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- PDB-6bkd: Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6bkd | |||||||||
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Title | Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to broadly neutralizing antibody AR3D | |||||||||
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![]() | IMMUNE SYSTEM / hepatitis C virus / HCV / broadly neutralizing antibodies / bNAbs / E2 core / IGHV1-69 | |||||||||
Function / homology | ![]() immunoglobulin complex / 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 / immunoglobulin mediated immune response / 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 / ribonucleoside triphosphate phosphatase activity ...immunoglobulin complex / 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 / immunoglobulin mediated immune response / 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 / ribonucleoside triphosphate phosphatase activity / lipid droplet / antigen binding / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / RNA helicase activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / blood microparticle / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / induction by virus of host autophagy / immune response / viral RNA genome replication / cysteine-type endopeptidase activity / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / extracellular space / zinc ion binding / ATP binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Tzarum, N. / Wilson, I.A. / Law, M. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Genetic and structural insights into broad neutralization of hepatitis C virus by human VH1-69 antibodies. Authors: Tzarum, N. / Giang, E. / Kong, L. / He, L. / Prentoe, J. / Augestad, E. / Hua, Y. / Castillo, S. / Lauer, G.M. / Bukh, J. / Zhu, J. / Wilson, I.A. / Law, M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 128.5 KB | Display | ![]() |
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PDB format | ![]() | 95.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 698.8 KB | Display | ![]() |
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Full document | ![]() | 712.9 KB | Display | |
Data in XML | ![]() | 23.3 KB | Display | |
Data in CIF | ![]() | 31.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6bkbSC ![]() 6bkcC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20707.395 Da / Num. of mol.: 1 / Mutation: N448D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() |
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#2: Antibody | Mass: 24458.566 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#3: Antibody | Mass: 23047.535 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
#4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.44 Å3/Da / Density % sol: 49.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 20% (w/v) PEG 6000, 0.1M Hepes, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 16, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0331 Å / Relative weight: 1 |
Reflection | Resolution: 3.25→50 Å / Num. obs: 9230 / % possible obs: 90.1 % / Redundancy: 8.1 % / Rpim(I) all: 0.07 / Rsym value: 0.23 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 3.3→3.36 Å / Redundancy: 8.1 % / Mean I/σ(I) obs: 1.2 / CC1/2: 0.56 / % possible all: 68.3 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6BKB Resolution: 3.25→49.33 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.1
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.25→49.33 Å
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Refine LS restraints |
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LS refinement shell |
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