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- PDB-4pl4: Crystal structure of murine IRE1 in complex with OICR464 inhibitor -

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Basic information

Entry
Database: PDB / ID: 4pl4
TitleCrystal structure of murine IRE1 in complex with OICR464 inhibitor
ComponentsSerine/threonine-protein kinase/endoribonuclease IRE1
KeywordsTRANSFERASE / HYDROLASE/INHIBITOR / Schiff base / hydroxy aryl aldehydes (HAA) / inhibitor complex / unfolded protein response / endoribonuclease / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


IRE1alpha activates chaperones / mRNA splicing, via endonucleolytic cleavage and ligation / AIP1-IRE1 complex / IRE1-TRAF2-ASK1 complex / positive regulation of ERAD pathway / insulin metabolic process / positive regulation of endoplasmic reticulum unfolded protein response / IRE1-RACK1-PP2A complex / platelet-derived growth factor receptor binding / nuclear inner membrane ...IRE1alpha activates chaperones / mRNA splicing, via endonucleolytic cleavage and ligation / AIP1-IRE1 complex / IRE1-TRAF2-ASK1 complex / positive regulation of ERAD pathway / 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 / positive regulation of JUN kinase activity / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / cellular response to vascular endothelial growth factor stimulus / endoplasmic reticulum unfolded protein response / positive regulation of vascular associated smooth muscle cell proliferation / Hsp70 protein binding / RNA endonuclease activity / positive regulation of RNA splicing / cellular response to glucose stimulus / Hsp90 protein binding / ADP binding / cellular response to hydrogen peroxide / protein autophosphorylation / endonuclease activity / protein phosphorylation / non-specific serine/threonine protein kinase / negative regulation of translation / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / enzyme binding / magnesium ion binding / protein homodimerization activity / mitochondrion / ATP binding
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 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / 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 / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-31K / ADENOSINE-5'-DIPHOSPHATE / Serine/threonine-protein kinase/endoribonuclease IRE1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsSanches, M. / Duffy, N. / Talukdar, M. / Thevakumaran, N. / Chiovitti, D. / Al-awar, R. / Patterson, J.B. / Sicheri, F.
Funding support Canada, United States, 3items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)MOP 84370 Canada
Multiple Myeloma Research Foundation Biotech Investment Award United States
Canadian Cancer Society Canada
CitationJournal: Nat Commun / Year: 2014
Title: Structure and mechanism of action of the hydroxy-aryl-aldehyde class of IRE1 endoribonuclease inhibitors.
Authors: Sanches, M. / Duffy, N.M. / Talukdar, M. / Thevakumaran, N. / Chiovitti, D. / Canny, M.D. / Lee, K. / Kurinov, I. / Uehling, D. / Al-Awar, R. / Poda, G. / Prakesch, M. / Wilson, B. / Tam, V. ...Authors: Sanches, M. / Duffy, N.M. / Talukdar, M. / Thevakumaran, N. / Chiovitti, D. / Canny, M.D. / Lee, K. / Kurinov, I. / Uehling, D. / Al-Awar, R. / Poda, G. / Prakesch, M. / Wilson, B. / Tam, V. / Schweitzer, C. / Toro, A. / Lucas, J.L. / Vuga, D. / Lehmann, L. / Durocher, D. / Zeng, Q. / Patterson, J.B. / Sicheri, F.
History
DepositionMay 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Derived calculations / Other ...Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: entity_src_gen / pdbx_database_status ...entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_oper_list / software / struct_keywords
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible ..._entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _software.classification / _struct_keywords.text
Revision 1.3Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 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 / refine_hist / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn_type.id
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
C: Serine/threonine-protein kinase/endoribonuclease IRE1
D: Serine/threonine-protein kinase/endoribonuclease IRE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)204,63814
Polymers201,3264
Non-polymers3,31310
Water00
1
A: Serine/threonine-protein kinase/endoribonuclease IRE1
B: Serine/threonine-protein kinase/endoribonuclease IRE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,0738
Polymers100,6632
Non-polymers2,4106
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Serine/threonine-protein kinase/endoribonuclease IRE1
D: Serine/threonine-protein kinase/endoribonuclease IRE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,5666
Polymers100,6632
Non-polymers9034
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)319.110, 62.310, 141.330
Angle α, β, γ (deg.)90.000, 99.570, 90.000
Int Tables number5
Space group name H-MC121
Detailsbiological unit is the same as asym.

