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Yorodumi- PDB-2cse: Features of Reovirus Outer-Capsid Protein mu1 Revealed by Electro... -
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-Basic information
Entry | Database: PDB / ID: 2cse | ||||||
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Title | Features of Reovirus Outer-Capsid Protein mu1 Revealed by Electron and Image Reconstruction of the virion at 7.0-A Resolution | ||||||
Components |
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Keywords | VIRUS / cryoEM / image processing / reovirus / membrane penetration protein / Icosahedral virus | ||||||
Function / homology | Function and homology information icosahedral viral capsid / host cell surface binding / viral inner capsid / symbiont-mediated suppression of host PKR/eIFalpha signaling / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / protein serine/threonine kinase inhibitor activity / host cell endoplasmic reticulum / host cell mitochondrion ...icosahedral viral capsid / host cell surface binding / viral inner capsid / symbiont-mediated suppression of host PKR/eIFalpha signaling / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / protein serine/threonine kinase inhibitor activity / host cell endoplasmic reticulum / host cell mitochondrion / 7-methylguanosine mRNA capping / viral life cycle / viral genome replication / viral capsid / mRNA guanylyltransferase activity / regulation of translation / mRNA guanylyltransferase / mRNA (guanine-N7)-methyltransferase / viral nucleocapsid / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / symbiont-mediated suppression of host innate immune response / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / hydrolase activity / RNA-directed RNA polymerase / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / nucleotide binding / GTP binding / apoptotic process / host cell plasma membrane / structural molecule activity / ATP hydrolysis activity / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Mammalian orthoreovirus 1 Mammalian orthoreovirus 3 | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7 Å | ||||||
Authors | Zhang, X. / Ji, Y. / Zhang, L. / Harrison, S.C. / Marinescu, D.C. / Nibert, M.L. / Baker, T.S. | ||||||
Citation | Journal: Structure / Year: 2005 Title: Features of reovirus outer capsid protein mu1 revealed by electron cryomicroscopy and image reconstruction of the virion at 7.0 Angstrom resolution. Authors: Xing Zhang / Yongchang Ji / Lan Zhang / Stephen C Harrison / Dan C Marinescu / Max L Nibert / Timothy S Baker / Abstract: Reovirus is a useful model for addressing the molecular basis of membrane penetration by one of the larger nonenveloped animal viruses. We now report the structure of the reovirus virion at ...Reovirus is a useful model for addressing the molecular basis of membrane penetration by one of the larger nonenveloped animal viruses. We now report the structure of the reovirus virion at approximately 7.0 A resolution as obtained by electron cryomicroscopy and three-dimensional image reconstruction. Several features of the myristoylated outer capsid protein mu1, not seen in a previous X-ray crystal structure of the mu1-sigma3 heterohexamer, are evident in the virion. These features appear to be important for stabilizing the outer capsid, regulating the conformational changes in mu1 that accompany perforation of target membranes, and contributing directly to membrane penetration during cell entry. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 2cse.cif.gz | 519.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2cse.ent.gz | 345.4 KB | Display | PDB format |
PDBx/mmJSON format | 2cse.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2cse_validation.pdf.gz | 369.6 KB | Display | wwPDB validaton report |
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Full document | 2cse_full_validation.pdf.gz | 369.5 KB | Display | |
Data in XML | 2cse_validation.xml.gz | 1.1 KB | Display | |
Data in CIF | 2cse_validation.cif.gz | 141.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/2cse ftp://data.pdbj.org/pub/pdb/validation_reports/cs/2cse | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) |
-Components
-Protein , 6 types, 27 molecules ABCPQRJKLTSDEFMNOGHIUVWXYZ1
#1: Protein | Mass: 76346.336 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 1 / Genus: Orthoreovirus / Species: Mammalian orthoreovirus / Strain: Lang / References: UniProt: P11077 #2: Protein | Mass: 41237.117 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 1 / Genus: Orthoreovirus / Species: Mammalian orthoreovirus / Strain: Lang / References: UniProt: P07939 #3: Protein | | Mass: 144098.766 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 3 / Genus: Orthoreovirus / Species: Mammalian orthoreovirus / Strain: Dearing / References: UniProt: P11079 #4: Protein | Mass: 142008.359 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 1 / Genus: Orthoreovirus / Species: Mammalian orthoreovirus / Strain: Lang / References: UniProt: Q9WAB2 #5: Protein | Mass: 47155.211 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 1 / Genus: Orthoreovirus / Species: Mammalian orthoreovirus / Strain: Lang / References: UniProt: P11314 #6: Protein | | Mass: 142510.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mammalian orthoreovirus 1 / Genus: Orthoreovirus / Species: Mammalian orthoreovirus / Strain: Lang / References: UniProt: P17376, UniProt: P0CK32*PLUS |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: HUMAN REOVIRUS VIRIONS (T3D) / Type: VIRUS / Details: The structure was monodisperse. |
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Details of virus | Host category: MAMMALIAN |
Buffer solution | Name: 10 mM TRIS / pH: 7.5 / Details: 10 mM TRIS |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Cryogen name: ETHANE / Details: PLUNGED INTO ETHANE |
-Electron microscopy imaging
EM imaging | Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Mode: BRIGHT FIELD / Specimen-ID: 1
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Image recording | Electron dose: 20 e/Å2 / Film or detector model: KODAK SO-163 FILM | |||||||||||||||||||||||||||||||||||||||
Image scans | Num. digital images: 54 |
-Processing
CTF correction | Details: CTF correction of each particle | ||||||||||||||||||||||||||||
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Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||
3D reconstruction | Method: PFT, OOR, POR / Resolution: 7 Å / Num. of particles: 7939 / Nominal pixel size: 2.3 Å / Actual pixel size: 2.21 Å / Magnification calibration: CROSS-CORRELATION / Symmetry type: POINT | ||||||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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