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Yorodumi- PDB-1gkg: Structure Determination and Rational Mutagenesis reveal binding s... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1gkg | ||||||
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Title | Structure Determination and Rational Mutagenesis reveal binding surface of immune adherence receptor, CR1 (CD35) | ||||||
Components | COMPLEMENT RECEPTOR TYPE 1 | ||||||
Keywords | COMPLEMENT / MODULE / SCR / SUSHI | ||||||
Function / homology | Function and homology information complement component C4b receptor activity / immune complex clearance by erythrocytes / complement component C3b receptor activity / positive regulation of serine-type endopeptidase activity / negative regulation of complement activation, alternative pathway / complement component C4b binding / negative regulation of immunoglobulin production / negative regulation of activation of membrane attack complex / negative regulation of complement activation, classical pathway / negative regulation of complement-dependent cytotoxicity ...complement component C4b receptor activity / immune complex clearance by erythrocytes / complement component C3b receptor activity / positive regulation of serine-type endopeptidase activity / negative regulation of complement activation, alternative pathway / complement component C4b binding / negative regulation of immunoglobulin production / negative regulation of activation of membrane attack complex / negative regulation of complement activation, classical pathway / negative regulation of complement-dependent cytotoxicity / negative regulation of complement activation / ATP export / T cell mediated immunity / positive regulation of activation of membrane attack complex / plasma membrane organization / negative regulation of plasma cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / complement component C3b binding / negative regulation of serine-type endopeptidase activity / complement receptor mediated signaling pathway / positive regulation of regulatory T cell differentiation / complement activation, alternative pathway / negative regulation of interleukin-2 production / plasma membrane raft / ficolin-1-rich granule membrane / negative regulation of type II interferon production / complement activation, classical pathway / negative regulation of T cell proliferation / secretory granule membrane / Regulation of Complement cascade / virus receptor activity / cytoskeleton / positive regulation of cell population proliferation / Neutrophil degranulation / cell surface / extracellular space / extracellular exosome / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | SOLUTION NMR / MOLECULAR DYNAMICS SIMULATED ANNEALING | ||||||
Authors | Smith, B.O. / Mallin, R.L. / Krych-Goldberg, M. / Wang, X. / Hauhart, R.E. / Bromek, K. / Uhrin, D. / Atkinson, J.P. / Barlow, P.N. | ||||||
Citation | Journal: Cell(Cambridge,Mass.) / Year: 2002 Title: Structure of the C3B Binding Site of Cr1 (Cd35), the Immune Adherence Receptor Authors: Smith, B. / Mallin, R. / Krych-Goldberg, M. / Wang, X. / Hauhart, R. / Bromek, K. / Uhrin, D. / Atkinson, J. / Barlow, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1gkg.cif.gz | 941.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1gkg.ent.gz | 788.1 KB | Display | PDB format |
PDBx/mmJSON format | 1gkg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gk/1gkg ftp://data.pdbj.org/pub/pdb/validation_reports/gk/1gkg | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 14706.579 Da / Num. of mol.: 1 / Fragment: MODULES 16 AND 17, OF SITE 2, RESIDUE 1002-1133 / Mutation: YES Source method: isolated from a genetically manipulated source Details: SECOND TWO MODULES OF SITE 2 IN CR1, A C3B/C4B BINDING SITE Source: (gene. exp.) HOMO SAPIENS (human) Description: RECOMBINANT TECHNOLOGY USING HUMAN GENE (NOT SYNTHETIC) Production host: PICHIA PASTORIS (fungus) / References: UniProt: P17927 |
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Compound details | CHAIN A ENGINEERED |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 13C, 15N-LABELED PROTEIN |
-Sample preparation
Sample conditions | Ionic strength: 20MM NACL / pH: 6.0 / Pressure: 1 atm / Temperature: 310 K |
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Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: MOLECULAR DYNAMICS SIMULATED ANNEALING / Software ordinal: 1 Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE | ||||||||||||
NMR ensemble | Conformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 120 / Conformers submitted total number: 24 |