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- PDB-3p23: Crystal structure of the Human kinase and RNase domains in comple... -

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Basic information

Entry
Database: PDB / ID: 3p23
TitleCrystal structure of the Human kinase and RNase domains in complex with ADP
ComponentsSerine/threonine-protein kinase/endoribonuclease IRE1
KeywordsHYDROLASE / Transferase / Kinase domain / Kinase and RNase function / ATP binding ssRNA binding / dephosphorylated
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 / positive regulation of endoplasmic reticulum unfolded protein response / 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 / 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 / mRNA catabolic process / positive regulation of JUN kinase activity / 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 vascular associated smooth muscle cell proliferation / Hsp70 protein binding / RNA endonuclease activity / 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 phosphorylation / non-specific serine/threonine protein kinase / 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
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 / Serine/threonine-protein kinase/endoribonuclease IRE1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsAli, M.M.U. / Pearl, L.H.
CitationJournal: Embo J. / Year: 2011
Title: Structure of the Ire1 autophosphorylation complex and implications for the unfolded protein response.
Authors: Ali, M.M. / Bagratuni, T. / Davenport, E.L. / Nowak, P.R. / Silva-Santisteban, M.C. / Hardcastle, A. / McAndrews, C. / Rowlands, M.G. / Morgan, G.J. / Aherne, W. / Collins, I. / Davies, F.E. / Pearl, L.H.
History
DepositionOct 1, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 23, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 21, 2013Group: Refinement description
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 / 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_label_asym_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.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

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


Theoretical massNumber of molelcules
Total (without water)199,69613
Polymers197,7944
Non-polymers1,9029
Water7,152397
1
A: Serine/threonine-protein kinase/endoribonuclease IRE1
B: Serine/threonine-protein kinase/endoribonuclease IRE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,8967
Polymers98,8972
Non-polymers9995
Water362
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)99,8006
Polymers98,8972
Non-polymers9034
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Serine/threonine-protein kinase/endoribonuclease IRE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9964
Polymers49,4481
Non-polymers5483
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
B: Serine/threonine-protein kinase/endoribonuclease IRE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9003
Polymers49,4481
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
C: Serine/threonine-protein kinase/endoribonuclease IRE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9003
Polymers49,4481
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
D: Serine/threonine-protein kinase/endoribonuclease IRE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9003
Polymers49,4481
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)109.850, 83.200, 116.080
Angle α, β, γ (deg.)90.00, 94.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Serine/threonine-protein kinase/endoribonuclease IRE1 / Inositol-requiring protein 1 / hIRE1p / Ire1-alpha / IRE1a / Endoplasmic reticulum-to-nucleus ...Inositol-requiring protein 1 / hIRE1p / Ire1-alpha / IRE1a / Endoplasmic reticulum-to-nucleus signaling 1 / Serine/threonine-protein kinase / Endoribonuclease


Mass: 49448.484 Da / Num. of mol.: 4 / Fragment: UNP residues 547-977
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERN1, IRE1 / Plasmid: modifie pfastbac / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): sf9/21
References: UniProt: O75460, 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.: 4 / Source method: obtained synthetically / Formula: Mg
#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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsSER TO THR CONFLICT AT THIS POSITION IN UNP ENTRY O75460

