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    - PDB-2nsu: Crystal structure of the ectodomain of human transferrin receptor... -

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    Basic information

    Entry
    Database: PDB / ID: 2nsu
    TitleCrystal structure of the ectodomain of human transferrin receptor fitted into a cryo-EM reconstruction of canine parvovirus and feline transferrin receptor complex
    DescriptorTransferrin receptor protein 1
    KeywordsMETAL TRANSPORT / transferrin receptor / virus-receptor complex
    Specimen sourceHomo sapiens / human
    MethodElectron microscopy (27 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsHafenstein, S. / Kostyuchenko, V.A. / Rossmann, M.G.
    CitationProc. Natl. Acad. Sci. U.S.A., 2007, 104, 6585-6589

    Proc. Natl. Acad. Sci. U.S.A., 2007, 104, 6585-6589 StrPapers
    Asymmetric binding of transferrin receptor to parvovirus capsids.
    Susan Hafenstein / Laura M Palermo / Victor A Kostyuchenko / Chuan Xiao / Marc C Morais / Christian D S Nelson / Valorie D Bowman / Anthony J Battisti / Paul R Chipman / Colin R Parrish / Michael G Rossmann

    DateDeposition: Nov 6, 2006 / Release: Mar 27, 2007 / Last modification: Feb 24, 2009

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    Assembly

    Deposited unit
    A: Transferrin receptor protein 1
    B: Transferrin receptor protein 1

    143 kDa, 2 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    143,2472
    Polyers143,2472
    Non-polymers00
    Water0

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

    #1polypeptide(L) / Transferrin receptor protein 1 / TfR1, TR, TfR, Trfr, CD71 antigen, T9, p90 / Fragment: THE ECTODOMAIN OF HUMAN TRANSFERRIN RECEPTOR / Source: Homo sapiens (gene. exp.) / References: UniProt: P02786

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    Experimental details

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    Experiment

    ExperimentMethod: ELECTRON MICROSCOPY
    EM experimentReconstruction method: SINGLE PARTICLE / Specimen type: VITREOUS ICE (CRYO EM)

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    Sample preparation

    Assembly of specimenName: MIXTURE OF EMPTY CANINE PARVOVIRUS CAPSIDS AND ECTODOMAINS OF FELINE TRANSFERRIN RECEPTORS
    Aggregation state: PARTICLE / Details: NOT AVAILABLE
    ComponentDetails: Based on PDB entry 1CX8
    Buffer solutionName: 0.02M TRIS-HCL
    Sample preparationpH: 7.5
    Specimen supportDetails: QUANTIFOIL 200
    VitrificationDetails: PLUNGED IN LIQUID ETHANE

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    Electron microscopy imaging

    MicroscopyMicroscope model: FEI/PHILIPS CM200 FEG / Date: Jan 22, 2003
    Electron gunElectron source: FEG / Accelerating voltage: 200 kV / Electron dose: 25.96 e/A2
    Electron lensMode: BRIGHTFIELD / Nominal magnification: 50000 X / Calibrated magnification: 54000 X / Nominal defocus max: 3900 nm / Nominal defocus min: 1700 nm / Cs: 2 mm
    CameraType: KODAK SO163 FILM
    EM image scansNumber digital images: 115
    RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionSoftware name: XMIPP, SPIDER, EMAN / Number of particles: 8566
    EM single particle entitySymmetry type: MIXED SYMMETRY
    3D reconstructionMethod: projection matching / Resolution: 27 A / Nominal pixel size: 2.6 A/pix / Actual pixel size: 2.6 A/pix / CTF correction method: CTF correction of each particle / Details: a modified version of XMIPP software was used
    Atomic model buildingMethod: MANUAL FITTING USING THE PROGRAM O / Ref protocol: RIGID BODY / Ref space: REAL / Target criteria: BEST VISUAL FIT USING THE PROGRAM O
    Least-squares processHighest resolution: 27 A
    Refine hist #LASTHighest resolution: 27 A
    Number of atoms included #LASTProtein: 10112 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 10112

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