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Components

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


Mass: 50331.383 Da / Num. of mol.: 4 / Fragment: UNP residues 550-977
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ern1, Ire1 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9EQY0, non-specific serine/threonine protein kinase, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-31K / 2-methoxy-6-methyl-4-(4-methyl-3,4-dihydro-2H-1,4-benzoxazin-7-yl)phenol


Mass: 285.338 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H19NO3
#3: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-PEU / 2,5,8,11,14,17,20,23,26,29,32,35,38,41,44,47,50,53,56,59,62,65,68,71,74,77,80-HEPTACOSAOXADOOCTACONTAN-82-OL / PEG 8000


Mass: 1221.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C55H112O28 / Comment: precipitant*YM
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
Has protein modificationY
Nonpolymer detailsTHE 31K LIGAND REPRESENTS THE FINAL BOUND PRODUCT. THE STARTING MATERIAL FOR 31K LIGAND IS 2- ...THE 31K LIGAND REPRESENTS THE FINAL BOUND PRODUCT. THE STARTING MATERIAL FOR 31K LIGAND IS 2-HYDROXY-3-METHOXY-5-(4-METHYL-3,4-DIHYDRO-2H-1,4-BENZOXAZIN-7-YL)BENZALDEHYDE. ALDEHYDE IS ELIMINATED THROUGH THE FORMATION OF A SCHIFF-BASE WITH ONE OF THE PROTEIN'S LYSINE RESIDUES.

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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: 3.44 Å3/Da / Density % sol: 64.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M HEPES, 12% PEG8000, 8% ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97919 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 4, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97919 Å / Relative weight: 1
ReflectionResolution: 3→46.6 Å / Num. obs: 53692 / % possible obs: 96.2 % / Redundancy: 2.25 % / Biso Wilson estimate: 60.47 Å2 / Net I/σ(I): 11.08
Reflection shellResolution: 3→3.18 Å / Redundancy: 2.24 % / Mean I/σ(I) obs: 1.33 / % possible all: 96.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation5.29 Å46.7 Å
Translation5.29 Å46.7 Å

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: dev_1175)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PL3

