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Yorodumi- PDB-4jzo: Three dimensional structure of broadly neutralizing human anti - ... -
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-Basic information
Entry | Database: PDB / ID: 4jzo | ||||||
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Title | Three dimensional structure of broadly neutralizing human anti - Hepatitis C virus (HCV) glycoprotein E2 Fab fragment HC84-27 | ||||||
Components |
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Keywords | immune system/viral protein / Fab fragment / Immunglobulin fold / Antibody / immune system-viral protein complex | ||||||
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 / RNA-directed RNA polymerase / ribonucleoprotein complex / 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 / structural molecule activity / host cell plasma membrane / virion membrane / 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) Hepatitis C virus | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å | ||||||
Authors | Krey, T. / Rey, F.A. | ||||||
Citation | Journal: Plos Pathog. / Year: 2013 Title: Structural basis of HCV neutralization by human monoclonal antibodies resistant to viral neutralization escape. Authors: Krey, T. / Meola, A. / Keck, Z.Y. / Damier-Piolle, L. / Foung, S.K. / Rey, F.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4jzo.cif.gz | 340.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4jzo.ent.gz | 276.9 KB | Display | PDB format |
PDBx/mmJSON format | 4jzo.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jz/4jzo ftp://data.pdbj.org/pub/pdb/validation_reports/jz/4jzo | HTTPS FTP |
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-Related structure data
Related structure data | 4jznC 2xzaS 3qot 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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2 |
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3 |
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4 |
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Unit cell |
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Details | The asymetric unit contains four Fab molecules each representing a heterodimer of heavy and light chain. Each Fab molecule binds one synthetic peptide. |
-Components
#1: Antibody | Mass: 27553.543 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMT Fab / Production host: Drosophila melanogaster (fruit fly) #2: Antibody | Mass: 23340.764 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pMT Fab / Production host: Drosophila melanogaster (fruit fly) #3: Protein/peptide | Mass: 1536.732 Da / Num. of mol.: 4 / Fragment: Residues 434-446 of HCV strain H77 polyprotein / Source method: obtained synthetically / Source: (synth.) Hepatitis C virus (isolate H) References: UniProt: P27958, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases, hepacivirin, nucleoside-triphosphate phosphatase, RNA helicase, RNA-directed RNA polymerase #4: 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: 2.29 Å3/Da / Density % sol: 46.25 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 23% PEG 3350 250mM Sodium Thiocyanate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 28, 2012 |
Radiation | Monochromator: LN2 cooled Fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→41.35 Å / Num. all: 91860 / Num. obs: 78908 / % possible obs: 85.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 1.6 % / Biso Wilson estimate: 41.25 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.22→2.34 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.184 / Mean I/σ(I) obs: 2 / % possible all: 71 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2XZA and 3QOT Resolution: 2.22→41.35 Å / Cor.coef. Fo:Fc: 0.9248 / Cor.coef. Fo:Fc free: 0.9059 / SU R Cruickshank DPI: 0.338 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 40.42 Å2
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Refine analyze | Luzzati coordinate error obs: 0.283 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.22→41.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.22→2.28 Å / Total num. of bins used: 20
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