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Yorodumi- PDB-4uca: N-terminal globular domain of the RSV Nucleoprotein in complex wi... -
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-Basic information
Entry | Database: PDB / ID: 4uca | ||||||
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Title | N-terminal globular domain of the RSV Nucleoprotein in complex with C- terminal peptide of the Phosphoprotein | ||||||
Components |
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Keywords | VIRAL PROTEIN / RIBONUCLEOPROTEIN / NUCLEOCAPSID / PHOSPHOPROTEIN / ANTIVIRAL COMPOUNDS / HALOGEN BOND | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / helical viral capsid / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / viral life cycle / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / PKR-mediated signaling / : / viral nucleocapsid ...symbiont-mediated suppression of host PKR/eIFalpha signaling / protein serine/threonine kinase inhibitor activity / helical viral capsid / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MDA-5 activity / viral life cycle / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / virion component / PKR-mediated signaling / : / viral nucleocapsid / host cell cytoplasm / ribonucleoprotein complex / RNA-dependent RNA polymerase activity / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA binding Similarity search - Function | ||||||
Biological species | HUMAN RESPIRATORY SYNCYTIAL VIRUS A2 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.22 Å | ||||||
Authors | Ouizougun-Oubari, M. / Pereira, N. / Tarus, B. / Galloux, M. / Tortorici, M.-A. / Hoos, S. / Baron, B. / England, P. / Bontems, F. / Rey, F.A. ...Ouizougun-Oubari, M. / Pereira, N. / Tarus, B. / Galloux, M. / Tortorici, M.-A. / Hoos, S. / Baron, B. / England, P. / Bontems, F. / Rey, F.A. / Eleouet, J.-F. / Sizun, C. / Slama-Schwok, A. / Duquerroy, S. | ||||||
Citation | Journal: J.Virol. / Year: 2015 Title: A Druggable Pocket at the Nucleocapsid/Phosphoprotein Interaction Site of the Human Respiratory Syncytial Virus. Authors: Ouizougun-Oubari, M. / Pereira, N. / Tarus, B. / Galloux, M. / Lassoued, S. / Fix, J. / Tortorici, M.A. / Hoos, S. / Baron, B. / England, P. / Desmaele, D. / Couvreur, P. / Bontems, F. / ...Authors: Ouizougun-Oubari, M. / Pereira, N. / Tarus, B. / Galloux, M. / Lassoued, S. / Fix, J. / Tortorici, M.A. / Hoos, S. / Baron, B. / England, P. / Desmaele, D. / Couvreur, P. / Bontems, F. / Rey, F.A. / Eleouet, J.F. / Sizun, C. / Slama-Schwok, A. / Duquerroy, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uca.cif.gz | 188.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uca.ent.gz | 151.6 KB | Display | PDB format |
PDBx/mmJSON format | 4uca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/4uca ftp://data.pdbj.org/pub/pdb/validation_reports/uc/4uca | HTTPS FTP |
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-Related structure data
Related structure data | 4uc6C 4uc7C 4uc8C 4uc9C 4ucbC 4uccC 4ucdC 4uceC 2wj8S C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26266.316 Da / Num. of mol.: 2 / Fragment: N-TERMINAL GLOBULAR DOMAIN, UNP RESIDUES 31-252 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HUMAN RESPIRATORY SYNCYTIAL VIRUS A2 / Plasmid: PET28 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P03418 #2: Protein/peptide | | Mass: 409.391 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) HUMAN RESPIRATORY SYNCYTIAL VIRUS A2 / References: UniProt: P03421*PLUS #3: Chemical | #4: Water | ChemComp-HOH / | Sequence details | N-TERMINAL MGS- AND C-TERMINAL -LEHHHHHH AMINO ACIDS COMES FROM CLONING ASP A300 PHE A301 ...N-TERMINAL MGS- AND C-TERMINAL -LEHHHHHH AMINO ACIDS COMES FROM CLONING ASP A300 PHE A301 CORRESPOND | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.1 Å3/Da / Density % sol: 41.54 % / Description: NONE |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 12, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 3.22→45 Å / Num. obs: 7219 / % possible obs: 96.9 % / Observed criterion σ(I): 0 / Redundancy: 4.4 % / Biso Wilson estimate: 62.47 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 7.7 |
Reflection shell | Resolution: 3.22→3.4 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.7 / % possible all: 86 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2WJ8 Resolution: 3.22→20 Å / Cor.coef. Fo:Fc: 0.9184 / Cor.coef. Fo:Fc free: 0.8784 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.52
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Displacement parameters | Biso mean: 68.2 Å2
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Refine analyze | Luzzati coordinate error obs: 0.659 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.22→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.22→3.6 Å / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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