4pl3


Resolution: 3→46.599 Å / FOM work R set: 0.7555 / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 30.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2759 2015 5.02 %
Rwork0.21 38116 -
obs0.2134 40131 72.14 %
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 235 Å2 / Biso mean: 86.73 Å2 / Biso min: 19.1 Å2
Refinement stepCycle: final / Resolution: 3→46.599 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12332 0 152 0 12484
Biso mean--69.95 --
Num. residues----1530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01212807
X-RAY DIFFRACTIONf_angle_d1.31717329
X-RAY DIFFRACTIONf_chiral_restr0.0911871
X-RAY DIFFRACTIONf_plane_restr0.0052207
X-RAY DIFFRACTIONf_dihedral_angle_d18.0664734
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0003-3.07540.4841460.38869774319
3.0754-3.15850.398770.30631161123832
3.1585-3.25140.4293770.3111588166542
3.2514-3.35630.33061010.26841937203852
3.3563-3.47620.30381130.27122235234859
3.4762-3.61540.33311320.25162601273369
3.6154-3.77990.31451500.23532935308578
3.7799-3.9790.25581520.21543348350089
3.979-4.22820.31282110.20183615382697
4.2282-4.55440.25631910.18113672386397
4.5544-5.01220.25131940.18033608380296
5.0122-5.73640.2662010.20153618381995
5.7364-7.22290.29351770.21183585376293
7.2229-46.60420.20771930.18333516370989
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)
10.6743-0.35580.31250.3999-0.35920.8472-0.0129-0.3224-0.00190.1251-0.205-0.2988-0.05160.50030.14970.477-0.1422-0.12460.86930.39660.457836.2928-11.425130.4124
21.7496-0.3507-0.25240.7599-0.15641.1166-0.0040.05810.21130.1359-0.2062-0.1038-0.22920.3405-0.0030.35280.0263-0.10340.20720.09790.214616.5114-2.822214.5244
31.56150.1871-0.31871.87710.04211.641-0.1178-0.1151-0.05870.3033-0.06650.2884-0.1938-0.01670.04650.40240.1194-0.04760.27150.00050.3449-5.7349-7.627815.0939
40.30070.0368-0.07290.2898-0.31270.420.02320.41380.3049-0.15710.29730.48250.0011-0.57470.08730.44310.1152-0.03680.85180.52080.695633.6333-23.019461.1161
51.10520.26510.06280.9716-0.19730.59340.1478-0.0850.19880.30310.0881-0.0545-0.208-0.11320.01190.35740.0650.09480.11010.10010.410853.9566-21.592978.9668
61.8627-0.3506-0.73011.57960.26481.03150.2664-0.39440.00110.3992-0.0682-0.3051-0.15920.18990.11610.4588-0.03180.06180.25540.17540.581374.5237-17.275177.1329
70.82320.2605-0.05570.7386-0.43570.85230.04030.14320.0445-0.18020.02820.18270.1552-0.1788-0.10210.3791-0.111-0.130.91770.37460.50225.309622.292267.7452
81.01160.3177-0.05981.6509-1.71041.8497-0.03520.25260.1951-0.17760.06490.3212-0.2491-0.23220.0180.41770.0722-0.00930.8390.30230.62286.555323.370877.1479
91.52150.2530.29582.2164-0.19441.8564-0.00540.20520.0953-0.15070.00070.29060.1168-0.23960.01940.3401-0.1683-0.06220.55950.12810.48517.436913.270981.9483
100.01080.02880.06950.1079-0.052.3760.00140.3876-0.0779-0.25380.1002-0.10820.0942-0.02880.01630.4166-0.1151-0.13890.56690.21470.622317.230417.099872.4239
111.51110.6623-0.79961.1946-0.74850.8181-0.13040.0256-0.0989-0.048-0.0639-0.0670.13640.0460.00880.3501-0.14240.00980.34740.19250.283822.023110.094489.4898
120.19660.48080.25462.96120.42220.5635-0.00650.0135-0.5565-0.1052-0.022-0.00570.44740.153-0.04910.6364-0.08970.13370.47920.17940.659814.0075-10.4966106.6427
131.12090.1024-0.33120.7317-0.04280.8493-0.0981-0.0631-0.0879-0.0343-0.1496-0.07690.3131-0.02510.03030.4821-0.22880.10310.63110.2440.515110.3351-4.1223112.4409
140.76120.09340.24390.2875-0.11260.66650.0310.0342-0.15170.0786-0.0515-0.29160.0610.227-0.0570.3332-0.0679-0.12541.13930.30740.71744.215-10.2402157.5301
152.651-0.4644-0.13510.48170.16351.4104-0.0415-0.06790.1283-0.01840.0434-0.1652-0.04920.17390.03090.349-0.1851-0.04451.21310.27990.736442.6122-1.8916140.8947
160.5859-0.0035-0.05680.73070.24320.9539-0.1430.087-0.0524-0.44670.0704-0.36390.12350.48560.02620.5317-0.12340.06841.05350.35860.620433.3841-7.3103126.8453
170.68350.5514-0.37211.3301-0.45150.32230.09010.12580.1795-0.47580.0579-0.439-0.04880.3213-0.06291.1975-0.35510.10021.09610.25831.302942.86085.2826105.6706
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 562 through 736 )B0
2X-RAY DIFFRACTION2chain 'B' and (resid 737 through 862 )B0
3X-RAY DIFFRACTION3chain 'B' and (resid 863 through 963 )B0
4X-RAY DIFFRACTION4chain 'A' and (resid 562 through 752 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 753 through 862 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 863 through 963 )A0
7X-RAY DIFFRACTION7chain 'C' and (resid 562 through 627 )C0
8X-RAY DIFFRACTION8chain 'C' and (resid 628 through 664 )C0
9X-RAY DIFFRACTION9chain 'C' and (resid 665 through 706 )C0
10X-RAY DIFFRACTION10chain 'C' and (resid 707 through 736 )C0
11X-RAY DIFFRACTION11chain 'C' and (resid 737 through 834 )C0
12X-RAY DIFFRACTION12chain 'C' and (resid 835 through 868 )C0
13X-RAY DIFFRACTION13chain 'C' and (resid 869 through 963 )C0
14X-RAY DIFFRACTION14chain 'D' and (resid 562 through 644 )D0
15X-RAY DIFFRACTION15chain 'D' and (resid 645 through 706 )D0
16X-RAY DIFFRACTION16chain 'D' and (resid 707 through 868 )D0
17X-RAY DIFFRACTION17chain 'D' and (resid 869 through 961 )D0

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