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Yorodumi- PDB-6uyd: Structure of Hepatitis C Virus Envelope Glycoprotein E2mc3-v1 red... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uyd | |||||||||||||||||||||
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Title | Structure of Hepatitis C Virus Envelope Glycoprotein E2mc3-v1 redesigned core from genotype 1a bound to broadly neutralizing antibody AR3C | |||||||||||||||||||||
Components |
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Keywords | VIRAL PROTEIN/IMMUNE SYSTEM / HCV / E2 core / Vaccine design / self-assembly nanoparticle / broadly neutralizing antibodies / bNAbs / VIRAL PROTEIN-IMMUNE SYSTEM 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 / kinase binding / SH3 domain binding / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / entry receptor-mediated virion attachment to host cell / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / RNA helicase activity / host cell endoplasmic reticulum membrane / host cell perinuclear region of cytoplasm / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / RNA helicase / ribonucleoprotein complex / induction by virus of host autophagy / RNA-directed RNA polymerase / 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 / host cell plasma membrane / structural molecule activity / 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 | Hepatitis C virus Homo sapiens (human) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.897 Å | |||||||||||||||||||||
Authors | Tzarum, N. / Wilson, I.A. / Zhu, J. | |||||||||||||||||||||
Funding support | United States, 6items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6uyd.cif.gz | 251.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uyd.ent.gz | 197 KB | Display | PDB format |
PDBx/mmJSON format | 6uyd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uyd_validation.pdf.gz | 394.9 KB | Display | wwPDB validaton report |
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Full document | 6uyd_full_validation.pdf.gz | 395 KB | Display | |
Data in XML | 6uyd_validation.xml.gz | 1.6 KB | Display | |
Data in CIF | 6uyd_validation.cif.gz | 15.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/6uyd ftp://data.pdbj.org/pub/pdb/validation_reports/uy/6uyd | HTTPS FTP |
-Related structure data
Related structure data | 6uyfC 6uygC 6uymC 4mwfS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Antibody , 2 types, 4 molecules HALB
#2: Antibody | Mass: 24627.498 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #3: Antibody | Mass: 23266.812 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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-Protein / Non-polymers , 2 types, 522 molecules EF
#1: Protein | Mass: 19500.826 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus (isolate H) / Production host: Homo sapiens (human) / References: UniProt: P27958*PLUS #6: Water | ChemComp-HOH / | |
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-Sugars , 2 types, 6 molecules
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / |
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-Details
Has ligand of interest | N |
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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: 2.93 Å3/Da / Density % sol: 57.97 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 20% (w/v) PEG 3500, 0.2M di-ammonium hydrogen phosphate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 20, 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: 1.897→30 Å / Num. obs: 121242 / % possible obs: 99 % / Redundancy: 4.5 % / CC1/2: 0.89 / Net I/σ(I): 25.8 |
Reflection shell | Resolution: 1.9→1.93 Å / Num. unique obs: 5954 / CC1/2: 0.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MWF Resolution: 1.897→29.914 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.25 / 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: 139.01 Å2 / Biso mean: 47.5896 Å2 / Biso min: 21.57 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.897→29.914 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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