+Open data
-Basic information
Entry | Database: PDB / ID: 1a1q | ||||||
---|---|---|---|---|---|---|---|
Title | HEPATITIS C VIRUS NS3 PROTEINASE | ||||||
Components | NS3 PROTEINASE | ||||||
Keywords | HYDROLASE / SERINE PROTEASE | ||||||
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 / 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 / viral envelope / host cell nucleus / virion attachment to host cell / 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 / SYNCHROTRON / HEAVY ATOMS: ISOMORPHOUS, ANOMALOUS SIGNALS / Resolution: 2.4 Å | ||||||
Authors | Love, R.A. / Parge, H.E. / Wickersham, J.A. / Hostomsky, Z. / Habuka, N. / Moomaw, E.W. / Adachi, T. / Hostomska, Z. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 1996 Title: The crystal structure of hepatitis C virus NS3 proteinase reveals a trypsin-like fold and a structural zinc binding site. Authors: Love, R.A. / Parge, H.E. / Wickersham, J.A. / Hostomsky, Z. / Habuka, N. / Moomaw, E.W. / Adachi, T. / Hostomska, Z. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1a1q.cif.gz | 31.2 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1a1q.ent.gz | 16.6 KB | Display | PDB format |
PDBx/mmJSON format | 1a1q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1a1q_validation.pdf.gz | 322.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1a1q_full_validation.pdf.gz | 322.9 KB | Display | |
Data in XML | 1a1q_validation.xml.gz | 849 B | Display | |
Data in CIF | 1a1q_validation.cif.gz | 5.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/a1/1a1q ftp://data.pdbj.org/pub/pdb/validation_reports/a1/1a1q | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
2 |
| ||||||||||||
3 |
| ||||||||||||
Unit cell |
| ||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 19894.604 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus / Genus: Hepacivirus / Strain: TYPE 1B / Description: EXPRESSED AS SOLUBLE PROTEIN / Gene: CDNA / Variant: BK ISOLATE / Plasmid: CDNA DERIVED FROM VIRAL RNA ISOLATED FROM PAT / Gene (production host): CDNA DERIVED FROM / Production host: Escherichia coli (E. coli) / References: UniProt: P26663 #2: Chemical | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 62 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 6.5 Details: VAPOR DIFFUSION. PROTEIN MIXED WITH WELL SOLUTION OF: 3.5M NACL, 150MM TRIS-HCL (PH 6.0), 5% PEG400., pH 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.995 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 1, 1995 / Details: MIRRORS |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.995 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→20 Å / Num. obs: 30000 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 20 Å2 / Rsym value: 0.079 / Net I/σ(I): 10 |
Reflection shell | Resolution: 2.4→2.5 Å / Redundancy: 3 % / Mean I/σ(I) obs: 4 / Rsym value: 0.29 / % possible all: 98 |
Reflection | *PLUS Num. measured all: 96285 / Rmerge(I) obs: 0.079 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: HEAVY ATOMS: ISOMORPHOUS, ANOMALOUS SIGNALS Resolution: 2.4→8 Å / Rfactor Rfree error: 0.02 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 Details: OF THE THREE MOLECULES IN THE ASYMMETRIC UNIT, THE CONFORMATION OF N TERMINAL REGION IS TRULY REPRESENTED BY CHAINS A AND C AND SHOWS A STRAND EXCHANGE PHENOMENON. HOWEVER, THIS COULD NOT BE ...Details: OF THE THREE MOLECULES IN THE ASYMMETRIC UNIT, THE CONFORMATION OF N TERMINAL REGION IS TRULY REPRESENTED BY CHAINS A AND C AND SHOWS A STRAND EXCHANGE PHENOMENON. HOWEVER, THIS COULD NOT BE CLEARLY SEEN IN CHAIN B SINCE THERE ARE SOME MISSING RESIDUES. FOR COMPLETE DESCRIPTION PLEASE SEE THE REFERENCED JOURNAL.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | NCS model details: RESTRAINTS / Rms dev Biso : 10 Å2 / Rms dev position: 1.5 Å / Weight Biso : 2 / Weight position: 200 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.5 Å / Rfactor Rfree error: 0.04 / Total num. of bins used: 12
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.32 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|