|Entry||Database: EMDB / ID: 1144|
|Title||The structure of the poliovirus 135S cell entry intermediate at 10-angstrom resolution reveals the location of an externalized polypeptide that binds to membranes.|
|Map data||Poliovirus 135S cell-entry intermediate produced by heating native virus for 3min. 50 degrees in 20mM HEPES pH 7.4, 2mM CaCl2|
|Sample||Poliovirus 135S particle:|
|Function / homology||Poliovirus 3A protein-like / Viral coat protein subunit / Peptidase C3A/C3B, picornaviral / Picornavirus/Calicivirus coat protein / Helicase, superfamily 3, single-stranded DNA/RNA virus / Poliovirus core protein 3a, soluble domain / P-loop containing nucleoside triphosphate hydrolase / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / picornavirus capsid protein ...Poliovirus 3A protein-like / Viral coat protein subunit / Peptidase C3A/C3B, picornaviral / Picornavirus/Calicivirus coat protein / Helicase, superfamily 3, single-stranded DNA/RNA virus / Poliovirus core protein 3a, soluble domain / P-loop containing nucleoside triphosphate hydrolase / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / picornavirus capsid protein / Picornavirus 2B protein / 3C cysteine protease (picornain 3C) / Picornavirus coat protein VP4 / RNA-directed RNA polymerase, catalytic domain / RNA dependent RNA polymerase / RNA helicase / Picornavirus core protein 2A / Picornavirus 2B protein / Picornavirus coat protein (VP4) / Poliovirus 3A protein like / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded RNA virus / Peptidase C3, picornavirus core protein 2A / suppression by virus of host translation initiation factor activity / positive stranded viral RNA replication / picornain 2A / pore-mediated entry of viral genome into host cell / suppression by virus of host mRNA export from nucleus / T=pseudo3 icosahedral viral capsid / suppression by virus of host RIG-I activity / picornain 3C / endocytosis involved in viral entry into host cell / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / pore formation by virus in membrane of host cell / integral to membrane of host cell / RNA helicase activity / nucleoside-triphosphate phosphatase / virion assembly / viral capsid / RNA-directed RNA polymerase / induction by virus of host autophagy / ion channel activity / protein complex oligomerization / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / cysteine-type endopeptidase activity / transcription, DNA-templated / host cell nucleus / virion attachment to host cell / structural molecule activity / RNA binding / membrane / ATP binding / Genome polyprotein|
Function and homology information
|Source||Human poliovirus 1 Mahoney (poliovirus)|
|Method||single particle reconstruction / cryo EM / 11 Å resolution|
|Authors||Bubeck D / Filman DJ / Cheng N / Steven AC / Hogle JM / Belnap DM|
|Citation||Journal: J. Virol. / Year: 2005|
Title: The structure of the poliovirus 135S cell entry intermediate at 10-angstrom resolution reveals the location of an externalized polypeptide that binds to membranes.
Authors: Doryen Bubeck / David J Filman / Naiqian Cheng / Alasdair C Steven / James M Hogle / David M Belnap
|Validation Report||PDB-ID: 1xyr|
SummaryFull reportAbout validation report
|Date||Deposition: Nov 6, 2004 / Header (metadata) release: Aug 4, 2005 / Map release: Sep 2, 2005 / Last update: Oct 24, 2012|
|Structure viewer||EM map: |
Downloads & links
|File||emd_1144.map.gz (map file in CCP4 format, 10114 KB)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 2.69 Å|
CCP4 map header:
-Entire Poliovirus 135S particle
|Entire||Name: Poliovirus 135S particle|
Details: Sedimentation coefficient = 135S. Poliovirus 135S particle produced by heating 160S particles at 50 deg. C for 3 minutes.
Oligomeric State: icosahedrally ordered capsid, 60 copies of VP1, VP2, VP3
Number of components: 1
-Component #1: virus, Human poliovirus 1 Mahoney
|Virus||Name: Human poliovirus 1 Mahoney / a.k.a: poliovirus / Class: VIRION / Details: 135S particle / Empty: No / Enveloped: No / Isolate: STRAIN|
|Species||Species: Human poliovirus 1 Mahoney (poliovirus)|
|Source (natural)||Host Species: Homo sapiens (human) / Host category: VERTEBRATES|
|Shell #1||Name of element: capsid / Diameter: 339 Å / T number(triangulation number): 1|
|Specimen||Specimen state: particle / Method: cryo EM|
|Sample solution||Buffer solution: 20 mM HEPES, 2 mM CaCl2 / pH: 7.4|
|Vitrification||Cryogen name: ETHANE / Method: Plunge frozen in liquid ethane. / Details: Vitrification occurred in ambient atmosphere.|
-Electron microscopy imaging
|Imaging||Microscope: FEI TECNAI 20|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 50000 X (nominal) / Imaging mode: BRIGHT FIELD|
|Specimen Holder||Holder: Side entry, liquid nitrogen-cooled, cryo specimen holder|
Model: GATAN LIQUID NITROGEN
|Image acquisition||Number of digital images: 44 / Scanner: ZEISS SCAI / Sampling size: 7 microns / Bit depth: 8 / Details: 22 defocal pairs were scanned.|
|Processing||Method: single particle reconstruction / Number of projections: 3641|
Details: Defocal pairs were used. Here, corresponding particle images from each micrograph are counted as one.
Applied symmetry: I (icosahedral)
|3D reconstruction||Algorithm: Fourier Bessel / Software: EM3DR2|
CTF correction: CTF and decay correction of each particle image
Resolution: 11 Å / Resolution method: FSC 0.333
Euler angles: Determined via PFT2 (used both amplitude and phase information to determine "best" view).
-Atomic model buiding
|Modeling #1||Refinement protocol: rigid body / Refinement space: RECIPROCAL|
Details: Protocol: rigid body. see paper for details of the model fitting
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