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Yorodumi- PDB-2m1k: Interaction of Human S100A6 (C3S) with V domain of Receptor for A... -
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-Basic information
Entry | Database: PDB / ID: 2m1k | ||||||
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Title | Interaction of Human S100A6 (C3S) with V domain of Receptor for Advanced Glycation End products (RAGE) | ||||||
Components |
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Keywords | PROTEIN BINDING / S100A6 C3S / RAGE V / heterotetrameric / HADDOCK model | ||||||
Function / homology | Function and homology information regulation of CD4-positive, alpha-beta T cell activation / negative regulation of blood circulation / advanced glycation end-product receptor activity / positive regulation of endothelin production / regulation of T cell mediated cytotoxicity / glucose mediated signaling pathway / negative regulation of long-term synaptic depression / positive regulation of monocyte extravasation / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / monoatomic ion transmembrane transporter activity ...regulation of CD4-positive, alpha-beta T cell activation / negative regulation of blood circulation / advanced glycation end-product receptor activity / positive regulation of endothelin production / regulation of T cell mediated cytotoxicity / glucose mediated signaling pathway / negative regulation of long-term synaptic depression / positive regulation of monocyte extravasation / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / monoatomic ion transmembrane transporter activity / positive regulation of dendritic cell differentiation / regulation of p38MAPK cascade / regulation of non-canonical NF-kappaB signal transduction / scavenger receptor activity / induction of positive chemotaxis / transcytosis / protein localization to membrane / positive regulation of monocyte chemotactic protein-1 production / positive regulation of heterotypic cell-cell adhesion / S100 protein binding / regulation of long-term synaptic potentiation / regulation of spontaneous synaptic transmission / laminin receptor activity / positive regulation of p38MAPK cascade / negative regulation of interleukin-10 production / tropomyosin binding / positive regulation of activated T cell proliferation / response to amyloid-beta / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / negative regulation of long-term synaptic potentiation / transport across blood-brain barrier / positive regulation of chemokine production / ruffle / positive regulation of interleukin-12 production / astrocyte activation / axonogenesis / positive regulation of interleukin-1 beta production / positive regulation of JNK cascade / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of non-canonical NF-kappaB signal transduction / regulation of synaptic plasticity / cytoplasmic side of plasma membrane / transmembrane signaling receptor activity / fibrillar center / response to wounding / positive regulation of fibroblast proliferation / positive regulation of interleukin-6 production / cellular response to amyloid-beta / nuclear envelope / calcium-dependent protein binding / cell junction / positive regulation of tumor necrosis factor production / neuron projection development / regulation of inflammatory response / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / collagen-containing extracellular matrix / postsynapse / positive regulation of ERK1 and ERK2 cascade / learning or memory / cell surface receptor signaling pathway / molecular adaptor activity / response to hypoxia / positive regulation of protein phosphorylation / apical plasma membrane / inflammatory response / calcium ion binding / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / signal transduction / protein homodimerization activity / zinc ion binding / extracellular exosome / extracellular region / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Gupta, A.A. / Yu, C. | ||||||
Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2013 Title: Interaction of the S100A6 mutant (C3S) with the V domain of the receptor for advanced glycation end products (RAGE). Authors: Mohan, S.K. / Gupta, A.A. / Yu, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2m1k.cif.gz | 2.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb2m1k.ent.gz | 2.2 MB | Display | PDB format |
PDBx/mmJSON format | 2m1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m1/2m1k ftp://data.pdbj.org/pub/pdb/validation_reports/m1/2m1k | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 10177.664 Da / Num. of mol.: 2 / Mutation: C3S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CACY, S100A6 / Plasmid: pET(20b)+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P06703 #2: Protein | Mass: 11217.007 Da / Num. of mol.: 2 / Fragment: UNP residues 23-121 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AGER, RAGE / Plasmid: pET(15b)+ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q15109 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR Details: Interaction of Human S100A6 (C3S) with V domain of Receptor for Advanced Glycation End products | ||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 1.0 mM [U-100% 13C; U-100% 15N] S100A6 C3S, 20 mM TRIS, 10 mM Calcium chloride, 0.01 % sodium azide, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0 / pH: 7 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 700 MHz |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 Details: HADDOCK STARTING STRUCTURES ARE PDB ENTRIES 1K9K AND 2E5E. MODELS 1-10 ARE SUPERIMPOSED, WHILE MODELS 11-20 ARE SUPERIMPOSED IN A DIFFERENT ORIENTATION. | ||||||||||||||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 / Representative conformer: 1 |