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Yorodumi- PDB-4dvk: Crystal structure of the glycoprotein Erns from the pestivirus BV... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4dvk | |||||||||
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Title | Crystal structure of the glycoprotein Erns from the pestivirus BVDV-1 strain NCP-7 | |||||||||
Components | E(rns) glycoprotein | |||||||||
Keywords | VIRAL PROTEIN / T2 Ribonuclease / virus envelope glycoprotein | |||||||||
Function / homology | Function and homology information pestivirus NS3 polyprotein peptidase / ribonuclease T2 / serine-type exopeptidase activity / ribonuclease T2 activity / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / clathrin-dependent endocytosis of virus by host cell ...pestivirus NS3 polyprotein peptidase / ribonuclease T2 / serine-type exopeptidase activity / ribonuclease T2 activity / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / 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 / host cell endoplasmic reticulum membrane / viral protein processing / RNA helicase / induction by virus of host autophagy / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / 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 / SAD / MAD / 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 | 4dvk.cif.gz | 88.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4dvk.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 4dvk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dv/4dvk ftp://data.pdbj.org/pub/pdb/validation_reports/dv/4dvk | HTTPS FTP |
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-Related structure data
Related structure data | 4dvlC 4dvnC 4dw3C 4dw4C 4dw5C 4dw7C 4dwaC 4dwcC 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: 18761.219 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 | alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-6)-[beta-D-mannopyranose-(1-3)]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)-[alpha-D-mannopyranose-(1-4)-alpha-D- ...beta-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)-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 , 2 types, 215 molecules
#6: Chemical | ChemComp-SO4 / #7: Water | ChemComp-HOH / | |
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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: 4.58 Å3/Da / Density % sol: 73.15 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / 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: SLS / Beamline: X06SA / Wavelength: 1.15961 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 2, 2007 |
Radiation | Monochromator: LN2 cooled Fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.15961 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. all: 37167 / Num. obs: 36126 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.2→2.32 Å / % possible all: 83.3 |
-Phasing
Phasing | Method: MAD |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.21→45.92 Å / Cor.coef. Fo:Fc: 0.9173 / Cor.coef. Fo:Fc free: 0.9131 / Occupancy max: 1 / Occupancy min: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 129.89 Å2 / Biso mean: 42.2937 Å2 / Biso min: 3 Å2
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Refine analyze | Luzzati coordinate error obs: 0.275 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.21→45.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.21→2.27 Å / Total num. of bins used: 18
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