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- PDB-2rio: Structure of the dual enzyme Ire1 reveals the basis for catalysis... -

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Basic information

Entry
Database: PDB / ID: 2rio
TitleStructure of the dual enzyme Ire1 reveals the basis for catalysis and regulation of non-conventional splicing
ComponentsSerine/threonine-protein kinase/endoribonuclease IRE1
KeywordsHYDROLASE / TRANSFERASE / Protein-nucleotide complex / ATP-binding / Endoplasmic reticulum / Glycoprotein / Kinase / Magnesium / Membrane / Metal-binding / Multifunctional enzyme / Nucleotide-binding / Phosphorylation / 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 / endoplasmic reticulum unfolded protein response / RNA endonuclease activity ...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 / 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 / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / endoplasmic reticulum / ATP binding / identical protein binding / metal ion 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 / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 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 / Up-down Bundle / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / STRONTIUM ION / Serine/threonine-protein kinase/endoribonuclease IRE1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsLee, K.P. / Dey, M. / Neculai, D. / Cao, C. / Dever, T.E. / Sicheri, F.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2008
Title: Structure of the dual enzyme ire1 reveals the basis for catalysis and regulation in nonconventional RNA splicing.
Authors: Lee, K.P. / Dey, M. / Neculai, D. / Cao, C. / Dever, T.E. / Sicheri, F.
History
DepositionOct 12, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 9, 2017Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.entity_id / _entity_src_gen.host_org_genus ..._entity_src_gen.entity_id / _entity_src_gen.host_org_genus / _entity_src_gen.host_org_species / _entity_src_gen.pdbx_beg_seq_num / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_vector_type / _entity_src_gen.pdbx_src_id / _entity_src_gen.plasmid_name
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999Residues 869-892(UNP numbering) were deleted. Residues 868 and 893 were fused together.

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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)101,1558
Polymers100,0772
Non-polymers1,0786
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.307, 130.307, 175.011
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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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: 50038.398 Da / Num. of mol.: 2 / Fragment: Cytoplasmic fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: IRE1, ERN1 / Plasmid: pProEx / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21
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 / Strontium


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


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.29 Å3/Da / Density % sol: 71.3 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 50mM Tris-Cl (pH 8.0), 200mM KOAc, 50mM SrOAc, 10mM MgCl2 and 10% PEG 8K , VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97883 Å
DetectorDate: Mar 24, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97883 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 66131 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 43.4 % / Rsym value: 0.061 / Net I/σ(I): 7.2
Reflection shellResolution: 2.4→3.11 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 8.1 / Num. unique all: 6634 / Rsym value: 0.31 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXSphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→19.83 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.887 / SU B: 6.61 / SU ML: 0.158 / Cross valid method: THROUGHOUT / ESU R: 0.23 / ESU R Free: 0.21 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The SAD DATASET USED FOR PHASING WAS COLLECT AT 3.0A RESOLUTION.
RfactorNum. reflection% reflectionSelection details
Rfree0.26637 3326 5.1 %RANDOM
Rwork0.22217 ---
obs0.22443 62174 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.687 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0.03 Å20 Å2
2---0.05 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6414 0 58 0 6472
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0226639
X-RAY DIFFRACTIONr_angle_refined_deg2.4951.9878958
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0875790
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.84823.531303
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.362151223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.5851548
X-RAY DIFFRACTIONr_chiral_restr0.230.2996
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024902
X-RAY DIFFRACTIONr_nbd_refined0.2460.22894
X-RAY DIFFRACTIONr_nbtor_refined0.3160.24369
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2166
X-RAY DIFFRACTIONr_metal_ion_refined0.2310.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.246
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.250.25
X-RAY DIFFRACTIONr_mcbond_it1.3241.53980
X-RAY DIFFRACTIONr_mcangle_it2.43326438
X-RAY DIFFRACTIONr_scbond_it3.7532741
X-RAY DIFFRACTIONr_scangle_it5.6954.52520
LS refinement shellResolution: 2.4→2.461 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.366 233 -
Rwork0.256 4554 -
obs-65619 100 %

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