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Yorodumi- PDB-1ncq: The structure of HRV14 when complexed with pleconaril, an antivir... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ncq | |||||||||
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Title | The structure of HRV14 when complexed with pleconaril, an antiviral compound | |||||||||
Components | (COAT PROTEIN ...) x 4 | |||||||||
Keywords | VIRUS / rhinovirus 14 / HRV / pleconaril / 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 / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Zhang, Y. / Simpson, A.A. / Bator, C.M. / Chakravarty, S. / Pevear, D.C. / Skochko, G.A. / Tull, T.M. / Diana, G. / Rossmann, M.G. | |||||||||
Citation | Journal: J.Virol. / Year: 2004 Title: Structural and virological studies of the stages of virus replication that are affected by antirhinovirus compounds Authors: Zhang, Y. / Simpson, A.A. / Ledford, R.M. / Bator, C.M. / Chakravarty, S. / Skochko, G.A. / Demenczuk, T.M. / Watanyar, A. / Pevear, D.C. / Rossmann, M.G. | |||||||||
History |
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Remark 999 | AUTHORS STATE THAT RESIDUE 170 (CHAIN B) CAN BE ILE OR LEU, AS SEEN IN OTHER DATABASE REFERENCE SEQUENCES. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ncq.cif.gz | 169.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ncq.ent.gz | 136.3 KB | Display | PDB format |
PDBx/mmJSON format | 1ncq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/1ncq ftp://data.pdbj.org/pub/pdb/validation_reports/nc/1ncq | HTTPS FTP |
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-Related structure data
-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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Symmetry | Point symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral)) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-COAT PROTEIN ... , 4 types, 4 molecules ABCD
#1: Protein | Mass: 32560.549 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 / Genus: Rhinovirus / Cell line: hela cells / Species: Human rhinovirus B / References: UniProt: P03303 |
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#2: Protein | Mass: 28501.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 / Genus: Rhinovirus / Cell line: hela cells / Species: Human rhinovirus B / References: UniProt: P03303 |
#3: Protein | Mass: 26236.754 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 / Genus: Rhinovirus / Cell line: hela cells / Species: Human rhinovirus B / References: UniProt: P03303 |
#4: Protein | Mass: 7183.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Human rhinovirus 14 / Genus: Rhinovirus / Cell line: hela cells / Species: Human rhinovirus B / References: UniProt: P03303 |
-Non-polymers , 2 types, 243 molecules
#5: Chemical | ChemComp-W11 / |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal grow | Details: The crystal was soaked in stabilization buffer containing 2ug/ml pleconaril before data collection | ||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 2.5→20 Å / Num. obs: 671838 / Observed criterion σ(I): 0 |
Reflection | *PLUS Num. measured all: 1675367 / Rmerge(I) obs: 70.3 / Rmerge F obs: 0.077 |
Reflection shell | *PLUS % possible obs: 26.3 % / Rmerge(I) obs: 0.456 |
-Processing
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.5→20 Å
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Refinement | *PLUS Rfactor Rfree: 0.216 / Rfactor Rwork: 0.217 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS
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