CTF correction: The whole micrograph / Resolution: 4.9 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Software: Chimera / Refinement protocol: flexible / Refinement space: REAL
    Details: Protocol: Rigid body and Molecular Dynamics Flexible Fitting. symmetry-restrained MDFF
    Input PDB model: 3KO1
    Chain ID: A
    Output model

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