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- PDB-4yzd: Crystal Structure of human phosphorylated IRE1alpha in complex wi... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4yzd | ||||||
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Title | Crystal Structure of human phosphorylated IRE1alpha in complex with ADP-Mg | ||||||
![]() | Serine/threonine-protein kinase/endoribonuclease IRE1 | ||||||
![]() | TRANSFERASE / active / ADP / complex / IRE1 | ||||||
Function / homology | ![]() peptidyl-serine trans-autophosphorylation / mRNA splicing, via endonucleolytic cleavage and ligation / AIP1-IRE1 complex / Ire1 complex / IRE1alpha activates chaperones / IRE1-TRAF2-ASK1 complex / insulin metabolic process / peptidyl-serine autophosphorylation / IRE1-RACK1-PP2A complex / platelet-derived growth factor receptor binding ...peptidyl-serine trans-autophosphorylation / mRNA splicing, via endonucleolytic cleavage and ligation / AIP1-IRE1 complex / Ire1 complex / IRE1alpha activates chaperones / IRE1-TRAF2-ASK1 complex / insulin metabolic process / peptidyl-serine autophosphorylation / IRE1-RACK1-PP2A complex / platelet-derived growth factor receptor binding / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / positive regulation of endoplasmic reticulum unfolded protein response / endothelial cell proliferation / nuclear inner membrane / IRE1-mediated unfolded protein response / mRNA catabolic process / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to vascular endothelial growth factor stimulus / cellular response to unfolded protein / regulation of macroautophagy / positive regulation of JUN kinase activity / positive regulation of vascular associated smooth muscle cell proliferation / RNA endonuclease activity / Hsp70 protein binding / response to endoplasmic reticulum stress / positive regulation of RNA splicing / cellular response to glucose stimulus / Hsp90 protein binding / ADP binding / cellular response to hydrogen peroxide / unfolded protein binding / protein autophosphorylation / non-specific serine/threonine protein kinase / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / enzyme binding / magnesium ion binding / endoplasmic reticulum / protein homodimerization activity / mitochondrion / ATP binding / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Concha, N.O. | ||||||
![]() | ![]() Title: Long-Range Inhibitor-Induced Conformational Regulation of Human IRE1 alpha Endoribonuclease Activity. Authors: Concha, N.O. / Smallwood, A. / Bonnette, W. / Totoritis, R. / Zhang, G. / Federowicz, K. / Yang, J. / Qi, H. / Chen, S. / Campobasso, N. / Choudhry, A.E. / Shuster, L.E. / Evans, K.A. / ...Authors: Concha, N.O. / Smallwood, A. / Bonnette, W. / Totoritis, R. / Zhang, G. / Federowicz, K. / Yang, J. / Qi, H. / Chen, S. / Campobasso, N. / Choudhry, A.E. / Shuster, L.E. / Evans, K.A. / Ralph, J. / Sweitzer, S. / Heerding, D.A. / Buser, C.A. / Su, D.S. / DeYoung, M.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 409.4 KB | Display | ![]() |
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PDB format | ![]() | 332.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 40.6 KB | Display | |
Data in CIF | ![]() | 54.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4yz9C ![]() 4yzcC ![]() 3p23S C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 46610.570 Da / Num. of mol.: 3 / Fragment: UNP residues 562-966 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: O75460, non-specific serine/threonine protein kinase, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters #2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.13 Å3/Da / Density % sol: 60.73 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: The crystals of pIRE1a with Mg2+-ADP were grown by mixing 2 ul protein solution (10 mg/ml pIRE1a (547-977) in 50 mM Hepes, pH 7.5, 200 mM NaCl, 5 mM DTT, 1 mM EDTA, 1 mM ADP (100mM ADP stock ...Details: The crystals of pIRE1a with Mg2+-ADP were grown by mixing 2 ul protein solution (10 mg/ml pIRE1a (547-977) in 50 mM Hepes, pH 7.5, 200 mM NaCl, 5 mM DTT, 1 mM EDTA, 1 mM ADP (100mM ADP stock was ~ pH 7.0), 1 mM MgCl2) with 2 ul reservoir solution (16 % PEG 3350, 200 mM Na+ Malonate pH 6.0) in sitting drops at room temperature. Seeding was used to initiate crystal growth. Crystals appeared the next day and grew to full size in 3 weeks. For data collection, the crystals were frozen in a solution of 20% ethylene glycol, 22% PEG 3350, 200 mM Na+ Malonate pH 6.0 and added to the protein drop before mounting the crystals on the loop. |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Sep 27, 2011 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.102→45.643 Å / Num. obs: 30914 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 84.26 Å2 / Rmerge(I) obs: 0.087 / Χ2: 1.055 / Net I/av σ(I): 15.225 / Net I/σ(I): 9.9 / Num. measured all: 118513 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3P23 Resolution: 3.102→45.643 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.11 / 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 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.102→45.643 Å
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Refine LS restraints |
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LS refinement shell |
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