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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: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 15% PEG 3350, 0.2M Ammonium Sulfate, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 85 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.92 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 1, 2009
RadiationMonochromator: double crystals monochromator, Kirkpatrick Baez horizontal and vertical focusing mirrors
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.7→58.8 Å / Num. all: 56524 / Num. obs: 56524 / % possible obs: 98.5 % / Observed criterion σ(F): 3.2 / Observed criterion σ(I): 2.7 / Redundancy: 3.2 % / Biso Wilson estimate: 39 Å2 / Rsym value: 0.09 / Net I/σ(I): 7.9
Reflection shellResolution: 2.7→2.74 Å / Mean I/σ(I) obs: 3.2 / Rsym value: 0.32 / % possible all: 98.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementResolution: 2.7→54.733 Å / SU ML: 1.55 / σ(F): 0.02 / Phase error: 35.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2944 2698 5.05 %
Rwork0.2355 --
obs0.2384 53417 92.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.776 Å2 / ksol: 0.346 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--24.3637 Å20 Å2-2.7075 Å2
2--28.0282 Å20 Å2
3----25.5278 Å2
Refinement stepCycle: LAST / Resolution: 2.7→54.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12414 0 117 397 12928
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00312840
X-RAY DIFFRACTIONf_angle_d0.91417377
X-RAY DIFFRACTIONf_dihedral_angle_d15.494718
X-RAY DIFFRACTIONf_chiral_restr0.0691889
X-RAY DIFFRACTIONf_plane_restr0.0042225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.74910.35911270.29832393X-RAY DIFFRACTION85
2.7491-2.8020.39731350.29332426X-RAY DIFFRACTION85
2.802-2.85920.39811400.28952514X-RAY DIFFRACTION87
2.8592-2.92130.38471340.2872504X-RAY DIFFRACTION89
2.9213-2.98930.40321410.28162581X-RAY DIFFRACTION89
2.9893-3.0640.33771380.27852555X-RAY DIFFRACTION89
3.064-3.14690.3271240.25142585X-RAY DIFFRACTION91
3.1469-3.23950.31521490.23922628X-RAY DIFFRACTION92
3.2395-3.3440.30741620.24422706X-RAY DIFFRACTION95
3.344-3.46350.32771610.23222747X-RAY DIFFRACTION96
3.4635-3.60220.31241340.21132777X-RAY DIFFRACTION97
3.6022-3.76610.24321350.21962802X-RAY DIFFRACTION97
3.7661-3.96460.25911480.20072778X-RAY DIFFRACTION96
3.9646-4.21290.27591440.19392780X-RAY DIFFRACTION97
4.2129-4.5380.24681440.19412750X-RAY DIFFRACTION96
4.538-4.99440.23951510.19532753X-RAY DIFFRACTION95
4.9944-5.71640.26751510.20862748X-RAY DIFFRACTION95
5.7164-7.19950.27941400.21832812X-RAY DIFFRACTION96
7.1995-54.74440.20771400.22322880X-RAY DIFFRACTION96
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)
10.0168-0.02770.01510.03020.00310.0709-0.0165-0.0255-0.1544-0.0423-0.02850.3108-0.1308-0.1955-0.00030.2743-0.0849-0.07390.86320.07810.335316.5598-36.826944.6355
20.0601-0.07580.0350.1611-0.02510.09980.13830.0294-0.0123-0.01570.0557-0.06190.21840.04740.14150.22120.0523-0.0058-0.23910.10380.175738.2171-34.551440.8909
30.0991-0.1391-0.02860.13310.08360.0495-0.02830.1582-0.00930.0552-0.04-0.10960.1092-0.0255-0.12190.11350.14550.0409-0.2126-0.21420.182958.6233-34.532917.1314
40.0543-0.02830.02680.03970.00970.02480.12440.07660.0480.01150.17860.27590.0196-0.26950.00020.2666-0.01390.03831.07960.22020.392515.7182-34.71875.1828
50.155-0.04610.08150.0935-0.05910.13080.12450.3188-0.07280.1082-0.1218-0.04170.0849-0.13660.00340.2001-0.0115-0.00620.63540.07140.187637.1695-37.732879.4369
60.0301-0.0033-0.0029-0.01950.05890.0275-0.0613-0.0729-0.0130.0496-0.00950.04460.08090.0545-0.03530.1709-0.14880.0008-0.4408-0.11170.163456.8085-40.8661103.218
70.03070.08670.01930.0273-0.03370.05310.0566-0.006-0.07070.0673-0.2061-0.2701-0.13410.2081-0.00040.1676-0.1129-0.02531.15010.05340.40411.3527-36.46716.6627
80.36710.05410.01040.05150.04030.09520.08380.17180.1833-0.1208-0.06540.03860.07770.03510.00360.2042-0.0877-0.01660.60340.04390.1747-10.4345-33.989820.2771
90.06910.0138-0.0385-0.0149-0.02340.0735-0.0695-0.05830.153-0.05880.02280.07990.0072-0.2105-0.00020.2999-0.0092-0.02610.88070.09660.3099-30.6966-33.793243.9226
100.0270.02590.01940.05440.0370.0270.112-0.08090.21680.0280.1123-0.04470.15690.24570.00030.20350.01560.03580.9609-0.0920.313112.2799-34.9384-13.8814
110.1153-0.06110.03760.0170.00810.15520.1030.02980.1117-0.0334-0.00260.03940.0280.13290.12030.2393-0.0302-0.013-0.0680.07920.2064-9.3104-38.007-18.3704
120.0407-0.0257-0.02840.04960.03730.08280.02830.3247-0.01770.18910.08370.001-0.1091-0.16240.00010.2620.03020.020.59030.09370.198-28.8817-40.2846-42.3841
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 564:655
2X-RAY DIFFRACTION2chain A and resid 656:830
3X-RAY DIFFRACTION3chain A and resid 831:963
4X-RAY DIFFRACTION4chain B and resid 564:655
5X-RAY DIFFRACTION5chain B and resid 656:830
6X-RAY DIFFRACTION6chain B and resid 831:963
7X-RAY DIFFRACTION7chain C and resid 564:655
8X-RAY DIFFRACTION8chain C and resid 656:830
9X-RAY DIFFRACTION9chain C and resid 831:963
10X-RAY DIFFRACTION10chain D and resid 564:655
11X-RAY DIFFRACTION11chain D and resid 656:830
12X-RAY DIFFRACTION12chain D and resid 831:963

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