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Yorodumi- PDB-1fc1: CRYSTALLOGRAPHIC REFINEMENT AND ATOMIC MODELS OF A HUMAN FC FRAGM... -
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-Basic information
Entry | Database: PDB / ID: 1fc1 | |||||||||
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Title | CRYSTALLOGRAPHIC REFINEMENT AND ATOMIC MODELS OF A HUMAN FC FRAGMENT AND ITS COMPLEX WITH FRAGMENT B OF PROTEIN A FROM STAPHYLOCOCCUS AUREUS AT 2.9-AND 2.8-ANGSTROMS RESOLUTION | |||||||||
Components | FC FRAGMENTFragment crystallizable region | |||||||||
Keywords | IMMUNOGLOBULIN | |||||||||
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 / Resolution: 2.9 Å | |||||||||
Authors | Deisenhofer, J. | |||||||||
Citation | Journal: Biochemistry / Year: 1981 Title: Crystallographic refinement and atomic models of a human Fc fragment and its complex with fragment B of protein A from Staphylococcus aureus at 2.9- and 2.8-A resolution. Authors: Deisenhofer, J. #1: Journal: Hoppe-Seyler's Z.Physiol.Chem. / Year: 1976 Title: Crystallographic Structural Studies of a Human Fc Fragment. II. A Complete Model Based on a Fourier Map at 3.5 Angstroms Resolution Authors: Deisenhofer, J. / Colman, P.M. / Epp, O. / Huber, R. #2: Journal: Hoppe-Seyler's Z.Physiol.Chem. / Year: 1976 Title: Crystallographic Structural Studies of a Human Fc-Fragment. I. An Electron-Density Map at 4 Angstroms Resolution and a Partial Model Authors: Deisenhofer, J. / Colman, P.M. / Huber, R. / Haupt, H. / Schwick, G. #3: Journal: FEBS Lett. / Year: 1974 Title: X-Ray Studies on Antibody Fragments Authors: Colman, P.M. / Epp, O. / Fehlhammer, H. / Bode, W. / Schiffer, M. / Lattman, E.E. / Jones, T.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fc1.cif.gz | 87.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fc1.ent.gz | 72.9 KB | Display | PDB format |
PDBx/mmJSON format | 1fc1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/1fc1 ftp://data.pdbj.org/pub/pdb/validation_reports/fc/1fc1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Atom site foot note | 1: THESE ATOMS WERE NOT FOUND IN THE ELECTRON DENSITY MAP. THEIR COORDINATES WERE GENERATED USING STEREOCHEMICAL CRITERIA 2: RESIDUE 374 OF EACH CHAIN IS A CIS-PROLINE. | ||||||||
Details | THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT CONTAINS ONE FC FRAGMENT WHICH CONSISTS OF TWO CHEMICALLY IDENTICAL POLYPEPTIDE CHAINS EACH WITH ATTACHED POLYSACCHARIDE. THESE TWO CHAINS ARE DESIGNATED CHAIN 1 AND CHAIN 2 BY THE DEPOSITOR AND REPRESENTED WITH CHAIN IDENTIFIERS A AND B BELOW. THE CH2 AND CH3 DOMAINS OF THE TWO CRYSTALLOGRAPHICALLY INDEPENDENT POLYPEPTIDE CHAINS ARE RELATED BY NON-CRYSTALLOGRAPHIC (APPROXIMATE) DIADS (SEE JRNL REFERENCE ABOVE FOR A COMPLETE DISCUSSION). THE FOLLOWING TRANSFORMATION, WHEN APPLIED TO THE CH2 DOMAIN OF CHAIN A (RESIDUES PRO A 238 THROUGH GLY A 341 TOGETHER WITH THE POLYSACCHARIDE), WILL YIELD APPROXIMATE COORDINATES FOR THE CH2 DOMAIN OF CHAIN B (RESIDUES PRO B 238 THROUGH GLY B 341 TOGETHER WITH THE POLYSACCHARIDE). TRNSF1 1 -0.99391 -0.03853 -0.10322 92.070 TRNSF2 1 -0.06679 0.95579 0.28635 -0.310 TRNSF3 1 0.08759 0.29136 -0.95207 11.160 THE FOLLOWING TRANSFORMATION, WHEN APPLIED TO THE CH3 DOMAIN OF CHAIN A (RESIDUES GLN A 342 THROUGH LEU A 443), WILL YIELD APPROXIMATE COORDINATES FOR THE CH3 DOMAIN OF CHAIN B (RESIDUES GLN B 342 THROUGH LEU B 443). TRNSF1 2 -0.99907 -0.03950 -0.01721 88.510 TRNSF2 2 -0.04232 0.97468 0.21956 -1.010 TRNSF3 2 0.00810 0.22008 -0.97544 24.570 |
-Components
#1: Protein | Mass: 25236.615 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Tissue: SERUM / References: UniProt: P01857 #2: Polysaccharide | Source method: isolated from a genetically manipulated source |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.94 Å3/Da / Density % sol: 58.1 % |
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Refinement | Highest resolution: 2.9 Å | ||||||||||||
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Refinement step | Cycle: LAST / Highest resolution: 2.9 Å
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