+Open data
-Basic information
Entry | Database: PDB / ID: 1r1a | ||||||||||||
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Title | CRYSTAL STRUCTURE OF HUMAN RHINOVIRUS SEROTYPE 1A (HRV1A) | ||||||||||||
Components |
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Keywords | VIRUS / RHINOVIRUS COAT PROTEIN / Icosahedral virus | ||||||||||||
Function / homology | Function and homology information symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization ...symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host gene expression / DNA replication / RNA helicase activity / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||||||||
Biological species | Human rhinovirus 1A | ||||||||||||
Method | X-RAY DIFFRACTION / Resolution: 3.2 Å | ||||||||||||
Authors | Kim, S. / Rossmann, M.G. | ||||||||||||
Citation | Journal: J.Mol.Biol. / Year: 1989 Title: Crystal structure of human rhinovirus serotype 1A (HRV1A). Authors: Kim, S.S. / Smith, T.J. / Chapman, M.S. / Rossmann, M.G. / Pevear, D.C. / Dutko, F.J. / Felock, P.J. / Diana, G.D. / McKinlay, M.A. #1: Journal: Nature / Year: 1985 Title: Structure of a Human Common Cold Virus and Functional Relationship to Other Picornaviruses Authors: Rossmann, M.G. / Arnold, E. / Erickson, J.W. / Frankenberger, E.A. / Griffith, J.P. / Hecht, H.-J. / Johnson, J.E. / Kamer, G. / Luo, M. / Mosser, A.G. / Rueckert, R.R. / Sherry, B. / Vriend, G. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r1a.cif.gz | 154.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r1a.ent.gz | 114.1 KB | Display | PDB format |
PDBx/mmJSON format | 1r1a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r1a_validation.pdf.gz | 475.1 KB | Display | wwPDB validaton report |
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Full document | 1r1a_full_validation.pdf.gz | 594.2 KB | Display | |
Data in XML | 1r1a_validation.xml.gz | 32.9 KB | Display | |
Data in CIF | 1r1a_validation.cif.gz | 45.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r1/1r1a ftp://data.pdbj.org/pub/pdb/validation_reports/r1/1r1a | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 32610.688 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rhinovirus 1A / Genus: Rhinovirus / Species: Human rhinovirus A / Plasmid: CLASSIFIED / Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P23008 |
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#2: Protein | Mass: 29114.764 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rhinovirus 1A / Genus: Rhinovirus / Species: Human rhinovirus A / Plasmid: CLASSIFIED / Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P23008 |
#3: Protein | Mass: 26176.998 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rhinovirus 1A / Genus: Rhinovirus / Species: Human rhinovirus A / Plasmid: CLASSIFIED / Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P23008 |
#4: Protein/peptide | Mass: 4583.816 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rhinovirus 1A / Genus: Rhinovirus / Species: Human rhinovirus A / Plasmid: CLASSIFIED / Cell line (production host): HeLa cells / Production host: Homo sapiens (human) / References: UniProt: P23008 |
#5: Polysaccharide | beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose / sucrose |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal grow | *PLUS Temperature: 6 ℃ / Method: microdialysis | |||||||||||||||
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Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||
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Refinement | Resolution: 3.2→10 Å /
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Refinement step | Cycle: LAST / Resolution: 3.2→10 Å
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Software | *PLUS Name: PROLSQ / Classification: refinement | ||||||||||||
Refinement | *PLUS Rfactor obs: 0.293 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |