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Yorodumi- PDB-6mej: Crystal structure of Hepatitis C virus envelope glycoprotein E2 e... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6mej | |||||||||
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Title | Crystal structure of Hepatitis C virus envelope glycoprotein E2 ectodomain in complex with human antibodies HEPC3 and HEPC46 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / HCV glycoprotein / broadly neutralizing antibodies | |||||||||
Function / homology | Function and homology information virus-mediated perturbation of host defense response => GO:0019049 / host cell mitochondrial membrane / host cell lipid droplet / lipid droplet / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / viral envelope / host cell nucleus / structural molecule activity ...virus-mediated perturbation of host defense response => GO:0019049 / host cell mitochondrial membrane / host cell lipid droplet / lipid droplet / viral nucleocapsid / clathrin-dependent endocytosis of virus by host cell / host cell endoplasmic reticulum membrane / viral envelope / host cell nucleus / structural molecule activity / virion membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) Hepacivirus C | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | |||||||||
Authors | Flyak, A.I. / Bjorkman, P.J. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Cell Host Microbe / Year: 2018 Title: HCV Broadly Neutralizing Antibodies Use a CDRH3 Disulfide Motif to Recognize an E2 Glycoprotein Site that Can Be Targeted for Vaccine Design. Authors: Flyak, A.I. / Ruiz, S. / Colbert, M.D. / Luong, T. / Crowe Jr., J.E. / Bailey, J.R. / Bjorkman, P.J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6mej.cif.gz | 443.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6mej.ent.gz | 361.4 KB | Display | PDB format |
PDBx/mmJSON format | 6mej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6mej_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6mej_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 6mej_validation.xml.gz | 42.7 KB | Display | |
Data in CIF | 6mej_validation.cif.gz | 58 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/me/6mej ftp://data.pdbj.org/pub/pdb/validation_reports/me/6mej | HTTPS FTP |
-Related structure data
Related structure data | 6medSC 6meeC 6mefC 6megSC 6mehC 6meiC 6mekC 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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Unit cell |
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-Components
-Protein , 1 types, 1 molecules C
#3: Protein | Mass: 28769.514 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepacivirus C / Plasmid: pCMV / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human) / References: UniProt: C1KH25 |
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-Antibody , 4 types, 4 molecules ABHL
#1: Antibody | Mass: 24681.619 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 22938.188 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human) |
#4: Antibody | Mass: 25759.807 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human) |
#5: Antibody | Mass: 23384.883 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: pTT5 / Cell line (production host): HEK293-6E / Production host: Homo sapiens (human) |
-Sugars , 3 types, 6 molecules
#6: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#7: 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 |
#8: Sugar | ChemComp-NAG / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.93 % / Mosaicity: 0.5 ° |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.8 / Details: 0.2 M Ammonium sulfate, 20% Peg 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1 Å | |||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2017 | |||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||
Reflection | Resolution: 2.6→78.27 Å / Num. obs: 45937 / % possible obs: 99.9 % / Redundancy: 3.1 % / Biso Wilson estimate: 64.62 Å2 / CC1/2: 0.976 / Rmerge(I) obs: 0.125 / Rpim(I) all: 0.085 / Rrim(I) all: 0.152 / Net I/σ(I): 5.6 / Num. measured all: 142433 / Scaling rejects: 109 | |||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 3.1 %
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MWF, 6MED, 6MEG Resolution: 2.8→78.271 Å / SU ML: 0.41 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 32 / 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: 193.09 Å2 / Biso mean: 75.0984 Å2 / Biso min: 24.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.8→78.271 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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