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Yorodumi- PDB-4oi7: RAGE recognizes nucleic acids and promotes inflammatory responses... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4oi7 | |||||||||
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Title | RAGE recognizes nucleic acids and promotes inflammatory responses to DNA | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN / SIGNALING PROTEIN/DNA / protein-DNA complex / Ig fold / DNA binding / extracellular receptor / SIGNALING PROTEIN-DNA complex | |||||||||
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 dendritic cell differentiation / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process ...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 dendritic cell differentiation / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / regulation of p38MAPK cascade / regulation of non-canonical NF-kappaB signal transduction / scavenger receptor activity / induction of positive chemotaxis / transcytosis / laminin receptor activity / protein localization to membrane / positive regulation of monocyte chemotactic protein-1 production / S100 protein binding / regulation of long-term synaptic potentiation / regulation of spontaneous synaptic transmission / positive regulation of heterotypic cell-cell adhesion / positive regulation of p38MAPK cascade / negative regulation of interleukin-10 production / positive regulation of activated T cell proliferation / TRAF6 mediated NF-kB activation / negative regulation of long-term synaptic potentiation / response to amyloid-beta / Advanced glycosylation endproduct receptor signaling / transport across blood-brain barrier / positive regulation of chemokine production / positive regulation of interleukin-12 production / positive regulation of interleukin-1 beta production / astrocyte activation / microglial cell activation / positive regulation of JNK cascade / regulation of synaptic plasticity / TAK1-dependent IKK and NF-kappa-B activation / fibrillar center / response to wounding / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / neuron projection development / cellular response to amyloid-beta / transmembrane signaling receptor activity / positive regulation of tumor necrosis factor production / signaling receptor activity / cell junction / amyloid-beta binding / positive regulation of NF-kappaB transcription factor activity / regulation of inflammatory response / postsynapse / positive regulation of ERK1 and ERK2 cascade / response to hypoxia / learning or memory / cell surface receptor signaling pathway / molecular adaptor activity / 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 | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.104 Å | |||||||||
Authors | Jin, T. / Jiang, J. / Xiao, T. | |||||||||
Citation | Journal: J.Exp.Med. / Year: 2013 Title: RAGE is a nucleic acid receptor that promotes inflammatory responses to DNA. Authors: Sirois, C.M. / Jin, T. / Miller, A.L. / Bertheloot, D. / Nakamura, H. / Horvath, G.L. / Mian, A. / Jiang, J. / Schrum, J. / Bossaller, L. / Pelka, K. / Garbi, N. / Brewah, Y. / Tian, J. / ...Authors: Sirois, C.M. / Jin, T. / Miller, A.L. / Bertheloot, D. / Nakamura, H. / Horvath, G.L. / Mian, A. / Jiang, J. / Schrum, J. / Bossaller, L. / Pelka, K. / Garbi, N. / Brewah, Y. / Tian, J. / Chang, C. / Chowdhury, P.S. / Sims, G.P. / Kolbeck, R. / Coyle, A.J. / Humbles, A.A. / Xiao, T.S. / Latz, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4oi7.cif.gz | 204.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4oi7.ent.gz | 161.4 KB | Display | PDB format |
PDBx/mmJSON format | 4oi7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/oi/4oi7 ftp://data.pdbj.org/pub/pdb/validation_reports/oi/4oi7 | HTTPS FTP |
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-Related structure data
Related structure data | 4oi8C 3o3uS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 24195.580 Da / Num. of mol.: 2 / Fragment: UNP residues 23-237 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AGER, RAGE / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q15109 #2: DNA chain | | Mass: 6761.380 Da / Num. of mol.: 1 / Source method: obtained synthetically #3: DNA chain | | Mass: 6743.352 Da / Num. of mol.: 1 / Source method: obtained synthetically #4: Chemical | ChemComp-EDO / #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.18 Å3/Da / Density % sol: 61.28 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: 12% PEG6000, 0.1 M Tris-HCl, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03 Å |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 22, 2010 |
Radiation | Monochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03 Å / Relative weight: 1 |
Reflection | Resolution: 3.1→50 Å / Num. all: 13957 / Num. obs: 13817 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Rmerge(I) obs: 0.14 |
Reflection shell | Resolution: 3.1→3.15 Å / Redundancy: 6 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 1.97 / Num. unique all: 575 / % possible all: 85.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3O3U Resolution: 3.104→43.138 Å / σ(F): 1.38 / Phase error: 26.77 / Stereochemistry target values: TWIN_LSQ_F
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.104→43.138 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 38.0286 Å / Origin y: -22.2532 Å / Origin z: -12.1861 Å
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Refinement TLS group |
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