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Yorodumi- PDB-1rmu: THREE-DIMENSIONAL STRUCTURES OF DRUG-RESISTANT MUTANTS OF HUMAN R... -
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-Basic information
Entry | Database: PDB / ID: 1rmu | |||||||||
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Title | THREE-DIMENSIONAL STRUCTURES OF DRUG-RESISTANT MUTANTS OF HUMAN RHINOVIRUS 14 | |||||||||
Components | (HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT ...) x 4 | |||||||||
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 / : ...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 / Resolution: 3 Å | |||||||||
Authors | Badger, J. / Krishnaswamy, S. / Kremer, M.J. / Oliveira, M.A. / Rossmann, M.G. / Heinz, B.A. / Rueckert, R.R. / Dutko, F.J. / Mckinlay, M.A. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 1989 Title: Three-dimensional structures of drug-resistant mutants of human rhinovirus 14. Authors: Badger, J. / Krishnaswamy, S. / Kremer, M.J. / Oliveira, M.A. / Rossmann, M.G. / Heinz, B.A. / Rueckert, R.R. / Dutko, F.J. / McKinlay, M.A. #1: Journal: To be Published Title: The Use of Molecular Replacement Phases for the Refinement of the Human Rhinovirus 14 Structure Authors: Arnold, E. / Rossmann, M.G. #2: Journal: To be Published 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. #3: Journal: To be Published Title: Structural Analysis of Antiviral Agents that Interact with the Capsid of Human Rhinoviruses Authors: Badger, J. / Minor, I. / Oliveira, M.A. / Smith, T.J. / Rossmann, M.G. #4: Journal: Proc.Natl.Acad.Sci.USA / Year: 1988 Title: Structural Analysis of a Series of Antiviral Agents Complexed with Human Rhinovirus 14 Authors: Badger, J. / Minor, I. / Kremer, M.J. / Oliveira, M.A. / Smith, T.J. / Griffith, J.P. / Guerin, D.M.A. / Krishnaswamy, S. / Luo, M. / Rossmann, M.G. / Mckinlay, M.A. / Diana, G.D. / Dutko, F. ...Authors: Badger, J. / Minor, I. / Kremer, M.J. / Oliveira, M.A. / Smith, T.J. / Griffith, J.P. / Guerin, D.M.A. / Krishnaswamy, S. / Luo, M. / Rossmann, M.G. / Mckinlay, M.A. / Diana, G.D. / Dutko, F.J. / Fancher, M. / Rueckert, R.R. / Heinz, B.A. #5: 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. #6: 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. #7: 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. #8: 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. #9: 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. #10: 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. #11: 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. #12: 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 | 1rmu.cif.gz | 159.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rmu.ent.gz | 122.2 KB | Display | PDB format |
PDBx/mmJSON format | 1rmu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rm/1rmu ftp://data.pdbj.org/pub/pdb/validation_reports/rm/1rmu | HTTPS FTP |
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-Related structure data
-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
-HUMAN RHINOVIRUS 14 COAT PROTEIN (SUBUNIT ... , 4 types, 4 molecules 1234
#1: Protein | Mass: 32620.580 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 |
-Non-polymers , 2 types, 262 molecules
#5: Chemical | ChemComp-TRS / |
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#6: Water | ChemComp-HOH / |
-Details
Nonpolymer details | THERE IS A TRIS ION BOUND AT THE PORE ENTRANCE. IT IS 6 ANGSTROMS FROM TYR 1 199. LARGE (UP TO 1.4 ...THERE IS A TRIS ION BOUND AT THE PORE ENTRANCE. IT IS 6 ANGSTROMS FROM TYR 1 199. LARGE (UP TO 1.4 ANGSTROM) CONFORMATI |
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-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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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Num. obs: 60503 / Num. measured all: 65507 / Rmerge(I) obs: 0.122 |
-Processing
Software | Name: REAL-SPACE / Version: REFINEMENT / Classification: refinement | ||||||||||||
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Refinement | Highest resolution: 3 Å | ||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3 Å
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