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Yorodumi- PDB-4p2y: Crystal structure of the human RAGE ectodomain (fragment VC1C2) i... -
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-Basic information
Entry | Database: PDB / ID: 4p2y | ||||||
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Title | Crystal structure of the human RAGE ectodomain (fragment VC1C2) in complex with mouse S100A6 | ||||||
Components |
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Keywords | SIGNALING PROTEIN / signaling complex / pattern recognition receptor / dimerization / EF-hand calcium binding protein | ||||||
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 / extrinsic component of cytoplasmic side of plasma membrane / 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 / 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 / positive regulation of interleukin-6 production / cellular response to amyloid-beta / transmembrane signaling receptor activity / calcium-dependent protein binding / positive regulation of tumor necrosis factor production / neuron projection development / cell junction / nuclear envelope / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / regulation of inflammatory response / collagen-containing extracellular matrix / postsynapse / molecular adaptor activity / positive regulation of ERK1 and ERK2 cascade / learning or memory / cell surface receptor signaling pathway / response to hypoxia / inflammatory response / positive regulation of protein phosphorylation / apical plasma membrane / calcium ion binding / protein-containing complex binding / perinuclear region of cytoplasm / cell surface / protein homodimerization activity / zinc ion binding / extracellular region / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å | ||||||
Authors | Yatime, L. / Andersen, G.R. | ||||||
Citation | Journal: Structure / Year: 2016 Title: The Structure of the RAGE:S100A6 Complex Reveals a Unique Mode of Homodimerization for S100 Proteins. Authors: Yatime, L. / Betzer, C. / Jensen, R.K. / Mortensen, S. / Jensen, P.H. / Andersen, G.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p2y.cif.gz | 177.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p2y.ent.gz | 138.1 KB | Display | PDB format |
PDBx/mmJSON format | 4p2y.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p2/4p2y ftp://data.pdbj.org/pub/pdb/validation_reports/p2/4p2y | HTTPS FTP |
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-Related structure data
Related structure data | 4ybhC 1k96S 4lp5S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Details | The biological assembly is a heterotetramer generated from the heterodimer in the asymmetric unit by the operation: -x, y, -z. |
-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 32680.297 Da / Num. of mol.: 1 Fragment: V, C1 and C2 domains (VC1C2 module), full-length ectodomain, UNP residues 23-323 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: AGER, RAGE / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): Shuffle T7 Express / References: UniProt: Q15109 |
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#2: Protein | Mass: 10192.740 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: S100a6, Cacy / Plasmid: pETM11 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P14069 |
-Non-polymers , 5 types, 207 molecules
#3: Chemical | ChemComp-ZN / #4: Chemical | ChemComp-CL / #5: Chemical | ChemComp-ACT / #6: Chemical | #7: 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: 3.61 Å3/Da / Density % sol: 65.9 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.2 M Zn acetate, 0.1 M Na cacodylate pH 6.5, 10% isopropanol |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.041 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Feb 19, 2012 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.041 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→35 Å / Num. obs: 27554 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Redundancy: 7 % / Biso Wilson estimate: 44.57 Å2 / Rmerge F obs: 0.998 / Rmerge(I) obs: 0.074 / Rrim(I) all: 0.08 / Χ2: 1.032 / Net I/σ(I): 15.56 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LP5, 1K96 Resolution: 2.3→27.242 Å / FOM work R set: 0.8478 / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.97 / Stereochemistry target values: ML
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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 max: 165.91 Å2 / Biso mean: 52.48 Å2 / Biso min: 17.59 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.3→27.242 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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