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Yorodumi- PDB-1r7e: NMR structure of the membrane anchor domain (1-31) of the nonstru... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1r7e | ||||||
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Title | NMR structure of the membrane anchor domain (1-31) of the nonstructural protein 5A (NS5A) of hepatitis C virus (Minimized average structure. Sample in 100mM SDS). | ||||||
Components | Genome polyprotein | ||||||
Keywords | MEMBRANE PROTEIN / Membrane anchor domain / HCV NS5A protein / peptide. | ||||||
Function / homology | Function and homology information positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet ...positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / positive regulation of cytokinesis / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / negative regulation of protein secretion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / endoplasmic reticulum-Golgi intermediate compartment membrane / kinase binding / SH3 domain binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / entry receptor-mediated virion attachment to host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / ribonucleoprotein complex / induction by virus of host autophagy / serine-type endopeptidase activity / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / virus-mediated perturbation of host defense response / RNA-dependent RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding Similarity search - Function | ||||||
Method | SOLUTION NMR / distance geometry, simulated annealing, molecular dynamics, energy minimization | ||||||
Model type details | minimized average | ||||||
Authors | Penin, F. / Brass, V. / Appel, N. / Ramboarina, S. / Montserret, R. / Ficheux, D. / Blum, H.E. / Bartenschlager, R. / Moradpour, D. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2004 Title: Structure and function of the membrane anchor domain of hepatitis C virus nonstructural protein 5A. Authors: Penin, F. / Brass, V. / Appel, N. / Ramboarina, S. / Montserret, R. / Ficheux, D. / Blum, H.E. / Bartenschlager, R. / Moradpour, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1r7e.cif.gz | 20.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1r7e.ent.gz | 12.6 KB | Display | PDB format |
PDBx/mmJSON format | 1r7e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1r7e_validation.pdf.gz | 246.4 KB | Display | wwPDB validaton report |
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Full document | 1r7e_full_validation.pdf.gz | 246.2 KB | Display | |
Data in XML | 1r7e_validation.xml.gz | 1.8 KB | Display | |
Data in CIF | 1r7e_validation.cif.gz | 1.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r7/1r7e ftp://data.pdbj.org/pub/pdb/validation_reports/r7/1r7e | HTTPS FTP |
-Related structure data
Related structure data | 1r7cC 1r7dC 1r7fC 1r7gC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 3770.423 Da / Num. of mol.: 1 Fragment: Nonstructural protein NS5A (P56)(residues 1973-2003 OF SWISS-PROT SEQUENCE P27958) Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence is naturally found in hepatitis C virus. References: UniProt: P27958 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.2mM NS5A[1-31], 10mM DTTd10 / Solvent system: 100mM SDS in H2O/D2O 95/5 (v/v) |
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Sample conditions | pH: 6 / Pressure: ambient / Temperature: 313 K |
-NMR measurement
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M |
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Radiation wavelength | Relative weight: 1 |
NMR spectrometer | Type: Varian UNITYPLUS / Manufacturer: Varian / Model: UNITYPLUS / Field strength: 500 MHz |
-Processing
NMR software |
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Refinement | Method: distance geometry, simulated annealing, molecular dynamics, energy minimization Software ordinal: 1 | ||||||||||||||||||||||||
NMR representative | Selection criteria: minimized average structure | ||||||||||||||||||||||||
NMR ensemble | Conformers submitted total number: 1 |