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Yorodumi- PDB-4rhv: THE USE OF MOLECULAR-REPLACEMENT PHASES FOR THE REFINEMENT OF THE... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4rhv | ||||||||||||
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Title | THE USE OF MOLECULAR-REPLACEMENT PHASES FOR THE REFINEMENT OF THE HUMAN RHINOVIRUS 14 STRUCTURE | ||||||||||||
Components |
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Keywords | VIRUS / RHINOVIRUS 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 / nucleoside-triphosphate phosphatase ...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 / DNA replication / RNA helicase activity / induction by virus of host autophagy / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / 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 / Resolution: 3 Å | ||||||||||||
Authors | Arnold, E. / Rossmann, M.G. | ||||||||||||
Citation | 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. #1: Journal: To be Published Title: Analysis of the Structure of Human Rhinovirus 14 Refined at a Resolution of 3.0 Angstroms Authors: Arnold, E. / Rossmann, M.G. #2: Journal: Acta Crystallogr.,Sect.A / Year: 1987 Title: The Structure Determination of a Common Cold Virus, Human Rhinovirus 14 Authors: Arnold, E. / Vriend, G. / Luo, M. / Griffith, J.P. / Kamer, G. / Erickson, J.W. / Johnson, J.E. / Rossmann, M.G. #3: Journal: Proc.Natl.Acad.Sci.USA / Year: 1987 Title: Implications of the Picornavirus Capsid Structure for Polyprotein Structure Authors: Arnold, E. / Luo, M. / Vriend, G. / Rossmann, M.G. / Palmenberg, A.C. / Parks, G.D. / Nicklin, M.J.H. / Wimmer, E. #4: Journal: Science / Year: 1986 Title: The Site of Attachment in Human Rhinovirus 14 for Antiviral Agents that Inhibit Uncoating Authors: Smith, T.J. / Kremer, M.J. / Luo, M. / Vriend, G. / Arnold, E. / Kamer, G. / Rossmann, M.G. / Mckinlay, M.A. / Diana, G.D. / Otto, M.J. #5: Journal: Chem.Scr. / Year: 1987 Title: The Structure of a Human Common Cold Virus (Rhinovirus 14) and its Evolutionary Relations to Other Viruses 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. / Vriend, 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. / Rueckert, R.R. / Sherry, B. / Vriend, G. #7: Journal: J.Mol.Biol. / Year: 1984 Title: Virion Orientation in Cubic Crystals of the Human Common Cold Virus Hrv14 Authors: Arnold, E. / Erickson, J.W. / Fout, G.S. / Frankenberger, E.A. / Hecht, H.-J. / Luo, M. / Rossmann, M.G. / Rueckert, R.R. #8: Journal: J.Mol.Biol. / Year: 1984 Title: Picornaviruses of Two Different Genera Have Similar Structures Authors: Luo, M. / Arnold, E. / Erickson, J.W. / Rossmann, M.G. / Boege, U. / Scraba, D.G. #9: Journal: Proc.Natl.Acad.Sci.USA / Year: 1983 Title: Crystallization of a Common Cold Virus, Human Rhinovirus 14. (Quote)Isomorphism(Quote) with Poliovirus Crystals Authors: Erickson, J.W. / Frankenberger, E.A. / Rossmann, M.G. / Fout, G.S. / Medappa, K.C. / Rueckert, R.R. | ||||||||||||
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 | 4rhv.cif.gz | 178.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4rhv.ent.gz | 138.8 KB | Display | PDB format |
PDBx/mmJSON format | 4rhv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4rhv_validation.pdf.gz | 445 KB | Display | wwPDB validaton report |
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Full document | 4rhv_full_validation.pdf.gz | 528.8 KB | Display | |
Data in XML | 4rhv_validation.xml.gz | 44 KB | Display | |
Data in CIF | 4rhv_validation.cif.gz | 58.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/4rhv ftp://data.pdbj.org/pub/pdb/validation_reports/rh/4rhv | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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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: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal grow | *PLUS pH: 7.2 / Method: vapor diffusion, hanging drop / Details: Arnold, E., (1984) J.Mol.Biol., 177, 417. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Components of the solutions | *PLUS
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-Processing
Refinement | Resolution: 3→6 Å / Rfactor Rwork: 0.16 / σ(F): 3 | ||||||||||||
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Refinement step | Cycle: LAST / Resolution: 3→6 Å
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Refinement | *PLUS Rfactor Rwork: 0.16 | ||||||||||||
Solvent computation | *PLUS | ||||||||||||
Displacement parameters | *PLUS |