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Yorodumi- PDB-1hri: STRUCTURE DETERMINATION OF ANTIVIRAL COMPOUND SCH 38057 COMPLEXED... -
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-Basic information
Entry | Database: PDB / ID: 1hri | |||||||||
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Title | STRUCTURE DETERMINATION OF ANTIVIRAL COMPOUND SCH 38057 COMPLEXED WITH HUMAN RHINOVIRUS 14 | |||||||||
Components |
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Keywords | VIRUS / COAT PROTEIN / 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 / structural molecule activity / virion attachment to host cell / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane / metal ion binding Similarity search - Function | |||||||||
Biological species | Human rhinovirus 14 | |||||||||
Method | X-RAY DIFFRACTION / Resolution: 3 Å | |||||||||
Authors | Zhang, A. / Nanni, R.G. / Oren, D.A. / Arnold, E. | |||||||||
Citation | 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. / Rozhon, E. / Cox, S. / Buontempo, P. / O'Connell, ...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. / Rozhon, E. / Cox, S. / Buontempo, P. / O'Connell, J. / Schwartz, J. / Miller, G. / Bauer, B. / Versace, R. / Pinto, P. / Ganguly, A. / Girijavallabhan, V. / Arnold, E. #1: Journal: To be Published Title: Sch 38057: A Picornavirus Capsid-Binding Molecule with Antiviral Activity After the Initial Stage of Viral Uncoating Authors: Rozhon, E. / Cox, S. / Buontempo, P. / O'Connell, J. / Slater, W. / De Martino, J. / Schwartz, J. / Miller, G. / Arnold, E. / Zhang, A. / Morrow, C. / Jablonski, S. / Pinto, P. / Versace, R. ...Authors: Rozhon, E. / Cox, S. / Buontempo, P. / O'Connell, J. / Slater, W. / De Martino, J. / Schwartz, J. / Miller, G. / Arnold, E. / Zhang, A. / Morrow, C. / Jablonski, S. / Pinto, P. / Versace, R. / Duelfer, T. / Girijavallabhan, V. #2: 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. #3: 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 Angstroms Authors: Arnold, E. / Rossmann, M.G. #4: 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. #5: 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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Remark 700 | SHEET THERE IS A BIFURCATED SHEET IN EACH OF CHAINS *1*, *2*, AND *3*. TO REPRESENT THIS FEATURE ...SHEET THERE IS A BIFURCATED SHEET IN EACH OF CHAINS *1*, *2*, AND *3*. TO REPRESENT THIS FEATURE REDUNDANT SHEETS ARE DEFINED. THUS SHEETS B11 AND B12 DIFFER ONLY IN STRAND 4, SHEETS B12 AND B22 DIFFER ONLY IN STRAND 4, AND SHEETS B13 AND B23 DIFFER IN STRANDS 1 AND 4 (DOUBLY BIFURCATED). |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hri.cif.gz | 152 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hri.ent.gz | 117.1 KB | Display | PDB format |
PDBx/mmJSON format | 1hri.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hr/1hri ftp://data.pdbj.org/pub/pdb/validation_reports/hr/1hri | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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5 |
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6 |
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Unit cell |
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Atom site foot note | 1: RESIDUE PRO 2 83 IS A CIS PROLINE. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Cell line (production host): HELA CELLS / Production host: Homo sapiens (human) / References: UniProt: P03303 |
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#2: Protein | Mass: 28501.361 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Cell line (production host): HELA CELLS / Production host: Homo sapiens (human) / References: UniProt: P03303 |
#3: Protein | Mass: 26236.754 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Cell line (production host): HELA CELLS / Production host: Homo sapiens (human) / References: UniProt: P03303 |
#4: Protein | Mass: 7183.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human rhinovirus 14 / Genus: Rhinovirus / Species: Human rhinovirus B / Cell line (production host): HELA CELLS / Production host: Homo sapiens (human) / References: UniProt: P03303 |
#5: Chemical | ChemComp-S57 / |
Sequence details | THE STRAIN USED IN THIS STUDY HAS A MUTATION AT RESIDUE 170 OF CHAIN 2. IN THE NATIVE VIRUS THIS ...THE STRAIN USED IN THIS STUDY HAS A MUTATION AT RESIDUE 170 OF CHAIN 2. IN THE NATIVE VIRUS THIS RESIDUE IS ILE. IN THE STRAIN USED IN THIS STUDY THIS RESIDUE IS LEU. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion, hanging dropDetails: taken from Arnold, E. et al (1984). J. Mol. Biol., 177, 417-430. | ||||||||||||||||||||||||||||||||||||||||||||||||
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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 |
Reflection | *PLUS Highest resolution: 3 Å / Lowest resolution: 30 Å / Num. obs: 147740 / Rmerge(I) obs: 0.12 |
Reflection shell | *PLUS Highest resolution: 3 Å / Lowest resolution: 3.5 Å / % possible obs: 19 % / Num. unique obs: 40195 |
-Processing
Software | Name: FRODO / Classification: model building | ||||||||||||
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Refinement | Highest resolution: 3 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3 Å
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