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Yorodumi- PDB-4bm7: Crystal Structure of IgG Fc F241A mutant with native glycosylation -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bm7 | |||||||||
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Title | Crystal Structure of IgG Fc F241A mutant with native glycosylation | |||||||||
Components | IG GAMMA-1 CHAIN C REGION | |||||||||
Keywords | IMMUNE SYSTEM / GLYCAN | |||||||||
Function / homology | Function and homology information complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | |||||||||
Authors | Yu, X. / Baruah, K. / Harvey, D.J. / Vasiljevic, S. / Alonzi, D.S. / Song, B. / Higgins, M.K. / Bowden, T.A. / Crispin, M. / Scanlan, C.N. | |||||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2013 Title: Engineering Hydrophobic Protein-Carbohydrate Interactions to Fine-Tune Monoclonal Antibodies. Authors: Yu, X. / Baruah, K. / Harvey, D.J. / Vasiljevic, S. / Alonzi, D.S. / Song, B. / Higgins, M.K. / Bowden, T.A. / Scanlan, C.N. / Crispin, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bm7.cif.gz | 186.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bm7.ent.gz | 146.7 KB | Display | PDB format |
PDBx/mmJSON format | 4bm7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/4bm7 ftp://data.pdbj.org/pub/pdb/validation_reports/bm/4bm7 | HTTPS FTP |
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-Related structure data
Related structure data | 3aveS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 26279.691 Da / Num. of mol.: 2 / Fragment: IMMUNOGLOBULIN GAMMA, FC, RESIDUES 101-329 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293T / Production host: HOMO SAPIENS (human) / References: UniProt: P01857 #2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Chemical | ChemComp-CL / | #4: Water | ChemComp-HOH / | Sequence details | SEQUENCE INCLUDES A SITE-DIRECTED F241A MUTATION FOR ANALYSIS OF EFFECTS UPON PROTEIN-CARBOHYDRATE ...SEQUENCE INCLUDES A SITE-DIRECTED F241A MUTATION FOR ANALYSIS OF EFFECTS UPON PROTEIN-CARBOHYDRA | |
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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: 2.75 Å3/Da / Density % sol: 55 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: 28% POLYETHYLENE GLYCOL MONOMETHYL ETHER 2,000 IN 0.1M BIS-TRIS BUFFER AT PH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.917 |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 5, 2011 / Details: MIRRORS |
Radiation | Monochromator: SINGLE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.917 Å / Relative weight: 1 |
Reflection | Resolution: 1.94→50 Å / Num. obs: 36211 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.4 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 6 % / Rmerge(I) obs: 0.75 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3AVE Resolution: 1.95→49.92 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 7.424 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.165 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.812 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→49.92 Å
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