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    - PDB-4ard: Structure of the immature retroviral capsid at 8A resolution by c... -

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    Basic information

    Entry
    Database: PDB / ID: 4ard
    TitleStructure of the immature retroviral capsid at 8A resolution by cryo- electron microscopy
    DescriptorCAPSID PROTEIN P27
    KeywordsVIRAL PROTEIN / RETROVIRUS / GAG
    Specimen sourceMASON-PFIZER MONKEY VIRUS / virus
    MethodElectron microscopy (7 A resolution / Helical / Vitreous ice cryoem)
    AuthorsBharat, T.A.M. / Davey, N.E. / Ulbrich, P. / Riches, J.D. / Marco, A.D. / Rumlova, M. / Sachse, C. / Ruml, T. / Briggs, J.A.G.
    CitationNature, 2012, 487, 385-389

    Nature, 2012, 487, 385-389 StrPapers
    Structure of the immature retroviral capsid at 8 Å resolution by cryo-electron microscopy.
    Tanmay A M Bharat / Norman E Davey / Pavel Ulbrich / James D Riches / Alex de Marco / Michaela Rumlova / Carsten Sachse / Tomas Ruml / John A G Briggs

    DateDeposition: Apr 23, 2012 / Release: May 30, 2012 / Last modification: Aug 1, 2012

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    Assembly

    Deposited unit
    A: CAPSID PROTEIN P27
    B: CAPSID PROTEIN P27

    25.8 kDa, 2 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    25,7712
    Polyers25,7712
    Non-polymers00
    Water0

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

    #1polypeptide(L) / CAPSID PROTEIN P27 / M-PMV DPRO CANC PROTEIN / Fragment: M-PMV CA-NTD, RESIDUES 318-433 / Source: MASON-PFIZER MONKEY VIRUS (gene. exp.) / References: UniProt: P07567

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    Experimental details

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    Experiment

    ExperimentMethod: ELECTRON MICROSCOPY
    EM experimentReconstruction method: HELICAL / Specimen type: VITREOUS ICE CRYOEM

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    Sample preparation

    Assembly of specimenName: M-PMV CANC GAG TUBES / Aggregation state: FILAMENT
    Buffer solutionName: 100MM NACL, 50MM TRIS-HCL, 1UM ZN
    Sample preparationpH: 7.7
    Specimen supportDetails: HOLEY CARBON
    VitrificationDetails: LIQUID ETHANE

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    Electron microscopy imaging

    MicroscopyMicroscope model: OTHER / Date: Jul 5, 2011
    Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 0.2 e/A2 / Illumination mode: LOW DOSE
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 47000 X / Nominal defocus max: 4000 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
    CameraType: KODAK SO163 FILM
    EM image scansNumber digital images: 46
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionSoftware name: SPIDER, AV3
    3D reconstructionMethod: HELICAL RECONSTRUCTION WITH 3D ASYMMETRIC UNIT AVERAGING
    Resolution: 7 A / Nominal pixel size: 1.53 A/pix / Actual pixel size: 1.53 A/pix / CTF correction method: DIVISION BY 3D CTF SQ
    Details: HELICAL RECONSTRUCTION WITH 3D ASYMMETRIC UNIT AVERAGING SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2090. (DEPOSITION ID: 10768).
    Atomic model buildingMethod: RIGID BODY / Ref protocol: NMR / Ref space: REAL
    Least-squares processHighest resolution: 7 A
    Refine hist #LASTHighest resolution: 7 A
    Number of atoms included #LASTProtein: 232 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 232

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