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- PDB-5hgi: Crystal structure of apo human IRE1 alpha -

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Basic information

Entry
Database: PDB / ID: 5hgi
TitleCrystal structure of apo human IRE1 alpha
ComponentsSerine/threonine-protein kinase/endoribonuclease IRE1
KeywordsTransferase/Oxidoreductase / Ser/Thr Protein kinase / RNase / Transferase-Oxidoreductase complex
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
KEN domain / Serine/threonine-protein kinase/endoribonuclease IRE1/2-like / KEN domain / KEN domain superfamily / Ribonuclease 2-5A / KEN domain profile. / domain in protein kinases, N-glycanases and other nuclear proteins / de novo design (two linked rop proteins) / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat ...KEN domain / Serine/threonine-protein kinase/endoribonuclease IRE1/2-like / KEN domain / KEN domain superfamily / Ribonuclease 2-5A / KEN domain profile. / domain in protein kinases, N-glycanases and other nuclear proteins / de novo design (two linked rop proteins) / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / : / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / Serine/threonine-protein kinase/endoribonuclease IRE1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.584 Å
AuthorsFeldman, H.C. / Tong, M. / Wang, L. / Meza-Acevedo, R. / Gobillot, T.A. / Gliedt, J.M. / Hari, S.B. / Mitra, A.K. / Backes, B.J. / Papa, F.R. ...Feldman, H.C. / Tong, M. / Wang, L. / Meza-Acevedo, R. / Gobillot, T.A. / Gliedt, J.M. / Hari, S.B. / Mitra, A.K. / Backes, B.J. / Papa, F.R. / Seeliger, M.A. / Maly, D.J.
CitationJournal: Acs Chem.Biol. / Year: 2016
Title: Structural and Functional Analysis of the Allosteric Inhibition of IRE1 alpha with ATP-Competitive Ligands.
Authors: Feldman, H.C. / Tong, M. / Wang, L. / Meza-Acevedo, R. / Gobillot, T.A. / Lebedev, I. / Gliedt, M.J. / Hari, S.B. / Mitra, A.K. / Backes, B.J. / Papa, F.R. / Seeliger, M.A. / Maly, D.J.
History
DepositionJan 8, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 22, 2016Group: Database references
Revision 1.2Aug 31, 2016Group: Database references
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Serine/threonine-protein kinase/endoribonuclease IRE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,62115
Polymers49,3031
Non-polymers1,31714
Water18010
1
A: Serine/threonine-protein kinase/endoribonuclease IRE1
hetero molecules

A: Serine/threonine-protein kinase/endoribonuclease IRE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,24130
Polymers98,6072
Non-polymers2,63528
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area6410 Å2
ΔGint-347 kcal/mol
Surface area36300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.039, 169.196, 104.138
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-1003-

CS

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Serine/threonine-protein kinase/endoribonuclease IRE1 / Endoplasmic reticulum-to-nucleus signaling 1 / Inositol-requiring protein 1 / hIRE1p / Ire1-alpha / IRE1a


Mass: 49303.266 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: The sequence begins from G547-L977 / Source: (gene. exp.) Homo sapiens (human) / Gene: ERN1, IRE1 / Plasmid: Bac-to-Bac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): SF9
References: UniProt: O75460, non-specific serine/threonine protein kinase, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters

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Non-polymers , 7 types, 24 molecules

#2: Chemical
ChemComp-CS / CESIUM ION


Mass: 132.905 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cs
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-DTT / 2,3-DIHYDROXY-1,4-DITHIOBUTANE / 1,4-DITHIOTHREITOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O2S2
#6: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6OS
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.04 Å3/Da / Density % sol: 59.53 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 9
Details: Crystallization buffer: 25 mM Bis-Tris Propane pH 9, 39% PEG 200, 250 mM CsCl, 10% glycerol. After setting up the crystallization drop with the mother liquor in a 1:1 uL ratio using the ...Details: Crystallization buffer: 25 mM Bis-Tris Propane pH 9, 39% PEG 200, 250 mM CsCl, 10% glycerol. After setting up the crystallization drop with the mother liquor in a 1:1 uL ratio using the liquid bridge method, 2-mercaptoethanol was added to the reservoir at a final concentration of 143 mM. Crystals were cryoprotected in the same reservoir crystallization buffer.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 9, 2014
RadiationMonochromator: Double flat Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.58→84.6 Å / Num. obs: 19194 / % possible obs: 99.72 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.05432 / Net I/σ(I): 20.47
Reflection shellResolution: 2.584→2.676 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.8543 / Mean I/σ(I) obs: 2.37 / % possible all: 99.68

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P23

3p23


Resolution: 2.584→44.343 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2475 986 5.14 %RANDOM
Rwork0.2126 ---
obs0.2145 19188 99.69 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.584→44.343 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2962 0 38 10 3010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043054
X-RAY DIFFRACTIONf_angle_d0.6414131
X-RAY DIFFRACTIONf_dihedral_angle_d16.3811819
X-RAY DIFFRACTIONf_chiral_restr0.043457
X-RAY DIFFRACTIONf_plane_restr0.004536
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.584-2.72020.33731490.27952540X-RAY DIFFRACTION100
2.7202-2.89060.32781450.27922557X-RAY DIFFRACTION100
2.8906-3.11380.32721470.27322576X-RAY DIFFRACTION100
3.1138-3.4270.23071360.25162579X-RAY DIFFRACTION100
3.427-3.92260.28741260.20632611X-RAY DIFFRACTION100
3.9226-4.94110.21911410.18592628X-RAY DIFFRACTION100
4.9411-44.34950.21491420.19812711X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.44160.2755-0.15780.32760.05580.172-0.41050.3476-1.5790.36380.2616-0.06061.13950.40810.00091.04250.14210.17910.9326-0.15641.1914-22.7875-42.2157-24.4421
22.0505-0.23110.26812.41290.71322.2541-0.12960.1273-0.1870.1745-0.04020.17680.17840.18320.00010.56110.02680.10610.61540.03360.6001-16.2995-20.6384-17.2681
32.2176-0.92150.48952.63980.76311.448-0.29360.1140.2704-0.5062-0.12150.0471-0.37220.12050.00050.8325-0.043-0.20280.62110.12230.6941-21.478310.3364-21.9897
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 562 through 619 )
2X-RAY DIFFRACTION2chain 'A' and (resid 620 through 834 )
3X-RAY DIFFRACTION3chain 'A' and (resid 835 through 964 )

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