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Yorodumi- PDB-2ijo: Crystal Structure of the West Nile virus NS2B-NS3 protease comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ijo | ||||||
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Title | Crystal Structure of the West Nile virus NS2B-NS3 protease complexed with bovine pancreatic trypsin inhibitor | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / WEST NILE VIRUS / PROTEASE / APROTININ / BPTI / NS2B / NS3 / FLAVIVIRUS / serine protease / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information RNA 5'-cap (guanine-N7)-methylation / RNA stabilization / RNA folding chaperone / DNA/DNA annealing activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / : / RNA strand annealing activity / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding ...RNA 5'-cap (guanine-N7)-methylation / RNA stabilization / RNA folding chaperone / DNA/DNA annealing activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of JAK1 activity / : / RNA strand annealing activity / trypsinogen activation / negative regulation of serine-type endopeptidase activity / sulfate binding / potassium channel inhibitor activity / negative regulation of platelet aggregation / zymogen binding / molecular function inhibitor activity / negative regulation of thrombin-activated receptor signaling pathway / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / flavivirin / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / positive regulation of viral genome replication / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT1 activity / serine protease inhibitor complex / ribonucleoside triphosphate phosphatase activity / protein-DNA complex / serine-type endopeptidase inhibitor activity / viral capsid / nucleoside-triphosphate phosphatase / double-stranded RNA binding / peptidase activity / mRNA (guanine-N7)-methyltransferase / methyltransferase cap1 / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / protease binding / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / protein dimerization activity / RNA helicase / induction by virus of host autophagy / ribonucleoprotein complex / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase activity / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / viral envelope / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / calcium ion binding / virion attachment to host cell / virion membrane / structural molecule activity / ATP hydrolysis activity / proteolysis / DNA binding / extracellular space / RNA binding / extracellular region / ATP binding / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | West Nile virus Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Aleshin, A.E. / Shiryaev, S.A. / Strongin, A.Y. / Liddington, R.C. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: Structural evidence for regulation and specificity of flaviviral proteases and evolution of the Flaviviridae fold. Authors: Aleshin, A.E. / Shiryaev, S.A. / Strongin, A.Y. / Liddington, R.C. | ||||||
History |
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Remark 400 | COMPOUND THE PROTEINS NS2B (CHAIN A) AND NS3 (CHAIN B) ARE CONNECTED THROUGH A LINKER AGGGGSGGGG. | ||||||
Remark 999 | SEQUENCE THIS IS THE SEQUENCE OF THE LINKER BETWEEN CHAINS A AND B. RESIDUE NUMBERS 1 THROUGH 5 IN ... SEQUENCE THIS IS THE SEQUENCE OF THE LINKER BETWEEN CHAINS A AND B. RESIDUE NUMBERS 1 THROUGH 5 IN COORDINATES FOR CHAIN B ARE ARBITRARY, SINCE ONLY THESE FIVE RESIDUES WERE VISIBLE IN ELECTRON DENSITY. THE SEQUENCE ALIGNMENT OF THESE FIVE RESIDUES IS ALSO ARBITRARY AND IS BASED ONLY ON THE DISTANCE CRITERIA TO THE NEXT VISIBLE RESIDUES. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ijo.cif.gz | 67.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ijo.ent.gz | 48.3 KB | Display | PDB format |
PDBx/mmJSON format | 2ijo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/2ijo ftp://data.pdbj.org/pub/pdb/validation_reports/ij/2ijo | HTTPS FTP |
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-Related structure data
Related structure data | 2ggvSC 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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1 |
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Unit cell |
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Details | NS2B cofactor and NS3 protease domain form heterodimer |
-Components
#1: Protein | Mass: 6078.417 Da / Num. of mol.: 1 / Fragment: NS2B cofactor domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) West Nile virus / Genus: Flavivirus / Plasmid: pET101 / Production host: Escherichia coli (E. coli) References: UniProt: Q203W3, UniProt: P06935*PLUS, flavivirin |
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#2: Protein | Mass: 20906.584 Da / Num. of mol.: 1 / Fragment: NS3 protease domain / Mutation: K104R Source method: isolated from a genetically manipulated source Source: (gene. exp.) West Nile virus / Genus: Flavivirus / Plasmid: pET101 / Production host: Escherichia coli (E. coli) References: UniProt: Q203W3, UniProt: P06935*PLUS, flavivirin |
#3: Protein | Mass: 6527.568 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P00974 |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 20% PEG 8000, 0.1M TRIS-HCL, 0.2M SODIUM CHLORIDE, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 170 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 28, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→40 Å / Num. all: 11411 / Num. obs: 11411 / % possible obs: 93 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Biso Wilson estimate: 47 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 24 |
Reflection shell | Resolution: 2.3→2.45 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.9 / % possible all: 70 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2GGV Resolution: 2.3→40 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 42.735 Å2 | ||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.735 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→40 Å
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Refine LS restraints |
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Xplor file |
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