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Yorodumi- PDB-6xq9: Receptor for Advanced Glycation End Products VC1 domain in comple... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6xq9 | ||||||
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Title | Receptor for Advanced Glycation End Products VC1 domain in complex with Fragments 1 & 13 | ||||||
Components | Advanced glycosylation end product-specific receptor | ||||||
Keywords | SIGNALING PROTEIN / RAGE / IG-like domain / receptor / Advanced Glycation End Products | ||||||
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 | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Salay, L.E. / Kozlyuk, N. / Gilston, B.A. / Gogliotti, R.D. / Christov, P.P. / Kim, K. / Ovee, M. / Waterson, A.G. / Chazin, W.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Proteins / Year: 2021 Title: A fragment-based approach to discovery of Receptor for Advanced Glycation End products inhibitors. Authors: Kozlyuk, N. / Gilston, B.A. / Salay, L.E. / Gogliotti, R.D. / Christov, P.P. / Kim, K. / Ovee, M. / Waterson, A.G. / Chazin, W.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6xq9.cif.gz | 199.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6xq9.ent.gz | 140.8 KB | Display | PDB format |
PDBx/mmJSON format | 6xq9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6xq9_validation.pdf.gz | 2 MB | Display | wwPDB validaton report |
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Full document | 6xq9_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 6xq9_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 6xq9_validation.cif.gz | 26.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xq/6xq9 ftp://data.pdbj.org/pub/pdb/validation_reports/xq/6xq9 | HTTPS FTP |
-Related structure data
Related structure data | 6xq1C 6xq3C 6xq5C 6xq6C 6xq7C 6xq8C 7lmlC 7lmwC 4lp4S 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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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: givenMatrix: (0.502026601379, -0.864851981748, 0.000584101949087), (-0.864848899824, -0.502026443228, -0.00241469939158), (0.00238159217812, 0.000707083400855, -0.999996914021)Vector: ...NCS oper: (Code: given Matrix: (0.502026601379, -0.864851981748, 0.000584101949087), Vector: |
-Components
#1: Protein | Mass: 23131.494 Da / Num. of mol.: 2 / Fragment: VC1 domain, resdues 23-231 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 #2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-V6S / #4: Chemical | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 3.32 Å3/Da / Density % sol: 63 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 2.5 M NaOAc (pH 7.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 24, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→50 Å / Num. obs: 52826 / % possible obs: 99.73 % / Redundancy: 5.7 % / Biso Wilson estimate: 31.43 Å2 / Rpim(I) all: 0.019 / Rrim(I) all: 0.063 / Net I/av σ(I): 29.94 / Net I/σ(I): 29.9 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 18.38 / Num. unique obs: 5258 / Rpim(I) all: 0.05 / Rrim(I) all: 0.166 / % possible all: 98.43 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LP4 Resolution: 2.3→34.06 Å / SU ML: 0.2929 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 26.6772 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.9 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→34.06 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.573947506322 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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