+Open data
-Basic information
Entry | Database: PDB / ID: 1vrh | |||||||||
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Title | HRV14/SDZ 880-061 COMPLEX | |||||||||
Components | (RHINOVIRUS 14) x 4 | |||||||||
Keywords | VIRUS / RHINOVIRUS COAT PROTEIN / ANTIVIRAL AGENTS / POLYPROTEIN / COAT PROTEIN / CORE PROTEIN / RNA POLYMERASE / HYDROLASE / THIOL PROTEASE / MYRISTYLATION / Icosahedral virus | |||||||||
Function / homology | Function and homology information lysis of host organelle involved in viral entry into host cell / 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 / : ...lysis of host organelle involved in viral entry into host cell / 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 / RNA helicase activity / DNA replication / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / 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 14 | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å | |||||||||
Authors | Oren, D.A. / Zhang, A. / Arnold, E. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: Synthesis and activity of piperazine-containing antirhinoviral agents and crystal structure of SDZ 880-061 bound to human rhinovirus 14. Authors: Oren, D.A. / Zhang, A. / Nesvadba, H. / Rosenwirth, B. / Arnold, E. #1: Journal: Antiviral Res. / Year: 1995 Title: Sdz 35-682, a New Picornavirus Capsid-Binding Agent with Potent Antiviral Activity Authors: Rosenwirth, B. / Oren, D.A. / Arnold, E. / Kis, Z.L. / Eggers, H.J. #2: Journal: J.Mol.Biol. / Year: 1993 Title: Structure Determination of Antiviral Compound Sch 38057 Complexed with Human Rhinovirus 14 Authors: Zhang, A. / Nanni, R.G. / Li, T. / Arnold, G.F. / Oren, D.A. / Jacobo-Molina, A. / Williams, R.L. / Kamer, G. / Rubenstein, D.A. / Li, Y. #3: Journal: Semin.Virol. / Year: 1992 Title: Three-Dimensional Structure-Activity Relationships for Antiviral Agents that Interact with Picornavirus Capsids Authors: Zhang, A. / Nanni, R.G. / Oren, D.A. / Rozhon, E.J. / Arnold, E. #4: Journal: J.Mol.Biol. / Year: 1990 Title: Analysis of the Structure of a Common Cold Virus, Human Rhinovirus 14, Refined at a Resolution of 3.0 A Authors: Arnold, E. / Rossmann, M.G. #5: Journal: Acta Crystallogr.,Sect.A / Year: 1988 Title: The Use of Molecular-Replacement Phases for the Refinement of the Human Rhinovirus 14 Structure Authors: Arnold, E. / Rossmann, M.G. #6: 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. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vrh.cif.gz | 169.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vrh.ent.gz | 134 KB | Display | PDB format |
PDBx/mmJSON format | 1vrh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vr/1vrh ftp://data.pdbj.org/pub/pdb/validation_reports/vr/1vrh | HTTPS FTP |
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-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: 32560.549 Da / Num. of mol.: 1 / Mutation: I(2 170)L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Production host: Homo sapiens (human) / References: UniProt: P03303 |
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#2: Protein | Mass: 28501.361 Da / Num. of mol.: 1 / Mutation: I(2 170)L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Production host: Homo sapiens (human) / References: UniProt: P03303 |
#3: Protein | Mass: 26236.754 Da / Num. of mol.: 1 / Mutation: I(2 170)L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Production host: Homo sapiens (human) / References: UniProt: P03303 |
#4: Protein | Mass: 7183.863 Da / Num. of mol.: 1 / Mutation: I(2 170)L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Production host: Homo sapiens (human) / References: UniProt: P03303 |
#5: Chemical | ChemComp-SD8 / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal grow | Details: 5 MG/ML OF SDZ 880-061 IN 200 MICROLITER DROPS FOR 3 - 4 CRYSTALS | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1.54 |
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Detector | Detector: FILM / Date: Jun 1, 1990 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Rmerge(I) obs: 0.119 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 30 Å / Num. obs: 147189 / % possible obs: 25.8 % |
Reflection shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 3.5 Å / % possible obs: 16 % / Num. unique obs: 35847 / Rmerge(I) obs: 0.195 |
-Processing
Software | Name: PURDUE / Version: DATA PROCESSING PACKAGE / Classification: data reduction | ||||||||||||
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Refinement | Highest resolution: 3 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3 Å
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