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Yorodumi- PDB-4dw5: Crystal structure of the glycoprotein Erns from the pestivirus BV... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dw5 | ||||||||||||
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Title | Crystal structure of the glycoprotein Erns from the pestivirus BVDV-1 in complex with a non-cleavable CpU dinucleotide | ||||||||||||
Components | E(rns) glycoprotein | ||||||||||||
Keywords | VIRAL PROTEIN / virus glycoprotein / T2 Ribonuclease | ||||||||||||
Function / homology | Function and homology information pestivirus NS3 polyprotein peptidase / ribonuclease T2 / serine-type exopeptidase activity / ribonuclease T2 activity / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / clathrin-dependent endocytosis of virus by host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases ...pestivirus NS3 polyprotein peptidase / ribonuclease T2 / serine-type exopeptidase activity / ribonuclease T2 activity / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / clathrin-dependent endocytosis of virus by host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / viral protein processing / host cell endoplasmic reticulum membrane / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / virion attachment to host cell / GTP binding / virion membrane / ATP hydrolysis activity / proteolysis / RNA binding / ATP binding / membrane Similarity search - Function | ||||||||||||
Biological species | Bovine viral diarrhea virus | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.21 Å | ||||||||||||
Authors | Krey, T. / Bontems, F. / Vonrhein, C. / Vaney, M.-C. / Bricogne, G. / Ruemenapf, T. / Rey, F.A. | ||||||||||||
Citation | Journal: Structure / Year: 2012 Title: Crystal Structure of the Pestivirus Envelope Glycoprotein E(rns) and Mechanistic Analysis of Its Ribonuclease Activity. Authors: Krey, T. / Bontems, F. / Vonrhein, C. / Vaney, M.C. / Bricogne, G. / Rumenapf, T. / Rey, F.A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4dw5.cif.gz | 98.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dw5.ent.gz | 75.1 KB | Display | PDB format |
PDBx/mmJSON format | 4dw5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4dw5_validation.pdf.gz | 2.9 MB | Display | wwPDB validaton report |
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Full document | 4dw5_full_validation.pdf.gz | 3 MB | Display | |
Data in XML | 4dw5_validation.xml.gz | 24.8 KB | Display | |
Data in CIF | 4dw5_validation.cif.gz | 31.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dw/4dw5 ftp://data.pdbj.org/pub/pdb/validation_reports/dw/4dw5 | HTTPS FTP |
-Related structure data
Related structure data | 4dvkSC 4dvlC 4dvnC 4dw3C 4dw4C 4dw7C 4dwaC 4dwcC S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 19005.492 Da / Num. of mol.: 2 / Fragment: N-terminal fragment Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bovine viral diarrhea virus / Strain: CP7 / Gene: Erns / Plasmid: pMT-BIP-based / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q96662 |
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-Sugars , 4 types, 11 molecules
#2: Polysaccharide | beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D- ...beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||||
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#3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-3)-alpha-D- ...beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
-Non-polymers , 6 types, 191 molecules
#6: Chemical | ChemComp-SO4 / #7: Chemical | ChemComp-CSQ / | #8: Chemical | ChemComp-CSV / | #9: Chemical | ChemComp-1PE / | #10: Chemical | ChemComp-U5P / | #11: Water | ChemComp-HOH / | |
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-Details
Has protein modification | Y |
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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: 4.45 Å3/Da / Density % sol: 72.36 % |
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Crystal grow | Temperature: 298 K / pH: 4.6 Details: 33% PEG2000 MME, 100mM Na-Acetate, 140mM (NH4)2SO4, 50mM KH2PO4, pH 4.6, vapor diffusion, temperature 298K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.99187 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 9, 2010 |
Radiation | Monochromator: CHANNEL CUT SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99187 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→47.14 Å / Num. obs: 33587 / % possible obs: 95 % / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.21→2.33 Å / % possible all: 68.2 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4DVK Resolution: 2.21→47.14 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.914 / Occupancy max: 1 / Occupancy min: 0 / SU R Cruickshank DPI: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 49.18 Å2
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Refine analyze | Luzzati coordinate error obs: 0.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.21→47.14 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.21→2.28 Å / Total num. of bins used: 17
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