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Yorodumi- PDB-8w4l: Crystal structure of closed conformation of human immunoglobulin ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8w4l | ||||||
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Title | Crystal structure of closed conformation of human immunoglobulin Fc in presence of EndoSz | ||||||
Components | Immunoglobulin gamma-1 heavy chain | ||||||
Keywords | IMMUNE SYSTEM / N-linked glycan / glycoside hydrolase / transglycosylation | ||||||
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: 3.1 Å | ||||||
Authors | Guan, H.H. / Lin, C.C. / Hsieh, Y.C. / Chen, C.J. | ||||||
Funding support | Taiwan, 1items
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Citation | Journal: Jacs Au / Year: 2024 Title: Structure-Based High-Efficiency Homogeneous Antibody Platform by Endoglycosidase Sz Provides Insights into Its Transglycosylation Mechanism. Authors: Hsieh, Y.C. / Guan, H.H. / Lin, C.C. / Huang, T.Y. / Chuankhayan, P. / Chen, N.C. / Wang, N.H. / Hu, P.L. / Tsai, Y.C. / Huang, Y.C. / Yoshimura, M. / Lin, P.J. / Hsieh, Y.H. / Chen, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8w4l.cif.gz | 104.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8w4l.ent.gz | 79.5 KB | Display | PDB format |
PDBx/mmJSON format | 8w4l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8w4l_validation.pdf.gz | 1.7 MB | Display | wwPDB validaton report |
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Full document | 8w4l_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 8w4l_validation.xml.gz | 18.9 KB | Display | |
Data in CIF | 8w4l_validation.cif.gz | 25 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w4/8w4l ftp://data.pdbj.org/pub/pdb/validation_reports/w4/8w4l | HTTPS FTP |
-Related structure data
Related structure data | 8w4gC 8w4iC 8w4mC 8w4nC 8x8gC 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
#1: Antibody | Mass: 25129.496 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DOX5 #2: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Type: oligosaccharide / Mass: 1916.745 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source #3: Polysaccharide | beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Type: oligosaccharide / Mass: 1787.631 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source #4: Chemical | 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: 3.76 Å3/Da / Density % sol: 69.17 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 100 mM MES PH 6.0 200 mM Zinc acetate 10 % PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Oct 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→28.72 Å / Num. obs: 14294 / % possible obs: 98.56 % / Redundancy: 11.2 % / CC1/2: 0.963 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 3.101→3.211 Å / Num. unique obs: 1265 / CC1/2: 0.742 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→28.72 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 25.79 / 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: 176.81 Å2 / Biso mean: 52.3686 Å2 / Biso min: 9.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.1→28.72 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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