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Yorodumi- PDB-1xf5: Complex HCV core-Fab 19D9D6-Protein L mutant (H74C, Y64W)in space... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1xf5 | ||||||
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Title | Complex HCV core-Fab 19D9D6-Protein L mutant (H74C, Y64W)in space group P21212 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Crystal packing / Fab / Protein L / Peptide complex | ||||||
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 / : ...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 endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / RNA helicase / induction by virus of host autophagy / ribonucleoprotein complex / RNA-directed RNA polymerase / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / host cell nucleus / virion attachment to host cell / 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 | Finegoldia magna (bacteria) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Menez, R. / Housden, N.G. / Harrison, S. / Jolivet-Reynaud, C. / Gore, M.G. / Stura, E.A. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2005 Title: Different crystal packing in Fab-protein L semi-disordered peptide complex. Authors: Menez, R. / Housden, N.G. / Harrison, S. / Jolivet-Reynaud, C. / Gore, M.G. / Stura, E.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1xf5.cif.gz | 216.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1xf5.ent.gz | 179.9 KB | Display | PDB format |
PDBx/mmJSON format | 1xf5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xf/1xf5 ftp://data.pdbj.org/pub/pdb/validation_reports/xf/1xf5 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 4909.684 Da / Num. of mol.: 2 / Fragment: residues 2-45 / Source method: obtained synthetically / Details: This sequence occurs naturally in HCV / References: UniProt: P26661 #2: Antibody | Mass: 24334.051 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) #3: Antibody | Mass: 23563.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) #4: Protein | Mass: 8887.018 Da / Num. of mol.: 2 / Mutation: Y64W,H74C Source method: isolated from a genetically manipulated source Source: (gene. exp.) Finegoldia magna (bacteria) / Strain: ATCC 29328 / Plasmid: PKK223-3 / Production host: Escherichia coli (E. coli) #5: 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: 2.67 Å3/Da / Density % sol: 53.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 9 Details: 10.3% MPEG 5K, 0.5M NaCl, 0.2M Tris-HCl, pH 9, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97564 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 12, 2002 |
Radiation | Monochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97564 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→20 Å / Num. all: 40443 / Num. obs: 39554 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 2.59→2.65 Å / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→19.92 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.6→19.92 Å
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LS refinement shell | Resolution: 2.6→2.66 Å
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