[English] 日本語
Yorodumi- PDB-6uyf: Structure of Hepatitis C Virus Envelope Glycoprotein E2mc3-v1 red... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uyf | |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Structure of Hepatitis C Virus Envelope Glycoprotein E2mc3-v1 redesigned core from genotype 6a bound to broadly neutralizing antibody AR3B | |||||||||||||||||||||
Components |
| |||||||||||||||||||||
Keywords | 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 | Function and homology information 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 / : ...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 / clathrin-dependent endocytosis of virus by host cell / viral nucleocapsid / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / induction by virus of host autophagy / 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 / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / RNA binding / zinc ion binding / ATP binding / plasma membrane / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Homo sapiens (human) Recombinant Hepatitis C virus HK6a/JFH-1 | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 Å | |||||||||||||||||||||
Authors | Tzarum, N. / Wilson, I.A. / Zhu, J. | |||||||||||||||||||||
Funding support | United States, 6items
| |||||||||||||||||||||
Citation | Journal: Sci Adv / Year: 2020 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6uyf.cif.gz | 140.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6uyf.ent.gz | 104.5 KB | Display | PDB format |
PDBx/mmJSON format | 6uyf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/6uyf ftp://data.pdbj.org/pub/pdb/validation_reports/uy/6uyf | HTTPS FTP |
---|
-Related structure data
Related structure data | 6uydC 6uygC 6uymC 6bkcS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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.) Homo sapiens (human) / Production host: Homo sapiens (human) |
---|---|
#2: Antibody | Mass: 23418.855 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
-Protein / Non-polymers , 2 types, 307 molecules E
#3: Protein | Mass: 19616.018 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Recombinant Hepatitis C virus HK6a/JFH-1 Production host: Homo sapiens (human) / References: UniProt: B9V0E2*PLUS |
---|---|
#7: Water | ChemComp-HOH / |
-Sugars , 3 types, 4 molecules
#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 / | |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.65 Å3/Da / Density % sol: 53.5 % |
---|---|
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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
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 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|