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    Yorodumi
    - PDB-1if0: PSEUDO-ATOMIC MODEL OF BACTERIOPHAGE HK97 PROCAPSID (PROHEAD II) -

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    Basic information

    Entry
    Database: PDB / ID: 1if0
    TitlePSEUDO-ATOMIC MODEL OF BACTERIOPHAGE HK97 PROCAPSID (PROHEAD II)
    DescriptorMAJOR CAPSID PROTEIN GP5
    KeywordsVirus / Bacteriophage / Capsid / cryoEM / Pseudo-atomic model. / Icosahedral virus
    Specimen sourceEnterobacteria phage HK97 / virus
    MethodElectron microscopy (12 A resolution / Single particle / Vitreous ice (cryo EM))
    AuthorsConway, J.F. / Wikoff, W.R. / Cheng, N. / Duda, R.L. / Hendrix, R.W. / Johnson, J.E. / Steven, A.C.
    CitationScience, 2001, 292, 744-748

    primary. Science, 2001, 292, 744-748 StrPapers
    Virus maturation involving large subunit rotations and local refolding.
    J F Conway / W R Wikoff / N Cheng / R L Duda / R W Hendrix / J E Johnson / A C Steven

    #1. Science, 2000, 289, 2129-2133
    Topologically Linked Protein Rings in the Bacteriophage HK97 Capsid
    Wikoff, W.R. / Liljas, L. / Duda, R.L. / Tsuruta, H. / Hendrix, R.W. / Johnson, J.E.

    #2. Science, 1995, 253, 86-99
    Proteolytic and Conformational Control of Virus Capsid Maturation: The Bacteriophage HK97 System
    Conway, J.F. / Duda, R.L. / Cheng, N. / Hendrix, R.W. / Steven, A.C.

    DateDeposition: Apr 11, 2001 / Release: May 2, 2001 / Last modification: Feb 24, 2009

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    Structure visualization

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    • Biological unit as complete icosahedral assembly
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    • Biological unit as icosahedral pentamer
    • Imaged by Jmol
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    • Biological unit as icosahedral 23 hexamer
    • Imaged by Jmol
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    • Deposited structure unit
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    Assembly

    Deposited unit
    A: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    B: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    C: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    D: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    E: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    F: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    G: PROTEIN (MAJOR CAPSID PROTEIN GP5)

    198 kDa, 7 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    197,9607
    Polyers197,9607
    Non-polymers00
    Water0

    Omokage search
    #1
    A: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    B: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    C: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    D: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    E: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    F: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    G: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    x 60
    complete icosahedral assembly / 11.9 MDa, 420 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    11,877,577420
    Polyers11,877,577420
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x60
    Download / Omokage search
    #2idetical with deposited unit in distinct coordinate / icosahedral asymmetric unit / Symmetry operations: (point symmetry)x1
    #3
    A: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    B: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    C: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    D: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    E: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    F: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    G: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    x 5
    icosahedral pentamer / 990 kDa, 35 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    989,79835
    Polyers989,79835
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x5
    #4
    A: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    B: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    C: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    D: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    E: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    F: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    G: PROTEIN (MAJOR CAPSID PROTEIN GP5)
    x 6
    icosahedral 23 hexamer / 1.19 MDa, 42 molecules
    Theoretical massNumber of molelcules
    Total
    (without water)
    1,187,75842
    Polyers1,187,75842
    Non-polymers00
    Water0
    / Symmetry operations: (point symmetry)x6
    PAUidetical with deposited unit in distinct coordinate / icosahedral asymmetric unit, std point frame / Symmetry operations: (transform to point frame)x1

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    Components

    #1polypeptide(L) / PROTEIN (MAJOR CAPSID PROTEIN GP5) / BACTERIOPHAGE HK97 CAPSID PROTEIN / Source: Enterobacteria phage HK97 (gene. exp.) / References: UniProt: P49861

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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 specimenAggregation state: PARTICLE

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    Electron microscopy imaging

    MicroscopyMicroscope model: FEI/PHILLIPS CM200FEG

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    Processing

    Image selectionNumber of particles: 981
    EM single particle entitySymmetry type: ICOSAHEDRAL
    3D reconstructionResolution: 12 A
    Details: IMAGE RECONSTRUCTION INCLUDING CONTRAST TRANSFER CORRECTION, WAS DONE AS DESCRIBED IN T.S.Baker & R.H.Cheng, J.Struct.Biol. 116, 120-130 (1996) and J.F.Conway & A.C.Steven, J.Struct.Biol. 128, 106 (1999). Nine focal pairs were analyzed, yielding 2939 particles, of which 981 were included in the final map. This map was calculated to 12 Angstroms, its resolution as assessed by Fourier Ring Correlation (cutoff 2 sigma), as calculated between reprojections of two maps from half data sets.
    Atomic model buildingRef space: REAL
    Least-squares processHighest resolution: 12 A
    Refine hist #LASTHighest resolution: 12 A
    Number of atoms included #LASTProtein: 1792 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 1792

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