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    Yorodumi
    - EMDB-5295: 3D reconstruction of negatively stained PCSK9 in complex with a Fab -

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    Basic information

    Entry
    Database: EMDB / ID: 5295
    Title3D reconstruction of negatively stained PCSK9 in complex with a Fab
    KeywordsPCSK9-Fab complex
    Samplehuman PCSK9 in complex with a Fab
    SourceHomo sapiens / human
    Map data3D reconstruction of negatively stained PCSK9-Fab complex
    Methodsingle particle reconstruction, at 25 A resolution
    AuthorsWu S / Avila-Sakar A / Kim J / Booth DS / Greenberg CH / Rossi A / Liao M / Alian A / Griner SL / Juge N / Mergel CM / Chaparro-Riggers J / Strop P / Tampe R / Edwards RH / Stroud RM / Craik CS / Cheng Y
    CitationStructure, 2012, 20, 582-592

    Structure, 2012, 20, 582-592 StrPapers
    Fabs enable single particle cryoEM studies of small proteins.
    Shenping Wu / Agustin Avila-Sakar / JungMin Kim / David S Booth / Charles H Greenberg / Andrea Rossi / Maofu Liao / Xueming Li / Akram Alian / Sarah L Griner / Narinobu Juge / Yadong Yu / Claudia M Mergel / Javier Chaparro-Riggers / Pavel Strop / Robert Tampé / Robert H Edwards / Robert M Stroud / Charles S Craik / Yifan Cheng

    DateDeposition: May 23, 2011 / Header (metadata) release: Oct 26, 2011 / Map release: May 29, 2012 / Last update: May 23, 2011

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    Structure visualization

    Movie
    • Surface view with section colored by density value
    • Surface level: 0.5
    • Imaged by UCSF CHIMERA
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    • Surface view colored by height
    • Surface level: 0.5
    • Imaged by UCSF CHIMERA
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    Supplemental images

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    Map

    Fileemd_5295.map.gz (map file in CCP4 format, 845 KB)
    Projections & slicesSize of images:
    AxesZ (Sec.)Y (Row.)X (Col.)
    60 pix
    4.26 A/pix
    = 255.6 A
    60 pix
    4.26 A/pix
    = 255.6 A
    60 pix
    4.26 A/pix
    = 255.6 A

    Surface

    Projections

    Slices (1/3)

    Slices (1/2)

    Slices (2/3)

    Images are generated by Spider package.

    Voxel sizeX=Y=Z: 4.26 A
    Density
    Contour Level:0.5 (by author), 0.5 (movie #1):
    Minimum - Maximum-0.82391357 - 3.13429093
    Average (Standard dev.)0.00072357 (0.1562008)
    Details

    EMDB XML:

    Space Group Number1
    Map Geometry
    Axis orderXYZ
    Dimensions606060
    Origin000
    Limit595959
    Spacing606060
    CellA=B=C: 255.6 A
    Alpha=beta=gamma: 90 deg.

    CCP4 map header:

    modeImage stored as Reals
    A/pix X/Y/Z4.264.264.26
    M x/y/z606060
    origin x/y/z0.0000.0000.000
    length x/y/z255.600255.600255.600
    alpha/beta/gamma90.00090.00090.000
    start NX/NY/NZ-62-62-62
    NX/NY/NZ125125125
    MAP C/R/S123
    start NC/NR/NS000
    NC/NR/NS606060
    D min/max/mean-0.8243.1340.001

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    Supplemental data

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    Sample components

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    Entire human PCSK9 in complex with a Fab

    EntireName: human PCSK9 in complex with a Fab / Number of components: 2 / Oligomeric State: monomer
    MassTheoretical: 120 kDa / Experimental: 120 kDa

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    Component #1: protein, PCSK9

    ProteinName: PCSK9 / Oligomeric Details: monomer / Recombinant expression: Yes / Number of Copies: 2
    MassTheoretical: 120 kDa / Experimental: 120 kDa
    SourceSpecies: Homo sapiens / human
    Source (engineered)Expression System: Escherichia coli / bacteria /

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    Experimental details

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    Sample preparation

    Specimen stateparticle
    Support film200 mesh copper grid
    Staininguranyl formate
    VitrificationInstrument: NONE / Cryogen name: NONE

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    Electron microscopy imaging

    ImagingMicroscope: FEI TECNAI 20
    Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Electron dose: 30 e/A2 / Illumination mode: FLOOD BEAM
    LensMagnification: 50000 X (nominal), 50000 X (calibrated) / Astigmatism: each particle / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1.5 nm
    Specimen HolderHolder: single tilt / Model: SIDE ENTRY, EUCENTRIC / Tilt Angle: 0 - 60 deg.
    CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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    Image processing

    ProcessingMethod: single particle reconstruction / Number of projections: 3876 / Applied symmetry: C1 (asymmetric)
    3D reconstructionAlgorithm: Fourier space / Software: Frealign / CTF correction: each particle / Resolution: 25 A / Resolution method: FSC 0.5

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    Atomic model buiding

    Modeling #1Refinement space: REAL
    Input PDB model: 2PMW

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