+Open data
-Basic information
Entry | Database: PDB / ID: 1jxp | ||||||
---|---|---|---|---|---|---|---|
Title | BK STRAIN HEPATITIS C VIRUS (HCV) NS3-NS4A | ||||||
Components |
| ||||||
Keywords | Viral protein complex / COMPLEX (VIRAL NONSTRUCTURAL PROTEINS) / HYDROLASE / SERINE PROTEINASE | ||||||
Function / homology | Function and homology information hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / 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 / SH3 domain binding / nucleoside-triphosphate phosphatase ...hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / 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 / SH3 domain binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by 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 / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / virion membrane / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding / membrane Similarity search - Function | ||||||
Biological species | Hepatitis C virus | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.2 Å | ||||||
Authors | Yan, Y. / Munshi, S. / Chen, Z. | ||||||
Citation | Journal: Protein Sci. / Year: 1998 Title: Complex of NS3 protease and NS4A peptide of BK strain hepatitis C virus: a 2.2 A resolution structure in a hexagonal crystal form. Authors: Yan, Y. / Li, Y. / Munshi, S. / Sardana, V. / Cole, J.L. / Sardana, M. / Steinkuehler, C. / Tomei, L. / De Francesco, R. / Kuo, L.C. / Chen, Z. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1jxp.cif.gz | 86.1 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1jxp.ent.gz | 66 KB | Display | PDB format |
PDBx/mmJSON format | 1jxp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1jxp_validation.pdf.gz | 389.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1jxp_full_validation.pdf.gz | 403.1 KB | Display | |
Data in XML | 1jxp_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 1jxp_validation.cif.gz | 16.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jx/1jxp ftp://data.pdbj.org/pub/pdb/validation_reports/jx/1jxp | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| x 6||||||||
Unit cell |
| ||||||||
Details | THERE ARE TWO NS3 PROTEASE-NS4A PEPTIDE COMPLEXES IN THE ASYMMETRIC UNIT. THE TWO HCV NS3 PROTEASE MOLECULES IN EACH COMPLEX ARE LABELED AS CHAIN A AND CHAIN B. THE TWO NS4A PEPTIDES IN EACH COMPLEX ARE LABELED AS C AND D. CHAIN A IS NUMBERED 1 - 186, CHAIN B IS NUMBERED 1 - 186, CHAIN C IS NUMBERED 220 - 235 AND CHAIN D IS NUMBERED 220 - 235. THERE IS ONE ZINC ATOM IN EACH COMPLEX. ZINC ATOMS ARE NUMBERED 190 AND 490. WATER MOLECULES ARE NUMBERED 601 - 921. |
-Components
#1: Protein | Mass: 19634.529 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus (isolate BK) / Genus: Hepacivirus / Species: Hepatitis C virus / Strain: BK STRAIN ISOLATE / Production host: Escherichia coli (E. coli) / References: UniProt: P26663 #2: Protein/peptide | Mass: 1686.097 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: HEPATITIS C VIRUS PROTEINS / Source: (gene. exp.) Hepatitis C virus (isolate BK) / Genus: Hepacivirus / Species: Hepatitis C virus / Strain: BK STRAIN ISOLATE / Production host: Escherichia coli (E. coli) / References: UniProt: P26663 #3: Chemical | #4: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 54 % | ||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.5 / Details: pH 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 56 % | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 113 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: DOUBLE MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→30 Å / Num. obs: 22953 / % possible obs: 94 % / Observed criterion σ(I): 0 / Redundancy: 15 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.2→2.28 Å / % possible all: 72 |
Reflection shell | *PLUS % possible obs: 72 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Rfactor Rwork: 0.245 / Rfactor obs: 0.245 / Highest resolution: 2.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 2.2 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å / Num. reflection obs: 21978 / σ(F): 2 / % reflection Rfree: 10 % / Rfactor Rfree: 0.352 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 2.31 |