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- PDB-6uyf: Structure of Hepatitis C Virus Envelope Glycoprotein E2mc3-v1 red... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6uyf | |||||||||||||||||||||
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Title | Structure of Hepatitis C Virus Envelope Glycoprotein E2mc3-v1 redesigned core from genotype 6a bound to broadly neutralizing antibody AR3B | |||||||||||||||||||||
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![]() | VIRAL PROEIN/IMMUNE SYSTEM / HCV / E2 core / Vaccine design / self-assembly nanoparticle / broadly neutralizing antibodies / bNAbs / VIRAL PROTEIN-IMMUNE SYSTEM complex / VIRAL PROEIN-IMMUNE SYSTEM complex | |||||||||||||||||||||
Function / homology | ![]() 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 / 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 / protein complex oligomerization ...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 / 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 / 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 / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / ribonucleoprotein complex / induction by virus of host autophagy / 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 / structural molecule activity / virion membrane / proteolysis / RNA binding / zinc ion binding / ATP binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||||||||
Method | ![]() ![]() ![]() | |||||||||||||||||||||
![]() | Tzarum, N. / Wilson, I.A. / Zhu, J. | |||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Proof of concept for rational design of hepatitis C virus E2 core nanoparticle vaccines. Authors: He, L. / Tzarum, N. / Lin, X. / Shapero, B. / Sou, C. / Mann, C.J. / Stano, A. / Zhang, L. / Nagy, K. / Giang, E. / Law, M. / Wilson, I.A. / Zhu, J. | |||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 140.8 KB | Display | ![]() |
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PDB format | ![]() | 104.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 470.5 KB | Display | ![]() |
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Full document | ![]() | 470.6 KB | Display | |
Data in XML | ![]() | 1.7 KB | Display | |
Data in CIF | ![]() | 9.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6uydC ![]() 6uygC ![]() 6uymC ![]() 6bkcS 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
-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 24035.156 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Antibody | Mass: 23418.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
-Protein / Non-polymers , 2 types, 307 molecules E![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#3: Protein | Mass: 19616.018 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() |
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#7: Water | ChemComp-HOH / |
-Sugars , 3 types, 4 molecules ![](data/chem/img/NAG.gif)
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #6: Sugar | ChemComp-NAG / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 8000, 0.1M HEPES pH=7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→50 Å / Num. obs: 38846 / % possible obs: 93.9 % / Redundancy: 4.6 % / Biso Wilson estimate: 29.87 Å2 / CC1/2: 0.96 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 2.06→2.1 Å / Num. unique obs: 1408 / CC1/2: 0.92 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6BKC Resolution: 2.06→43.65 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.83 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 112.74 Å2 / Biso mean: 35.9401 Å2 / Biso min: 15.57 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.06→43.65 Å
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Refine LS restraints |
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LS refinement shell |
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