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    - PDB-2bk1: The pore structure of pneumolysin, obtained by fitting the alpha ... -

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    Basic information

    Entry
    Database: PDB / ID: 2bk1
    TitleThe pore structure of pneumolysin, obtained by fitting the alpha carbon trace of perfringolysin O into a cryo-EM map
    DescriptorPERFRINGOLYSIN O
    KeywordsTOXIN / CYTOLYSIS / HEMOLYSIS / THIOL-ACTIVATED CYTOLYSIN / CRYOEM / CYTOLYTIC PROTEIN
    Specimen sourceClostridium perfringens / bacteria
    MethodElectron microscopy (29 A resolution / Single particle / Vitreous ice)
    AuthorsTilley, S.J. / Orlova, E.V. / Gilbert, R.J.C. / Andrew, P.W. / Saibil, H.R.
    CitationCell, 2005, 121, 247-256

    primary. Cell, 2005, 121, 247-256 StrPapers
    Structural basis of pore formation by the bacterial toxin pneumolysin.
    Sarah J Tilley / Elena V Orlova / Robert J C Gilbert / Peter W Andrew / Helen R Saibil

    #1. Cell(Cambridge,Mass.), 1997, 89, 685- StrPapers
    Structure of a Cholesterol-Binding, Thiol-Activated Cytolysin and a Model of its Membrane Form
    Rossjohn, J. / Feil, S.C. / Mckinstry, W.J. / Tweten, R.K. / Parker, M.W.

    DateDeposition: Feb 10, 2005 / Release: May 4, 2005 / Last modification: Jan 16, 2013

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    • Biological unit as complete point assembly
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    • Simplified surface model + fitted atomic model
    • EMDB-1107
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    • Simplified surface model + fitted atomic model
    • EMDB-1108
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    Assembly

    Deposited unit
    A: PERFRINGOLYSIN O

    50.1 kDa, 1 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    50,0961
    Polyers50,0961
    Non-polymers00
    Water0

    Omokage search
    #1
    A: PERFRINGOLYSIN O
    x 38
    complete point assembly / 1.9 MDa, 38 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    1,903,66738
    Polyers1,903,66738
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x38
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    #2idetical with deposited unit in distinct coordinate / point asymmetric unit / Symmetry operations: (point symmetry)x1
    PAUidetical with deposited unit in distinct coordinate / point asymmetric unit, std point frame / Symmetry operations: (transform to point frame)x1

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    Components

    #1polypeptide(L) / PERFRINGOLYSIN O / THETA-TOXIN, THIOL-ACTIVATED CYTOLYSIN / Fragment: RESIDUES 53-500 / Source: CLOSTRIDIUM PERFRINGENS (gene. exp.) / References: UniProt: P19995

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    Experimental details

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    Experiment

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

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    Sample preparation

    Assembly of specimenName: PNEUMOLYSIN / Aggregation state: PARTICLE
    Details: THE SAMPLE CONSISTS OF PNEUMOLYSIN IN A MEMBRANE-INSERTED PORE STATE
    Buffer solutionName: 8 MM NA2HP04, 1.5MM KH2PO4, 2.5 MM KCL, 0.25 MM NACL
    Sample preparationSample conc.: 0.05 mg/ml
    Specimen supportDetails: HOLEY CARBON
    VitrificationDetails: PLUNGED INTO ETHANE

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    Electron microscopy imaging

    MicroscopyMicroscope model: FEI TECHNAI F20
    Details: SAMPLES WERE MAINTAINED AT LIQUID NITROGEN TEMPERATURES IN THE ELECTRON MICROSCOPE.
    Electron gunElectron source: FEG / Accelerating voltage: 200 kV / Electron dose: 2000 e/A2 / Illumination mode: LOW DOSE
    Electron lensMode: BRIGHT FIELD / Nominal magnification: 42000 X / Nominal defocus max: 3200 nm / Nominal defocus min: 1100 nm / Cs: 2 mm
    Specimen holderTemperature: 100 K / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
    CameraType: KODAK SO-163 FILM
    EM image scansNumber digital images: 135
    Radiation wavelengthRelative weight: 1

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    Processing

    Image selectionNumber of particles: 88
    EM single particle entitySymmetry type: CYCLIC
    3D reconstructionResolution: 29 A / Nominal pixel size: 3.5 A/pix / CTF correction method: PHASE FLIPPING
    Details: RESIDUES 134-142 ARE MISSING FROM THE SEQUENCE. RESIDUES CORRESPONDING TO TO TM1 AND TM2 (187-220,284-315) WERE MODELLED AS A POLY-ALANINE FLAT BETA HAIRPINS. THE OLIGOMER CAN BE GENERATED BY APPLYING 38-FOLD ROTATIONAL SYMMETRY.
    Atomic model buildingMethod: THE CRYSTAL STRUCTURE OF PERFRINOGLYSIN O (1PFO, ROSSJOHN ET AL., 1998, CELL 89, 685)WAS PLACED INTO THE CRYO-EM DENSITY MAP (EMD-1107). THE ALPHA CARBON TRACE OF PERFRINGOLYSIN 0 WAS MANUALLY POSITIONED INTO THE CRYO-EM DENSITY CORRESPONDING TO THE POSITION OF ONE SUBUNIT. THE BEST FIT WAS OBTAINED BY SEPARATING THE MONOMER INTO SIX RIGID BODIES: DOMAIN 1(91-172, 231-272 354-373), DOMAIN 2 UPPER (53- 62, 83-90, 374-381), DOMAIN 2 LOWER (63-82, 382-390), DOMAIN 3 (177-186, 221-230, 273-283, 316-353), DOMAIN 3 HAIRPINS (187- 220, 284-315), AND DOMAIN 4 (391-500). THE COMPLETE OLIGOMER (38-MER) WAS GENERATED AND CHECKED FOR CLOSE CONTACTS BOTH BY EYE AND USING THE CCP4 PROGRAM CONTACT.TO IMPROVE THE FIT SECTIONS CORRESPONDING TO 3 SUBUNITS WERE EXTRACTED FROM THE 38-MER MAP (EMD-1107) AND A 44-MER MAP AND ALIGNED. THE WEIGHTED AVERAGE WAS CALCULATED AND THE IMPROVED MAP USED FOR THE FINAL MANUAL FITTING. THE TWO SECTIONS ARE CONSISTENT TO A RESOLUTION OF 28 ANGSTROMS (0.5 CORRELATION FSC) AND THE WEIGHTED AVERAGE MAP WAS RECONSTRUCTED FROM 131 PARTICLES.
    Least-squares processHighest resolution: 29 A
    Refine hist #LASTHighest resolution: 29 A
    Number of atoms included #LASTProtein: 444 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 444

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