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Yorodumi- PDB-4n0y: Structure of the Hepatitis C Envelope Glycoprotein E1 antigenic r... -
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-Basic information
Entry | Database: PDB / ID: 4n0y | ||||||
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Title | Structure of the Hepatitis C Envelope Glycoprotein E1 antigenic region 314-324 bound to the cross-neutralizing antibody IGH526 | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Immunoglobulin Fold / Amidated c-terminus | ||||||
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 / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / Toll-like receptor 2 binding / : / viral capsid assembly / adhesion receptor-mediated virion attachment to host cell / TBC/RABGAPs / hepacivirin ...positive regulation of hexokinase activity / modulation by virus of host cellular process / translocation of peptides or proteins into host cell cytoplasm / symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / 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 / lipid droplet / 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 / membrane => GO:0016020 / 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 / endoplasmic reticulum membrane / virion attachment to host cell / 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 / extracellular region / ATP binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Hepatitis C virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.749 Å | ||||||
Authors | Kong, L. / Wilson, I.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2015 Title: Structure of Hepatitis C Virus Envelope Glycoprotein E1 Antigenic Site 314-324 in Complex with Antibody IGH526. Authors: Kong, L. / Kadam, R.U. / Giang, E. / Ruwona, T.B. / Nieusma, T. / Culhane, J.C. / Stanfield, R.L. / Dawson, P.E. / Wilson, I.A. / Law, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4n0y.cif.gz | 104.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4n0y.ent.gz | 82.8 KB | Display | PDB format |
PDBx/mmJSON format | 4n0y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n0/4n0y ftp://data.pdbj.org/pub/pdb/validation_reports/n0/4n0y | 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
-Protein/peptide , 1 types, 1 molecules A
#3: Protein/peptide | Mass: 1366.678 Da / Num. of mol.: 1 / Fragment: antigenic site (UNP residues 314-324) / Source method: obtained synthetically / Source: (synth.) Hepatitis C virus / References: UniProt: R9TE34, UniProt: P27958*PLUS |
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-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 24567.486 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293 Freestyle / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 22848.189 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): 293 Freestyle / Production host: Homo sapiens (human) |
-Non-polymers , 3 types, 348 molecules
#4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CL / | #6: 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: 2.77 Å3/Da / Density % sol: 55.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4 Details: 20% (w/v) PEG 6000, 1M lithium chloride and 0.1 M citric acid, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 25, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.033 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→30.67 Å / Num. obs: 55627 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 1.75→1.78 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.749→30.664 Å / SU ML: 0.18 / σ(F): 1.33 / Phase error: 19.98 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.749→30.664 Å
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Refine LS restraints |
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LS refinement shell |
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