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    - EMDB-1547: Structure of GroEL in complex with non-native capsid protein gp23... -

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    Basic information

    Entry
    Database: EMDB / ID: 1547
    TitleStructure of GroEL in complex with non-native capsid protein gp23, Bacteriophage T4 co-chaperone gp31 and ADPAlF3
    Keywordschaperonin / bacteriophage T4 / capsid protein gp23 / GroEL / co-chaperone gp31
    SampleGroEL-gp31-gp23(1)-ADPALF3
    SourceEscherichia coli / bacteria /
    Enterobacteria phage T4 / virus / Bacteriophage T4
    Synthetic construct
    Map dataVolume contains GroEL in complex with non-native capsid protein gp23, co-chaperonin gp31 and ADPAlF3
    Methodsingle particle reconstruction, at 10.2 A resolution
    AuthorsClare DK / Bakkes PJ / van Heerikhuizen H / van der Vies SM / Saibil HR
    CitationNature, 2009, 457, 107-110

    Nature, 2009, 457, 107-110 StrPapers
    Chaperonin complex with a newly folded protein encapsulated in the folding chamber.
    D K Clare / P J Bakkes / H van Heerikhuizen / S M van der Vies / H R Saibil

    DateDeposition: Sep 2, 2008 / Header (metadata) release: Sep 3, 2008 / Map release: Apr 2, 2009 / Last update: Sep 2, 2008

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.15
    • Imaged by UCSF CHIMERA
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    • Surface view colored by cylindrical radius
    • Surface level: 0.15
    • Imaged by UCSF CHIMERA
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    • Surface view with fitted model
    • Atomic models: : PDB-2cgt
    • Surface level: 0.15
    • Imaged by UCSF CHIMERA
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    Map

    Fileemd_1547.map.gz (map file in CCP4 format, 16001 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)X (Row.)Y (Col.)
    160 pix
    2.8 A/pix
    = 448. A
    160 pix
    2.8 A/pix
    = 448. A
    160 pix
    2.8 A/pix
    = 448. A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 2.8 A
    Density
    Contour Level:0.0947, 0.15 (movie #1):
    Minimum - Maximum-1.94969 - 3.39623
    Average (Standard dev.)0.00648203 (0.0950591)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderYXZ
    Dimensions160160160
    Origin-81-81-81
    Limit787878
    Spacing160160160
    CellA=B=C: 448 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z2.82.82.8
    M x/y/z160160160
    origin x/y/z0.0000.0000.000
    length x/y/z448.000448.000448.000
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-81-81-81
    NX/NY/NZ160160160
    MAP C/R/S213
    start NC/NR/NS-81-81-81
    NC/NR/NS160160160
    D min/max/mean-1.9503.3960.006

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    Supplemental data

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    Sample components

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    Entire GroEL-gp31-gp23(1)-ADPALF3

    EntireName: GroEL-gp31-gp23(1)-ADPALF3
    Details: one copy of gp23 is bound to GroEL in the opposite ring to that of the co-chaperonin gp31
    Number of components: 4
    Oligomeric State: tetradecamer of GroEL bound to a heptamer of gp31 and a monomer of gp23
    MassTheoretical: 950 kDa / Experimental: 950 kDa / Measured by: sequence

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    Component #1: protein, GroEL

    ProteinName: GroEL / a.k.a: GroEL / Oligomeric Details: tetradecamer / Number of Copies: 1 / Recombinant expression: Yes
    MassTheoretical: 56 kDa / Experimental: 56 kDa
    SourceSpecies: Escherichia coli / bacteria / / Strain: MC1009
    Source (engineered)Expression System: Escherichia coli / bacteria / / Vector: pSL6
    Source (natural)Location in cell: Cytoplasm
    External referencesGene Ontology: GO: 0005515 / InterPro: InterPro: 001844

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    Component #2: protein, gp31

    ProteinName: gp31 / a.k.a: bacteriophage T4 co-chaperonin / Oligomeric Details: heptamer / Recombinant expression: Yes / Number of Copies: 1
    MassTheoretical: 12 kDa / Experimental: 12 kDa
    SourceSpecies: Enterobacteria phage T4 / virus / Bacteriophage T4
    Source (engineered)Expression System: Escherichia coli / bacteria / / Vector: pAR1
    Source (natural)Location in cell: Cytoplasm
    External referencesInterPro: InterPro: 016416

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    Component #3: protein, gp23

    ProteinName: gp23 / a.k.a: Major capsid protein / Oligomeric Details: monomer / Number of Copies: 1 / Recombinant expression: Yes
    MassTheoretical: 56 kDa / Experimental: 56 kDa
    SourceSpecies: Enterobacteria phage T4 / virus / Bacteriophage T4
    Source (engineered)Expression System: Escherichia coli / bacteria / / Vector: pET2331
    Source (natural)Location in cell: Cytoplasm
    External referencesInterPro: InterPro: 010762

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    Component #4: ligand, ADPAlF3

    LigandName: ADPAlF3 / a.k.a: Non-hydrolysable ATP analogue / Oligomeric Details: monomer / Recombinant expression: No / Number of Copies: 14
    SourceSpecies: Synthetic construct

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Sample solutionSpecimen conc.: 1 mg/ml
    Buffer solution: 40 mM Tris-HCl pH 7.5, 10 mM KCl, 10 mM MgCl2, 2.5 mM ADPAlF3 After nucleotide addition the sample was incubated for 15 minutes before vitrification
    pH: 7.5
    Support film400 mesh R2/2 c-flat grids
    StainingCryo
    VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Temperature: 100 K / Method: blot for 2-3 seconds before plunging / Details: Vitrification instrument: manual plunger

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI F20 / Date: Jun 1, 2006
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 15 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal), 50000 X (calibrated) / Astigmatism: corrected at 150,00 times / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3000 nm
    Specimen HolderHolder: side entry / Model: GATAN LIQUID NITROGEN / Temperature: 100 K
    CameraDetector: KODAK SO-163 FILM

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    Image acquisition

    Image acquisitionNumber of digital images: 150 / Scanner: ZEISS SCAI / Sampling size: 1.4 microns / Bit depth: 8 / OD range: 0.5

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 7300 / Details: No symmetry was applied / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: SIRT
    Euler angles: SPIDER:theta 90-110 degrees, phi 0-360 degrees. Mirror option was on.
    Software: SPIDER / CTF correction: Each particle / Details: No symmetry was applied to the reconstruction / Resolution: 10.2 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Software: URO / Refinement protocol: rigid body / Target criteria: cross-correlation coefficient / Refinement space: RECIPROCAL
    Details: Protocol: Individual domains fitted as rigid bodies. The domains were separately fitted in URO
    Input PDB model: 2CGT
    Output model

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