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- PDB-6shc: Crystal structure of human IRE1 luminal domain Q105C -

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Basic information

Entry
Database: PDB / ID: 6shc
TitleCrystal structure of human IRE1 luminal domain Q105C
ComponentsSerine/threonine-protein kinase/endoribonuclease IRE1
KeywordsSIGNALING PROTEIN / IRE1 / unfolded protein response / ER stress / protein quality control
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 / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters ...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 / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / platelet-derived growth factor receptor binding / 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 / regulation of macroautophagy / cellular response to vascular endothelial growth factor stimulus / cellular response to unfolded protein / positive regulation of JUN kinase activity / RNA endonuclease activity / positive regulation of vascular associated smooth muscle cell proliferation / Hsp70 protein binding / response to endoplasmic reticulum stress / positive regulation of RNA splicing / ADP binding / cellular response to glucose stimulus / Hsp90 protein 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
Serine/threonine-protein kinase/endoribonuclease IRE1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.55 Å
AuthorsYan, Y. / Ron, D.
Funding support United Kingdom, 2items
OrganizationGrant numberCountry
Wellcome TrustWellcome 200848/Z/16/Z United Kingdom
Wellcome TrustWellcome 100140 United Kingdom
CitationJournal: Elife / Year: 2019
Title: Unstructured regions in IRE1 alpha specify BiP-mediated destabilisation of the luminal domain dimer and repression of the UPR.
Authors: Amin-Wetzel, N. / Neidhardt, L. / Yan, Y. / Mayer, M.P. / Ron, D.
History
DepositionAug 6, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)41,0061
Polymers41,0061
Non-polymers00
Water0
1
A: Serine/threonine-protein kinase/endoribonuclease IRE1

A: Serine/threonine-protein kinase/endoribonuclease IRE1


Theoretical massNumber of molelcules
Total (without water)82,0132
Polymers82,0132
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area1230 Å2
ΔGint-12 kcal/mol
Surface area26320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)182.772, 182.772, 68.449
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z+1/2
#9: y,x,-z+2/3
#10: -y,-x,-z+1/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+5/6

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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: 41006.367 Da / Num. of mol.: 1 / Mutation: Q105C, C109S, C148S, C332S
Source method: isolated from a genetically manipulated source
Details: Four mutations has been introduced into the construct: Q105C, C109S, C148S, C332S.
Source: (gene. exp.) Homo sapiens (human) / Gene: ERN1, IRE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Origami B
References: UniProt: O75460, non-specific serine/threonine protein kinase, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters

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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: 5.34 Å3/Da / Density % sol: 76.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5 / Details: 9% MPD, 0.1M Hepes pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.916 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.916 Å / Relative weight: 1
ReflectionResolution: 3.55→91.39 Å / Num. obs: 8590 / % possible obs: 100 % / Redundancy: 19.3 % / Biso Wilson estimate: 143.03 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.18 / Rpim(I) all: 0.058 / Rrim(I) all: 0.189 / Net I/σ(I): 11.7
Reflection shellResolution: 3.55→3.89 Å / Rmerge(I) obs: 2.242 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 1996 / CC1/2: 0.797 / Rpim(I) all: 0.719 / Rrim(I) all: 2.355

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2hz6

2hz6


Resolution: 3.55→54.79 Å / SU ML: 0.6921 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 42.6377
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3318 443 5.18 %
Rwork0.3233 8111 -
obs0.3239 8554 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 126.62 Å2
Refinement stepCycle: LAST / Resolution: 3.55→54.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1784 0 0 0 1784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00271830
X-RAY DIFFRACTIONf_angle_d0.60592538
X-RAY DIFFRACTIONf_chiral_restr0.0425307
X-RAY DIFFRACTIONf_plane_restr0.0055331
X-RAY DIFFRACTIONf_dihedral_angle_d2.65971044
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.55-4.060.38621410.36462639X-RAY DIFFRACTION99.82
4.06-5.120.32961350.2942660X-RAY DIFFRACTION99.79
5.12-54.790.32291670.32832812X-RAY DIFFRACTION99.83

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