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- PDB-6w3b: Structure of apo unphosphorylated IRE1 -

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Basic information

Entry
Database: PDB / ID: 6w3b
TitleStructure of apo unphosphorylated IRE1
ComponentsSerine/threonine-protein kinase/endoribonuclease IRE1
KeywordsTRANSFERASE / Kinase / UPR
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 / positive regulation of endoplasmic reticulum unfolded protein response / 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 / positive regulation of endoplasmic reticulum unfolded protein response / IRE1-RACK1-PP2A complex / platelet-derived growth factor receptor binding / nuclear inner membrane / endothelial cell proliferation / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / IRE1-mediated unfolded protein response / mRNA catabolic process / positive regulation of JUN kinase activity / 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 vascular associated smooth muscle cell proliferation / Hsp70 protein binding / RNA endonuclease activity / 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 phosphorylation / non-specific serine/threonine protein kinase / 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
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 / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily / Serine/threonine-protein kinase, active site ...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 / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / WD40/YVTN repeat-like-containing domain superfamily / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Serine/threonine-protein kinase/endoribonuclease IRE1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.57 Å
AuthorsWallweber, H. / Mortara, K. / Ferri, E. / Rudolph, J. / Wang, W.
CitationJournal: Nat Commun / Year: 2020
Title: Activation of the IRE1 RNase through remodeling of the kinase front pocket by ATP-competitive ligands.
Authors: Ferri, E. / Le Thomas, A. / Wallweber, H.A. / Day, E.S. / Walters, B.T. / Kaufman, S.E. / Braun, M.G. / Clark, K.R. / Beresini, M.H. / Mortara, K. / Chen, Y.A. / Canter, B. / Phung, W. / ...Authors: Ferri, E. / Le Thomas, A. / Wallweber, H.A. / Day, E.S. / Walters, B.T. / Kaufman, S.E. / Braun, M.G. / Clark, K.R. / Beresini, M.H. / Mortara, K. / Chen, Y.A. / Canter, B. / Phung, W. / Liu, P.S. / Lammens, A. / Ashkenazi, A. / Rudolph, J. / Wang, W.
History
DepositionMar 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 9, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)49,5611
Polymers49,5611
Non-polymers00
Water30617
1
A: Serine/threonine-protein kinase/endoribonuclease IRE1

A: Serine/threonine-protein kinase/endoribonuclease IRE1


Theoretical massNumber of molelcules
Total (without water)99,1232
Polymers99,1232
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_654-x+1,y,-z-1/21
Unit cell
Length a, b, c (Å)68.039, 167.588, 103.494
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 49561.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERN1, IRE1 / Cell line (production host): Sf9 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.98 Å3/Da / Density % sol: 58.67 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1 M Hepes pH 7.5, 42% PEG200, 1 M lithium chloride, 3% w/v 6-aminohexanoic acid

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 1, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.57→44.028 Å / Num. obs: 36280 / % possible obs: 99.8 % / Redundancy: 9.8 % / Biso Wilson estimate: 69.59 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.021 / Rrim(I) all: 0.067 / Net I/σ(I): 23.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.57-2.579101.15520112010.7370.3761.217298
11.853-44.02880.02718782340.9990.010.02960.9100

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Processing

Software
NameVersionClassification
PHENIX1.12-2829_finalrefinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HGI

5hgi


Resolution: 2.57→44.028 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 27.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2459 1851 5.1 %
Rwork0.2035 34429 -
obs0.2057 36280 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 177.69 Å2 / Biso mean: 78.6263 Å2 / Biso min: 41.04 Å2
Refinement stepCycle: final / Resolution: 2.57→44.028 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3204 0 0 17 3221
Biso mean---67.82 -
Num. residues----398
LS refinement shellResolution: 2.5702→2.6397 Å
RfactorNum. reflection% reflection
Rfree0.3441 --
Rwork0.3023 2664 -
obs--99.9 %
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)
10.85970.2980.63740.297-0.08190.8229-0.26160.02350.46060.0940.3266-0.1071-0.7352-0.476600.82560.1611-0.0150.58470.09930.818923.35541.606-23.263
21.7885-0.1762-0.01940.9426-0.15271.8044-0.0402-0.0067-0.03450.0451-0.0881-0.03890.0064-0.215-00.46030.026-0.06410.5358-0.01310.492414.7819.077-16.099
31.0874-0.71360.1791.8924-0.28011.4173-0.18280.0039-0.2-0.1605-0.0145-0.08290.3266-0.1828-00.6984-0.08360.15190.5704-0.07470.633221.443-10.445-22.59
40.1214-0.03870.03110.3681-0.36250.3288-0.11580.19230.19540.0139-0.0263-0.2126-0.0578-0.17450.00010.46380.02250.10250.49520.06090.717.3564.876-12.339
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 562:644 )A562 - 644
2X-RAY DIFFRACTION2( CHAIN A AND RESID 645:832 )A645 - 832
3X-RAY DIFFRACTION3( CHAIN A AND RESID 833:963 )A833 - 963
4X-RAY DIFFRACTION4( CHAIN A AND RESID 1001:1017 )A1001 - 1017

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