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Yorodumi- PDB-4z7g: Crystal structure of human IRE1 cytoplasmic kinase-RNase region - apo -
+Open data
-Basic information
Entry | Database: PDB / ID: 4z7g | ||||||
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Title | Crystal structure of human IRE1 cytoplasmic kinase-RNase region - apo | ||||||
Components | Serine/threonine-protein kinase/endoribonuclease IRE1 | ||||||
Keywords | TRANSFERASE / Kinase / RNase / Unfolded protein response | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å | ||||||
Authors | Bayliss, R. / Joshi, A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Oncotarget / Year: 2015 Title: Molecular mechanisms of human IRE1 activation through dimerization and ligand binding. Authors: Joshi, A. / Newbatt, Y. / McAndrew, P.C. / Stubbs, M. / Burke, R. / Richards, M.W. / Bhatia, C. / Caldwell, J.J. / McHardy, T. / Collins, I. / Bayliss, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4z7g.cif.gz | 317.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z7g.ent.gz | 259.5 KB | Display | PDB format |
PDBx/mmJSON format | 4z7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4z7g_validation.pdf.gz | 439.8 KB | Display | wwPDB validaton report |
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Full document | 4z7g_full_validation.pdf.gz | 450.8 KB | Display | |
Data in XML | 4z7g_validation.xml.gz | 26.7 KB | Display | |
Data in CIF | 4z7g_validation.cif.gz | 36.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z7/4z7g ftp://data.pdbj.org/pub/pdb/validation_reports/z7/4z7g | HTTPS FTP |
-Related structure data
Related structure data | 4z7hC 3p23S 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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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 47755.820 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ERN1, IRE1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: O75460, non-specific serine/threonine protein kinase, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.08 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: Apo-hIRE1 was crystallized by hanging-drop vapor diffusion by mixing IRE1 (at 2 mg/mL) with reservoir solution containing 18-20% PEG3350, 0.2 M sodium malonate and 0.1 Bis-Trispropane (pH 6.5) in a 1:1 ratio |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 27, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→85.33 Å / Num. obs: 32479 / % possible obs: 99.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 74.12 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 2.6→2.72 Å / Redundancy: 3.5 % / Rmerge(I) obs: 1.475 / Mean I/σ(I) obs: 0.8 / % possible all: 99.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3P23 Resolution: 2.6→85.33 Å / Cor.coef. Fo:Fc: 0.9305 / Cor.coef. Fo:Fc free: 0.9247 / SU R Cruickshank DPI: 0.449 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.408 / SU Rfree Blow DPI: 0.243 / SU Rfree Cruickshank DPI: 0.253
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Displacement parameters | Biso mean: 100.97 Å2
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Refine analyze | Luzzati coordinate error obs: 0.486 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.6→85.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.69 Å / Total num. of bins used: 16
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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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