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- PDB-3lj0: IRE1 complexed with ADP and Quercetin -

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Basic information

Entry
Database: PDB / ID: 3lj0
TitleIRE1 complexed with ADP and Quercetin
ComponentsSerine/threonine-protein kinase/endoribonuclease IRE1
KeywordsTRANSFERASE / HYDROLASE / kinase / flavonol / activator / dimer / ATP-binding / Endoplasmic reticulum / Glycoprotein / Magnesium / Membrane / Metal-binding / Multifunctional enzyme / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Transcription / Transcription regulation / Transmembrane / Unfolded protein response
Function / homology
Function and homology information


IRE1alpha activates chaperones / Ire1 complex / IRE1-TRAF2-ASK1 complex / fungal-type cell wall organization / inositol metabolic process / protein localization to Golgi apparatus / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / IRE1-mediated unfolded protein response / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / endoplasmic reticulum unfolded protein response ...IRE1alpha activates chaperones / Ire1 complex / IRE1-TRAF2-ASK1 complex / fungal-type cell wall organization / inositol metabolic process / protein localization to Golgi apparatus / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / IRE1-mediated unfolded protein response / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / endoplasmic reticulum unfolded protein response / RNA endonuclease activity / response to endoplasmic reticulum stress / mRNA processing / unfolded protein binding / non-specific serine/threonine protein kinase / protein kinase activity / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / endoplasmic reticulum / ATP binding / metal ion binding / identical protein binding / nucleus
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 / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / de novo design (two linked rop proteins) ...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 / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / de novo design (two linked rop proteins) / 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
ADENOSINE-5'-DIPHOSPHATE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / STRONTIUM ION / Serine/threonine-protein kinase/endoribonuclease IRE1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsLee, K.P.K. / Sicheri, F.
CitationJournal: Mol.Cell / Year: 2010
Title: Flavonol activation defines an unanticipated ligand-binding site in the kinase-RNase domain of IRE1.
Authors: Wiseman, R.L. / Zhang, Y. / Lee, K.P. / Harding, H.P. / Haynes, C.M. / Price, J. / Sicheri, F. / Ron, D.
History
DepositionJan 25, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 12, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 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_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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


Theoretical massNumber of molelcules
Total (without water)102,23910
Polymers100,5572
Non-polymers1,6838
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7640 Å2
ΔGint-140 kcal/mol
Surface area34870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)131.020, 131.020, 175.820
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1111A8 - 434
2111B8 - 434

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Components

#1: Protein Serine/threonine-protein kinase/endoribonuclease IRE1 / Endoplasmic reticulum-to-nucleus signaling 1 / Serine/threonine-protein kinase / Endoribonuclease


Mass: 50278.336 Da / Num. of mol.: 2
Fragment: UNP residues 658-1115, Protein kinase domain, KEN domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: ERN1, IRE1, YHR079C / Plasmid: pProEx / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P32361, non-specific serine/threonine protein kinase, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sr
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-QUE / 3,5,7,3',4'-PENTAHYDROXYFLAVONE / QUERCETIN


Mass: 302.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H10O7
Has protein modificationY

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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: 4.33 Å3/Da / Density % sol: 71.61 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 6.5
Details: 10% PEG 8K, 50 mM Na-Cacodylate pH 6.5, 300 mM KCl, 100 mM SrOAc, 10 mM MgCl2, 2mM ADP, quercetin, hanging drop, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2009
RadiationMonochromator: Si-111 crystals / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.95→65.51 Å / Num. all: 35428 / Num. obs: 35428 / % possible obs: 98.6 % / Redundancy: 2.8 % / Rsym value: 0.138

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Processing

Software
NameVersionClassificationNB
SCALA3.3.9data scaling
REFMAC5.5.0072refinement
PDB_EXTRACT3.005data extraction
MOSFLMdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2RIO

2rio


Resolution: 3.2→65.51 Å / Cor.coef. Fo:Fc: 0.9 / Cor.coef. Fo:Fc free: 0.897 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.67 / ESU R Free: 0.361 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.224 1389 5 %RANDOM
Rwork0.217 ---
obs0.217 27630 97.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 185.22 Å2 / Biso mean: 58.899 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1-1.25 Å20.62 Å20 Å2
2--1.25 Å20 Å2
3----1.87 Å2
Refinement stepCycle: LAST / Resolution: 3.2→65.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6261 0 102 0 6363
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0216501
X-RAY DIFFRACTIONr_angle_refined_deg1.1291.9958839
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.9365803
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.22523.162272
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.41915.0571047
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3191543
X-RAY DIFFRACTIONr_chiral_restr0.0740.2993
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214857
Refine LS restraints NCSNumber: 3081 / Type: TIGHT POSITIONAL / Rms dev position: 0.17 Å / Weight position: 0.05
LS refinement shellResolution: 3.2→3.283 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.278 87 -
Rwork0.306 1956 -
all-2043 -
obs--99.71 %

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