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Yorodumi- PDB-5fpy: Structure of hepatitis C virus (HCV) full-length NS3 complex with... -
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-Basic information
Entry | Database: PDB / ID: 5fpy | ||||||
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Title | Structure of hepatitis C virus (HCV) full-length NS3 complex with small-molecule ligand 5-bromo-1-methyl-1H-indole-2-carboxylic acid (AT21457) in an alternate binding site. | ||||||
Components | SERINE PROTEASE NS3 | ||||||
Keywords | HYDROLASE / HEPATITIS C VIRUS / HCV / NS3 COMPLEX / PROTEASE-HELICASE / PROTEIN-LIGAND COMPLEX / FRAGMENT SCREENING / ALTERNATE BINDING SITE / AT21457. | ||||||
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 / channel activity / SH3 domain binding ...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 / channel activity / SH3 domain binding / monoatomic ion transmembrane transport / nucleoside-triphosphate phosphatase / 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 / apoptotic process / host cell plasma membrane / virion membrane / structural molecule activity / 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 / MOLECULAR REPLACEMENT / Resolution: 2.52 Å | ||||||
Authors | Davies, T.G. / Jhoti, H. / Ludlow, R.F. / Saini, H.K. / Tickle, I.J. / Verdonk, M. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2015 Title: Detection of Secondary Binding Sites in Proteins Using Fragment Screening. Authors: Ludlow, R.F. / Verdonk, M.L. / Saini, H.K. / Tickle, I.J. / Jhoti, H. #1: Journal: Structure / Year: 1999 Title: Molecular Views of Viral Polyprotein Processing Revealed by the Crystal Structure of the Hepatitis C Virus Bifunctional Protease-Helicase. Authors: Yao, N. / Reichert, P. / Taremi, S.S. / Prosise, W.W. / Weber, P.C. #2: Journal: Nat.Chem.Biol. / Year: 2012 Title: Discovery of an Allosteric Mechanism for the Regulation of Hcv Ns3 Protein Function. Authors: Saalau-Bethell, S.M. / Woodhead, A.J. / Chessari, G. / Carr, M.G. / Coyle, J. / Graham, B. / Hiscock, S.D. / Murray, C.W. / Pathuri, P. / Rich, S.J. / Richardson, C.J. / Williams, P.A. / Jhoti, H. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BC" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5fpy.cif.gz | 264.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fpy.ent.gz | 211.3 KB | Display | PDB format |
PDBx/mmJSON format | 5fpy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fpy_validation.pdf.gz | 920.2 KB | Display | wwPDB validaton report |
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Full document | 5fpy_full_validation.pdf.gz | 928.1 KB | Display | |
Data in XML | 5fpy_validation.xml.gz | 51.3 KB | Display | |
Data in CIF | 5fpy_validation.cif.gz | 75.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fp/5fpy ftp://data.pdbj.org/pub/pdb/validation_reports/fp/5fpy | HTTPS FTP |
-Related structure data
Related structure data | 5fp5C 5fp6C 5fpdC 5fpeC 5fpmC 5fpnC 5fpoC 5fprC 5fpsSC 5fptC C: citing same article (ref.) S: Starting model for refinement |
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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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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.91357, 0.40632, -0.01705), Vector: |
-Components
#1: Protein | Mass: 70869.391 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HEPATITIS C VIRUS (ISOLATE BK) / Strain: GENOTYPE 1B / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) References: UniProt: P26663, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases #2: Chemical | #3: Water | ChemComp-HOH / | Nonpolymer details | 5-BROMO-1-METHYL-1H-INDOLE-2-CARBOXYLIC | Sequence details | N-TERM HIS TAG (37). DELETION 1-2. DELETION 632-686. | |
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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: 2.63 Å3/Da / Density % sol: 52.94 % / Description: NONE |
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Crystal grow | pH: 6.6 Details: 0.2M MES/NAOH, 14% W/V PEG 6000, 10% V/V MPD. PROTEIN CONC. = 6 MG/ML., pH 6.6 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 17, 2009 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0723 Å / Relative weight: 1 |
Reflection | Resolution: 2.52→47 Å / Num. obs: 52097 / % possible obs: 96.3 % / Observed criterion σ(I): -3.7 / Redundancy: 2.7 % / Biso Wilson estimate: 52.63 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.4 |
Reflection shell | Resolution: 2.52→2.59 Å / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.2 / % possible all: 97.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 5FPS Resolution: 2.52→46.99 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.89 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 0.558 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.82 / SU Rfree Blow DPI: 0.293 / SU Rfree Cruickshank DPI: 0.288 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY DISORDERED REGIONS WERE DELETED. THERE'S ALSO A HINT OF THE LIGAND PARALLEL-STACKING WITH TRP A501 BUT ...Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY DISORDERED REGIONS WERE DELETED. THERE'S ALSO A HINT OF THE LIGAND PARALLEL-STACKING WITH TRP A501 BUT DENSITY IS NOT SUFFICIENTLY GOOD TO BE CERTAIN.
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Displacement parameters | Biso mean: 46.83 Å2
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Refine analyze | Luzzati coordinate error obs: 0.26 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.52→46.99 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.52→2.58 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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