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Yorodumi- PDB-8w0x: Crystal structure of broadly neutralizing antibody hcab40 in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8w0x | ||||||||||||
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Title | Crystal structure of broadly neutralizing antibody hcab40 in complex with Hepatitis C virus envelope glycoprotein E2 ectodomain | ||||||||||||
Components |
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Keywords | IMMUNE SYSTEM/VIRAL PROTEIN / HCV glycoprotein / broadly neutralizing antibodies / IMMUNE SYSTEM / IMMUNE SYSTEM-VIRAL PROTEIN complex | ||||||||||||
Function / homology | Function and homology information host cell lipid droplet / host cell mitochondrion / lipid droplet / viral nucleocapsid / host cell endoplasmic reticulum membrane / ribonucleoprotein complex / viral envelope / apoptotic process / structural molecule activity / virion membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Hepacivirus hominis Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.12 Å | ||||||||||||
Authors | Flyak, A.I. / Wilcox, X.E. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Immunity / Year: 2024 Title: Convergent evolution and targeting of diverse E2 epitopes by human broadly neutralizing antibodies are associated with HCV clearance. Authors: Ogega, C.O. / Skinner, N.E. / Schoenle, M.V. / Wilcox, X.E. / Frumento, N. / Wright, D.A. / Paul, H.T. / Sinnis-Bourozikas, A. / Clark, K.E. / Figueroa, A. / Bjorkman, P.J. / Ray, S.C. / ...Authors: Ogega, C.O. / Skinner, N.E. / Schoenle, M.V. / Wilcox, X.E. / Frumento, N. / Wright, D.A. / Paul, H.T. / Sinnis-Bourozikas, A. / Clark, K.E. / Figueroa, A. / Bjorkman, P.J. / Ray, S.C. / Flyak, A.I. / Bailey, J.R. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8w0x.cif.gz | 280.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8w0x.ent.gz | 228.3 KB | Display | PDB format |
PDBx/mmJSON format | 8w0x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/8w0x ftp://data.pdbj.org/pub/pdb/validation_reports/w0/8w0x | HTTPS FTP |
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-Related structure data
Related structure data | 8w0vC 8w0wC 8w0yC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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
#1: Protein | Mass: 28946.479 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hepacivirus hominis / Plasmid: pCMV / Cell line (production host): HEK293expi / Production host: Homo sapiens (human) / References: UniProt: A0A2P0NE15 |
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-Antibody , 2 types, 2 molecules HL
#2: Antibody | Mass: 25968.047 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): HEK293expi / Production host: Homo sapiens (human) |
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#3: Antibody | Mass: 23448.020 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): HEK293expi / Production host: Homo sapiens (human) |
-Sugars , 6 types, 9 molecules
#4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]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 #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: 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 | Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source #9: Sugar | |
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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: 3.46 Å3/Da / Density % sol: 64.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M Sodium malonate and 12% PEG 3,350 |
-Data collection
Diffraction | Mean temperature: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Dec 9, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.87→40.04 Å / Num. obs: 25984 / % possible obs: 99.9 % / Redundancy: 19.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.047 / Rrim(I) all: 0.209 / Χ2: 0.84 / Net I/σ(I): 8.9 / Num. measured all: 511303 |
Reflection shell | Resolution: 2.87→3.03 Å / % possible obs: 100 % / Redundancy: 20.5 % / Rmerge(I) obs: 5.876 / Num. measured all: 76157 / Num. unique obs: 3711 / CC1/2: 0.451 / Rpim(I) all: 1.321 / Rrim(I) all: 6.025 / Χ2: 0.69 / Net I/σ(I) obs: 0.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.12→40.04 Å / SU ML: 0.4 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.82 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.12→40.04 Å
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Refine LS restraints |
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LS refinement shell |
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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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