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Yorodumi- PDB-6uym: Structure of Hepatitis C Virus Envelope Glycoprotein E2mc3-v6 red... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6uym | |||||||||||||||||||||
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Title | Structure of Hepatitis C Virus Envelope Glycoprotein E2mc3-v6 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 / IMMUNE SYSTEM / VIRAL PROTEIN-IMMUNE SYSTEM complex | |||||||||||||||||||||
Biological species | Hepatitis C virus Homo sapiens (human) | |||||||||||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.848 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 | 6uym.cif.gz | 235.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6uym.ent.gz | 185.4 KB | Display | PDB format |
PDBx/mmJSON format | 6uym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6uym_validation.pdf.gz | 394.2 KB | Display | wwPDB validaton report |
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Full document | 6uym_full_validation.pdf.gz | 395.4 KB | Display | |
Data in XML | 6uym_validation.xml.gz | 2 KB | Display | |
Data in CIF | 6uym_validation.cif.gz | 13.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uy/6uym ftp://data.pdbj.org/pub/pdb/validation_reports/uy/6uym | HTTPS FTP |
-Related structure data
Related structure data | 6uydC 6uyfC 6uygC 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
#1: Protein | Mass: 19286.709 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepatitis C virus (isolate H) / Strain: isolate H / Production host: Homo sapiens (human) #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) #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Sugar | ChemComp-NAG / 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: 2.73 Å3/Da / Density % sol: 54.89 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG 3500, 0.2M Na-thiocyanate, pH=6.9 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 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: 2.848→30 Å / Num. obs: 29145 / % possible obs: 88.5 % / Redundancy: 3.7 % / CC1/2: 0.96 / Net I/σ(I): 14.2 |
Reflection shell | Resolution: 2.85→2.9 Å / Num. unique obs: 836 / CC1/2: 0.88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MWF Resolution: 2.848→29.474 Å / SU ML: 0.39 / Cross valid method: THROUGHOUT / σ(F): 2 / Phase error: 33.04 / 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: 137.05 Å2 / Biso mean: 66.289 Å2 / Biso min: 29.72 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.848→29.474 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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