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    Yorodumi
    - PDB-2xky: Single particle analysis of Kir2.1NC_4 in negative stain -

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    Entry
    Database: PDB / ID: 2xky
    TitleSingle particle analysis of Kir2.1NC_4 in negative stain
    DescriptorINWARD RECTIFIER POTASSIUM CHANNEL 2
    KeywordsMETAL TRANSPORT / ION CHANNEL / MEMBRANE PROTEIN
    Specimen sourceMus musculus / mammal / MOUSE /
    MethodElectron microscopy + Solution scattering (17.2 A resolution / Single particle / Negative stain)
    AuthorsFomina, S. / Howard, T.D. / Sleator, O.K. / Golovanova, M. / O'Ryan, L. / Leyland, M.L. / Grossmann, J.G. / Collins, R.F. / Prince, S.M.
    CitationBiochim. Biophys. Acta, 2011, 1808, 2374-2389

    primary. Biochim. Biophys. Acta, 2011, 1808, 2374-2389 StrPapers
    Self-directed assembly and clustering of the cytoplasmic domains of inwardly rectifying Kir2.1 potassium channels on association with PSD-95.
    Svetlana Fomina / Tina D Howard / Olivia K Sleator / Marina Golovanova / Liam O'Ryan / Mark L Leyland / J Günter Grossmann / Richard F Collins / Stephen M Prince

    #1. Nat.Neurosci., 2005, 8, 279- StrPapers
    Cytoplasmic Domain Structures of Kir2.1 And Kir3.1 Show Sites for Modulating Gating and Rectification.
    Pegan, S. / Arrabit, C. / Zhou, W. / Kwiatkowski, W. / Collins, A. / Slesinger, P.A. / Choe, S.

    DateDeposition: Jul 15, 2010 / Release: Jul 20, 2011 / Last modification: Aug 10, 2011

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    Assembly

    Deposited unit
    I: INWARD RECTIFIER POTASSIUM CHANNEL 2
    J: INWARD RECTIFIER POTASSIUM CHANNEL 2
    K: INWARD RECTIFIER POTASSIUM CHANNEL 2
    L: INWARD RECTIFIER POTASSIUM CHANNEL 2

    140 kDa, 4 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    139,9224
    Polyers139,9224
    Non-polymers00
    Water0

    Omokage search
    #1idetical with deposited unit / defined by author&software (PISA) / Symmetry operations: (identity)x1
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    Components

    #1polypeptide(L) / INWARD RECTIFIER POTASSIUM CHANNEL 2 / HOMOTETRAMER OF FUSED N, C TERMINI / POTASSIUM CHANNEL, INWARDLY RECTIFYING SUBFAMILY J MEMBER 2, INWARD RECTIFIER K(+) CHANNEL KIR2.1, IRK-1 / Fragment: KIR2.1 CYTOPLASMIC DOMAIN, RESIDUES 1-67,189-428 / Source: MUS MUSCULUS (gene. exp.) / References: UniProt: P35561

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    Experimental details

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    Experiment

    Experiment
    Method
    ELECTRON MICROSCOPY
    SOLUTION SCATTERING
    EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: NEGATIVE STAIN

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    Sample preparation

    Assembly of specimenName: MOUSE KIR2.1, CYTOPLASMIC DOMAIN / Aggregation state: PARTICLE
    Buffer solutionName: 20MM TRIS/HCL, 150MM NACL, 1MM REDUCED GSH, 1MM EDTA, 50MM L-GLUTAMIC ACID, 50MM L-ARGININE
    Sample preparationpH: 7.5 / Sample conc.: 1 mg/ml
    Specimen supportDetails: CARBON

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    Data collection

    MicroscopyMicroscope model: OTHER / Details: LOW DOSE
    Electron gunElectron source: TUNGSTEN HAIRPIN / Accelerating voltage: 100 kV / Illumination mode: FLOOD BEAM
    Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1250 nm / Nominal defocus min: 600 nm / Cs: 2 mm
    Specimen holderTilt angle max: 0.1 deg. / Tilt angle min: 0 deg.
    CameraType: GATAN ORIUS CCD CAMERA
    EM image scansNumber digital images: 22
    Radiation wavelengthRelative weight: 1
    Soln scatter

    Buffer name: 20MM TRIS/HCL, 150MM NACL, 1MM REDUCED GSH, 1MM EDTA, 50MM L-GLUTAMIC ACID, 50MM L-ARGININE / Conc. range: 0.5-4.8 / Data reduction software list: OTOKO/GNOM / Detector type: MULTIWIRE 2-D / Mean guiner radius: 4.53 nm / Number of time frames: 60 / Protein length: 16 / Source beamline: STATION 2.1 / Source class: Y / Source type: SRS / Temperature: 277 K

    TypeID
    x-ray1
    modelling2

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    Processing

    Image selectionSoftware name: EMAN / Number of particles: 49012
    3D reconstructionResolution: 17.2 A / Nominal pixel size: 2.93 A/pix / Actual pixel size: 2.93 A/pix
    CTF correction method: PARAMETERS DETERMINED USING SCATTERING CURVE
    Details: THE COORDINATES DEPOSITED ARE FROM A COMBINED SAXS/EM STUDY. THE DOMAINS IN THE PROTEINS (HIGH RESOLUTION STRUCTURES FROM THE PDB) ARE POSITIONED RELATIVE TO ONE ANOTHER USING A SAXS CURVE, THIS COMPOSITE STRUCTURE IS THEN FITTED INTO AN EM MAP. MODEL GENERATED FROM SAXS REFINEMENT USING BUNCH. PETOUKHOV, M. V. AND SVERGUN, D. I. (2005). BIOPHYS J 89, 1237-50. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1764. (DEPOSITION ID: 7401).
    Atomic model buildingMethod: A MAP WAS GENERATED FROM THE SAXS MODEL COORDINATES AT A RESOLUTION MATCHING THE EXPERIMENTAL MAP. T HIS CALCULATED MAP WAS FITTED INTO THE EXPERIMENTAL MAP BY MAXIMIZING THE CROSS-CORRELATION WITH THE EXPERIMENTAL MAP. THE COORDINATES WERE THEN REPLACED IN THE CALCULATED MAP TO GENERATE THE FINAL ENTRY.
    Ref protocol: DOCKED USING CHIMERA / Ref space: REAL
    Least-squares processHighest resolution: 17.2 A
    Refine hist #LASTHighest resolution: 17.2 A
    Number of atoms included #LASTProtein: 1236 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1236
    Soln scatter modelMethod: RIGID BODY MODELLING
    Conformer selection criteria: CONFORMERS WERE CONSISTENT, BEST AGREEMENT WITH EXPERIMENTAL DATA DEPOSITED (CHI=2.6).
    Details: NUMBER OF TIME FRAMES USED 25(60S, 4.25M CAMERA), 35(60S, 1M CAMERA). PROTEIN CONCENTRATION 0.5 MG/ML (4.25M CAMERA), 4.8 MG/ML (1M CAMERA)
    Entry fitting list: PROGRAM PRE-BUNCH, 1U4F, C_4 SYMMETRY + SEQUENCE DATA
    Number of conformers calculated: 20 / Number of conformers submitted: 1 / Software author list: PETOUKHOV, M. V. & SVERGUN, D. I. / Software list: SASREF7/BUNCH8

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