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Yorodumi- PDB-6vsz: Crystal structure of a human afucosylated IgG1 Fc expressed in to... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6vsz | ||||||||||||
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Title | Crystal structure of a human afucosylated IgG1 Fc expressed in tobacco plants (Nicotiana benthamiana) | ||||||||||||
Components | Immunoglobulin gamma-1 heavy chain | ||||||||||||
Keywords | IMMUNE SYSTEM / immunoglobulin / crystallizable fragment / IgG1 / Fc | ||||||||||||
Function / homology | Function and homology information immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome / plasma membrane Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||||||||
Authors | Tolbert, W.D. / Pazgier, M. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J.Virol. / Year: 2021 Title: Enhanced Ability of Plant-Derived PGT121 Glycovariants To Eliminate HIV-1-Infected Cells. Authors: Anand, S.P. / Ding, S. / Tolbert, W.D. / Prevost, J. / Richard, J. / Gil, H.M. / Gendron-Lepage, G. / Cheung, W.F. / Wang, H. / Pastora, R. / Saxena, H. / Wakarchuk, W. / Medjahed, H. / ...Authors: Anand, S.P. / Ding, S. / Tolbert, W.D. / Prevost, J. / Richard, J. / Gil, H.M. / Gendron-Lepage, G. / Cheung, W.F. / Wang, H. / Pastora, R. / Saxena, H. / Wakarchuk, W. / Medjahed, H. / Wines, B.D. / Hogarth, M. / Shaw, G.M. / Martin, M.A. / Burton, D.R. / Hangartner, L. / Evans, D.T. / Pazgier, M. / Cossar, D. / McLean, M.D. / Finzi, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vsz.cif.gz | 192.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vsz.ent.gz | 153.3 KB | Display | PDB format |
PDBx/mmJSON format | 6vsz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vsz_validation.pdf.gz | 414.2 KB | Display | wwPDB validaton report |
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Full document | 6vsz_full_validation.pdf.gz | 416.8 KB | Display | |
Data in XML | 6vsz_validation.xml.gz | 2.3 KB | Display | |
Data in CIF | 6vsz_validation.cif.gz | 6.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/6vsz ftp://data.pdbj.org/pub/pdb/validation_reports/vs/6vsz | HTTPS FTP |
-Related structure data
Related structure data | 6vslC 3aveS 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
#1: Antibody | Mass: 23918.043 Da / Num. of mol.: 2 / Fragment: crystallizable fragment (UNP residues 236-446) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Nicotiana benthamiana (plant) / References: UniProt: P0DOX5 #2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.86 Å3/Da / Density % sol: 56.96 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 15% PEG4000, 0.1 M HEPES, pH 7.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 16, 2019 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→50 Å / Num. obs: 15294 / % possible obs: 88 % / Redundancy: 3.6 % / CC1/2: 0.99 / Rpim(I) all: 0.047 / Rsym value: 0.083 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2235 / CC1/2: 0.68 / Rpim(I) all: 0.497 / Rsym value: 0.902 / % possible all: 90.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 3AVE Resolution: 2.6→50 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.8
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→50 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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