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Yorodumi- PDB-4z0x: Structure of Hepatitis C Virus Envelope glycoprotein E2 antigenic... -
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-Basic information
Entry | Database: PDB / ID: 4z0x | |||||||||
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Title | Structure of Hepatitis C Virus Envelope glycoprotein E2 antigenic region 434-446 bound to the broadly neutralizing antibody HC26AM | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / HCV / Broadly neutralizing Antibody | |||||||||
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 / SH3 domain binding / kinase binding / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / entry receptor-mediated virion attachment to host cell / 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 / 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 | Homo sapiens (human) Hepacivirus C | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Rangarajan, S. / Shahid, S. / Mariuzza, R.A. | |||||||||
Citation | Journal: Hepatology / Year: 2016 Title: Affinity maturation of a broadly neutralizing human monoclonal antibody that prevents acute hepatitis C virus infection in mice. Authors: Keck, Z.Y. / Wang, Y. / Lau, P. / Lund, G. / Rangarajan, S. / Fauvelle, C. / Liao, G.C. / Holtsberg, F.W. / Warfield, K.L. / Aman, M.J. / Pierce, B.G. / Fuerst, T.R. / Bailey, J.R. / ...Authors: Keck, Z.Y. / Wang, Y. / Lau, P. / Lund, G. / Rangarajan, S. / Fauvelle, C. / Liao, G.C. / Holtsberg, F.W. / Warfield, K.L. / Aman, M.J. / Pierce, B.G. / Fuerst, T.R. / Bailey, J.R. / Baumert, T.F. / Mariuzza, R.A. / Kneteman, N.M. / Foung, S.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z0x.cif.gz | 120.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z0x.ent.gz | 76.5 KB | Display | PDB format |
PDBx/mmJSON format | 4z0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z0/4z0x ftp://data.pdbj.org/pub/pdb/validation_reports/z0/4z0x | HTTPS FTP |
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-Related structure data
Related structure data | 3qot 4aixS 4ajoS 4dagS 4dn3S 4hjoS 4jzoS 4qhkS 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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-Components
#1: Antibody | Mass: 11163.318 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) |
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#2: Antibody | Mass: 13055.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli BL21(DE3) (bacteria) |
#3: Protein/peptide | Mass: 1422.629 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Hepacivirus C / References: UniProt: P27958*PLUS |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.73 Å3/Da / Density % sol: 30 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: Sodium Phosphat monobasic, potassium phosphate dibasic, sodium phosphate dibasic/citric acid PH range: 4-4.5 / Temp details: K |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 10, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.075 Å / Relative weight: 1 |
Reflection | Resolution: 2→41.19 Å / Num. obs: 15612 / % possible obs: 96 % / Redundancy: 12.7 % / Biso Wilson estimate: 18.39 Å2 / Rmerge(I) obs: 0.145 / Net I/σ(I): 14.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entries 4JZO, 4HJO, 3QOT, 4DN3 (VH) & 4AIX, 4AJO, 4QHK, 4DAG (VL) Resolution: 2→41.19 Å / SU ML: 0.2373 / Cross valid method: FREE R-VALUE / σ(F): 0.03 / Phase error: 23.4025 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 21.29 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→41.19 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 8.72356495545 Å / Origin y: 20.7620457166 Å / Origin z: -10.2712779296 Å
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Refinement TLS group | Selection details: all |