+Open data
-Basic information
Entry | Database: PDB / ID: 6vxg | ||||||
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Title | Structure of the C-terminal Domain of RAGE and Its Inhibitor | ||||||
Components | Advanced glycosylation end product-specific receptor | ||||||
Keywords | SIGNALING PROTEIN/INHIBITOR / Inhibitor / Complex / Diabetes / Receptor for Advanced Glycated End Products / Inflammation / SIGNALING PROTEIN / SIGNALING PROTEIN-INHIBITOR complex | ||||||
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 / positive regulation of dendritic cell differentiation ...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 / 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 / positive regulation of activated T cell proliferation / response to amyloid-beta / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / transport across blood-brain barrier / negative regulation of long-term synaptic potentiation / positive regulation of chemokine production / positive regulation of interleukin-12 production / positive regulation of interleukin-1 beta production / astrocyte activation / positive regulation of JNK cascade / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / regulation of synaptic plasticity / fibrillar center / response to wounding / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to amyloid-beta / transmembrane signaling receptor activity / positive regulation of interleukin-6 production / neuron projection development / positive regulation of tumor necrosis factor production / cell junction / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / regulation of inflammatory response / postsynapse / molecular adaptor activity / learning or memory / positive regulation of ERK1 and ERK2 cascade / cell surface receptor signaling pathway / response to hypoxia / inflammatory response / positive regulation of protein phosphorylation / apical plasma membrane / protein-containing complex binding / cell surface / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Ramirez, L. / Shekhtman, A. | ||||||
Funding support | United States, 1items
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Citation | Journal: Sci Transl Med / Year: 2021 Title: Small-molecule antagonism of the interaction of the RAGE cytoplasmic domain with DIAPH1 reduces diabetic complications in mice. Authors: Manigrasso, M.B. / Rabbani, P. / Egana-Gorrono, L. / Quadri, N. / Frye, L. / Zhou, B. / Reverdatto, S. / Ramirez, L.S. / Dansereau, S. / Pan, J. / Li, H. / D'Agati, V.D. / Ramasamy, R. / ...Authors: Manigrasso, M.B. / Rabbani, P. / Egana-Gorrono, L. / Quadri, N. / Frye, L. / Zhou, B. / Reverdatto, S. / Ramirez, L.S. / Dansereau, S. / Pan, J. / Li, H. / D'Agati, V.D. / Ramasamy, R. / DeVita, R.J. / Shekhtman, A. / Schmidt, A.M. #1: Journal: J. Biol. Chem. / Year: 2012 Title: Signal transduction in receptor for advanced glycation end products (RAGE): solution structure of C-terminal rage (ctRAGE) and its binding to mDia1. Authors: Rai, V. / Maldonado, A.Y. / Burz, D.S. / Reverdatto, S. / Yan, S.F. / Schmidt, A.M. / Shekhtman, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6vxg.cif.gz | 144.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6vxg.ent.gz | 103.3 KB | Display | PDB format |
PDBx/mmJSON format | 6vxg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6vxg_validation.pdf.gz | 475.1 KB | Display | wwPDB validaton report |
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Full document | 6vxg_full_validation.pdf.gz | 600.3 KB | Display | |
Data in XML | 6vxg_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 6vxg_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vx/6vxg ftp://data.pdbj.org/pub/pdb/validation_reports/vx/6vxg | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 5035.241 Da / Num. of mol.: 1 / Fragment: C-terminal residues 363-404 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AGER, RAGE / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q15109 |
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#2: Chemical | ChemComp-RQV / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 300 uM [U-100% 13C; U-100% 15N] C-terminal RAGE, 90% H2O/10% D2O Details: Recombinant protein bound to small molecule ligand (N-(4-(7-cyano-4-(morpholin-4-ylmethyl)quinoline-2-yl)phenyl)acetamide) Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 300 uM / Component: C-terminal RAGE / Isotopic labeling: [U-100% 13C; U-100% 15N] |
Sample conditions | Details: 10 mM potassium phosphate buffer, pH 7.0 / Ionic strength: 10 mM / Label: condition_1 / pH: 7 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz / Details: QCI HCN cryoprobe |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 | ||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 200 / Conformers submitted total number: 20 |