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- PDB-6w3a: Structure of unphosphorylated IRE1 in complex with G-7658 -

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Basic information

Entry
Database: PDB / ID: 6w3a
TitleStructure of unphosphorylated IRE1 in complex with G-7658
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 / 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
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. / 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
Similarity search - Domain/homology
Chem-SJM / Serine/threonine-protein kinase/endoribonuclease IRE1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.606 Å
AuthorsFerri, E. / Wang, W. / Joachim, R. / Mortara, K.
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 1.2Jun 16, 2021Group: Derived calculations / Category: pdbx_struct_assembly / pdbx_struct_assembly_gen
Revision 1.3Oct 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
B: Serine/threonine-protein kinase/endoribonuclease IRE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,1084
Polymers99,1232
Non-polymers9852
Water75742
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint1 kcal/mol
Surface area33280 Å2
Unit cell
Length a, b, c (Å)77.114, 82.387, 164.027
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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.: 2
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: Chemical ChemComp-SJM / ~{N}-[6-methyl-5-[3-[2-[[(3~{S})-piperidin-3-yl]amino]pyrimidin-4-yl]pyridin-2-yl]oxy-naphthalen-1-yl]but-2-ynamide


Mass: 492.572 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C29H28N6O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 0.2 M magnesium formate, 20 %w/v PEG 3350, and 1% CYMAL-1

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 31, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.606→82.013 Å / Num. obs: 25334 / % possible obs: 91.5 % / Redundancy: 6.7 % / Biso Wilson estimate: 46.77 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.061 / Rrim(I) all: 0.16 / Net I/σ(I): 10.4 / Num. measured all: 170557
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
2.606-2.83771.227887712670.7310.4941.3251.551
7.887-82.0136.30.03794712660.9990.0130.03335.996.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5HGI

5hgi


Resolution: 2.606→58.124 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 35.38 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2902 1331 5.26 %
Rwork0.2469 23977 -
obs0.2492 25308 77.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 447.06 Å2 / Biso mean: 69.8148 Å2 / Biso min: 10.17 Å2
Refinement stepCycle: final / Resolution: 2.606→58.124 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5594 0 76 42 5712
Biso mean--29.77 45.18 -
Num. residues----734
LS refinement shellResolution: 2.606→2.6991 Å
RfactorNum. reflection% reflection
Rfree0.3349 5 -
Rwork0.3206 190 -
obs--33.36 %
Refinement TLS params.Method: refined / Origin x: 96.4536 Å / Origin y: -8.1553 Å / Origin z: 31.5024 Å
111213212223313233
T-0.1713 Å2-0.1286 Å2-0.0966 Å2--0.5493 Å2-0.2809 Å2---0.1384 Å2
L1.1855 °2-0.4946 °20.2907 °2-1.3403 °2-0.2544 °2--0.1584 °2
S0.2435 Å °0.9255 Å °0.1089 Å °-0.2707 Å °-0.551 Å °-0.0988 Å °0.2642 Å °0.2888 Å °-0.202 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA562 - 964
2X-RAY DIFFRACTION1allB562 - 964
3X-RAY DIFFRACTION1allY1
4X-RAY DIFFRACTION1allZ2
5X-RAY DIFFRACTION1allS1 - 51

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