+Open data
-Basic information
Entry | Database: PDB / ID: 1hei | ||||||
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Title | STRUCTURE OF THE HEPATITIS C VIRUS RNA HELICASE DOMAIN | ||||||
Components | HCV HELICASE | ||||||
Keywords | HELICASE / RNA / HEPATITIS / HCV / ATPASE / NTPASE | ||||||
Function / homology | Function and homology information positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet ...positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / Toll-like receptor 2 binding / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / symbiont-mediated suppression of host TRAF-mediated signal transduction / transformation of host cell by virus / positive regulation of cytokinesis / symbiont-mediated perturbation of host cell cycle G1/S transition checkpoint / negative regulation of protein secretion / 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 / endoplasmic reticulum-Golgi intermediate compartment membrane / kinase binding / SH3 domain binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / entry receptor-mediated virion attachment to 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 / virus-mediated perturbation of host defense response / 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 / viral envelope / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / proteolysis / RNA binding / zinc ion binding / ATP binding Similarity search - Function | ||||||
Biological species | Hepatitis C virus | ||||||
Method | X-RAY DIFFRACTION / MIRAS / Resolution: 2.1 Å | ||||||
Authors | Yao, N. / Weber, P. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1997 Title: Structure of the hepatitis C virus RNA helicase domain. Authors: Yao, N. / Hesson, T. / Cable, M. / Hong, Z. / Kwong, A.D. / Le, H.V. / Weber, P.C. #1: Journal: J.Virol. / Year: 1996 Title: The Qrxgrxgrxxxg Motif of the Vaccinia Virus Dexh Box RNA Helicase Nph-II is Required for ATP Hydrolysis and RNA Unwinding But not for RNA Binding Authors: Gross, C.H. / Shuman, S. #2: Journal: Arch.Biochem.Biophys. / Year: 1995 Title: Expression, Isolation, and Characterization of the Hepatitis C Virus ATPase/RNA Helicase Authors: Jin, L. / Peterson, D.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hei.cif.gz | 181.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hei.ent.gz | 140.7 KB | Display | PDB format |
PDBx/mmJSON format | 1hei.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/he/1hei ftp://data.pdbj.org/pub/pdb/validation_reports/he/1hei | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 48357.910 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus (isolate 1) / Genus: Hepacivirus / Species: Hepatitis C virus / Strain: H / Variant: 1A / Production host: Escherichia coli (E. coli) / Strain (production host): M15 / References: UniProt: P27958 #2: Chemical | #3: 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: 2.4 Å3/Da / Density % sol: 50 % Description: HG AND SM DERIVATIZED CRYSTALS WERE USED IN MIRAS | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 50MM CA ACETATE, 20MM NACACODYLATE PH 6.5, 8% PEG5000 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 7.5 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 95 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Feb 10, 1996 / Details: MIRROR |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→26 Å / Num. obs: 51694 / % possible obs: 88 % / Observed criterion σ(I): 0 / Redundancy: 12 % / Biso Wilson estimate: 25 Å2 / Rsym value: 0.052 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.1→2.18 Å / Mean I/σ(I) obs: 3 / Rsym value: 0.27 / % possible all: 74 |
Reflection | *PLUS Num. measured all: 676708 / Rmerge(I) obs: 0.052 |
Reflection shell | *PLUS % possible obs: 70 % / Rmerge(I) obs: 0.27 |
-Processing
Software |
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Refinement | Method to determine structure: MIRAS / Resolution: 2.1→8 Å / Isotropic thermal model: GAUSS / Cross valid method: FREE R / σ(F): 0
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Displacement parameters | Biso mean: 36 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å / Luzzati d res low obs: 8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.19 Å / Total num. of bins used: 8
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Xplor file |
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Refinement | *PLUS Num. reflection obs: 51577 / Num. reflection Rfree: 2579 / Rfactor obs: 0.22 / Rfactor Rfree: 0.32 / Rfactor Rwork: 0.22 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.39 / Rfactor Rwork: 0.32 |