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Yorodumi- PDB-4hzl: Neutralizing antibody mAb#8 in complex with the Epitope II of HCV... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4hzl | ||||||
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Title | Neutralizing antibody mAb#8 in complex with the Epitope II of HCV E2 envelope protein | ||||||
Components |
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Keywords | IMMUNE SYSTEM / Ig domain / neutralizing antibody | ||||||
Function / homology | Function and homology information symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / : / : / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / 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 ...symbiont-mediated suppression of host TRAF-mediated signal transduction => GO:0039527 / : / : / hepacivirin / host cell mitochondrial membrane / host cell lipid droplet / 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 / lipid droplet / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / 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 / induction by virus of host autophagy / serine-type endopeptidase activity / cysteine-type endopeptidase activity / RNA-directed RNA polymerase / viral RNA genome replication / RNA-dependent RNA polymerase 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 / structural molecule activity / virion membrane / RNA binding / zinc ion binding / extracellular region / ATP binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Mus musculus (house mouse) Recombinant Hepatitis C virus H77/JFH1_V787A Q1247L | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å | ||||||
Authors | Deng, L. / Zhang, P. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2013 Title: Structural evidence for a bifurcated mode of action in the antibody-mediated neutralization of hepatitis C virus. Authors: Deng, L. / Zhong, L. / Struble, E. / Duan, H. / Ma, L. / Harman, C. / Yan, H. / Virata-Theimer, M.L. / Zhao, Z. / Feinstone, S. / Alter, H. / Zhang, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4hzl.cif.gz | 341 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4hzl.ent.gz | 282.9 KB | Display | PDB format |
PDBx/mmJSON format | 4hzl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4hzl_validation.pdf.gz | 461.8 KB | Display | wwPDB validaton report |
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Full document | 4hzl_full_validation.pdf.gz | 490.5 KB | Display | |
Data in XML | 4hzl_validation.xml.gz | 36.2 KB | Display | |
Data in CIF | 4hzl_validation.cif.gz | 49.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hz/4hzl ftp://data.pdbj.org/pub/pdb/validation_reports/hz/4hzl | HTTPS FTP |
-Related structure data
Related structure data | 1zeaS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS oper:
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Details | Protein molecule complex contains Fab fragments of an IgG antibody in complex with a peptide antigen |
-Components
#1: Antibody | Mass: 23744.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) #2: Antibody | Mass: 23884.422 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) #3: Protein/peptide | Mass: 1980.184 Da / Num. of mol.: 2 / Fragment: Epitope II residues 430-446 / Source method: isolated from a natural source Source: (natural) Recombinant Hepatitis C virus H77(5'UTR-NS2)/JFH1_V787A,Q1247L Strain: H77 / References: UniProt: F5BWY6 #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: 3.33 Å3/Da / Density % sol: 63.11 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.1 M Tris-HCl buffer (pH 8.0) 16% (wt/vol) polyethylene glycol 10,000, 0.2 M ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 1, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.85→50 Å / Num. obs: 30296 / % possible obs: 99.8 % / Rmerge(I) obs: 0.135 / Net I/σ(I): 10.8 |
Reflection shell | Resolution: 2.85→3 Å / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 3.8 / % possible all: 53.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ZEA Resolution: 2.85→50 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.836 / SU B: 32.53 / SU ML: 0.325 / Cross valid method: THROUGHOUT / ESU R: 1.07 / ESU R Free: 0.385 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 47.489 Å2
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Refinement step | Cycle: LAST / Resolution: 2.85→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5
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LS refinement shell | Resolution: 2.85→2.924 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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