+Open data
-Basic information
Entry | Database: PDB / ID: 2l7u | ||||||||||||
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Title | Structure of CEL-PEP-RAGE V domain complex | ||||||||||||
Components |
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Keywords | ALLERGEN / V domain / Cleavage on pair of basic residues / Lipid-binding / Metal-binding / Phosphoprotein / Secreted | ||||||||||||
Function / homology | Function and homology information regulation of CD4-positive, alpha-beta T cell activation / advanced glycation end-product receptor activity / negative regulation of blood circulation / regulation of T cell mediated cytotoxicity / positive regulation of endothelin production / 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 / advanced glycation end-product receptor activity / negative regulation of blood circulation / regulation of T cell mediated cytotoxicity / positive regulation of endothelin production / 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 / cellular response to calcium ion starvation / transcytosis / laminin receptor activity / protein localization to membrane / positive regulation of monocyte chemotactic protein-1 production / positive regulation of heterotypic cell-cell adhesion / enterobactin binding / S100 protein binding / regulation of long-term synaptic potentiation / regulation of spontaneous synaptic transmission / negative regulation of mitochondrial depolarization / 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 / toxic substance binding / small molecule binding / positive regulation of chemokine production / cellular response to starvation / positive regulation of interleukin-12 production / positive regulation of interleukin-1 beta production / astrocyte activation / fatty acid binding / 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 / positive regulation of interleukin-6 production / transmembrane signaling receptor activity / neuron projection development / positive regulation of tumor necrosis factor production / pyridoxal phosphate binding / cell junction / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / regulation of inflammatory response / postsynapse / blood microparticle / molecular adaptor activity / learning or memory / cell surface receptor signaling pathway / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / inflammatory response / apical plasma membrane / positive regulation of protein phosphorylation / protein-containing complex binding / cell surface / protein-containing complex / DNA binding / extracellular region / identical protein binding / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) Bos taurus (cattle) | ||||||||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||||||||
Model details | lowest energy, model 1 | ||||||||||||
Authors | Xue, J. / Rai, V. / Schmidt, A. / Frolov, S. / Reverdatto, S. / Singer, D. / Chabierski, S. / Xie, J. / Burz, D. / Shekhtman, A. / Hoffman, R. | ||||||||||||
Citation | Journal: Structure / Year: 2011 Title: Advanced glycation end product recognition by the receptor for AGEs. Authors: Xue, J. / Rai, V. / Singer, D. / Chabierski, S. / Xie, J. / Reverdatto, S. / Burz, D.S. / Schmidt, A.M. / Hoffmann, R. / Shekhtman, A. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2l7u.cif.gz | 909 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2l7u.ent.gz | 765.2 KB | Display | PDB format |
PDBx/mmJSON format | 2l7u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/2l7u ftp://data.pdbj.org/pub/pdb/validation_reports/l7/2l7u | HTTPS FTP |
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-Related structure data
Similar structure data | |
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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: 11571.323 Da / Num. of mol.: 1 / Fragment: Ig-like V-type domain residues 23-125 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AGER, RAGE / Production host: Escherichia coli (E. coli) / References: UniProt: Q15109 |
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#2: Protein/peptide | Mass: 922.889 Da / Num. of mol.: 1 / Fragment: Sequence database residues 148-154 / Source method: obtained synthetically / Source: (synth.) Bos taurus (cattle) / References: UniProt: P02769 |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details |
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Sample |
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Sample conditions | Ionic strength: 130 / pH: 6.5 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 1 | ||||||||||||||||
NMR constraints | NOE constraints total: 1027 / NOE intraresidue total count: 328 / NOE long range total count: 0 / NOE medium range total count: 323 / NOE sequential total count: 375 / Protein chi angle constraints total count: 0 / Protein other angle constraints total count: 0 / Protein phi angle constraints total count: 79 / Protein psi angle constraints total count: 71 | ||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||
NMR ensemble | Average torsion angle constraint violation: 0.54 ° Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 30 / Conformers submitted total number: 25 / Maximum lower distance constraint violation: 0 Å / Maximum torsion angle constraint violation: 4 ° / Maximum upper distance constraint violation: 0.17 Å / Torsion angle constraint violation method: CYANA | ||||||||||||||||
NMR ensemble rms | Distance rms dev: 0.015 Å / Distance rms dev error: 0.005 Å |