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- PDB-4yzd: Crystal Structure of human phosphorylated IRE1alpha in complex wi... -

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Basic information

Entry
Database: PDB / ID: 4yzd
TitleCrystal Structure of human phosphorylated IRE1alpha in complex with ADP-Mg
ComponentsSerine/threonine-protein kinase/endoribonuclease IRE1
KeywordsTRANSFERASE / active / ADP / complex / IRE1
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 / magnesium ion binding / enzyme 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 / 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 / Serine/threonine-protein kinase/endoribonuclease IRE1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.102 Å
AuthorsConcha, N.O.
CitationJournal: Mol.Pharmacol. / Year: 2015
Title: Long-Range Inhibitor-Induced Conformational Regulation of Human IRE1 alpha Endoribonuclease Activity.
Authors: Concha, N.O. / Smallwood, A. / Bonnette, W. / Totoritis, R. / Zhang, G. / Federowicz, K. / Yang, J. / Qi, H. / Chen, S. / Campobasso, N. / Choudhry, A.E. / Shuster, L.E. / Evans, K.A. / ...Authors: Concha, N.O. / Smallwood, A. / Bonnette, W. / Totoritis, R. / Zhang, G. / Federowicz, K. / Yang, J. / Qi, H. / Chen, S. / Campobasso, N. / Choudhry, A.E. / Shuster, L.E. / Evans, K.A. / Ralph, J. / Sweitzer, S. / Heerding, D.A. / Buser, C.A. / Su, D.S. / DeYoung, M.P.
History
DepositionMar 24, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 11, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 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 / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _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

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)141,1628
Polymers139,8323
Non-polymers1,3305
Water48627
1
A: Serine/threonine-protein kinase/endoribonuclease IRE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0623
Polymers46,6111
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Serine/threonine-protein kinase/endoribonuclease IRE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0623
Polymers46,6111
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Serine/threonine-protein kinase/endoribonuclease IRE1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0382
Polymers46,6111
Non-polymers4271
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)191.751, 122.492, 77.876
Angle α, β, γ (deg.)90.00, 107.07, 90.00
Int Tables number5
Space group name H-MC121

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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: 46610.570 Da / Num. of mol.: 3 / Fragment: UNP residues 562-966
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERN1, IRE1 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
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.: 2 / Source method: isolated from a natural source / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

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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: 3.13 Å3/Da / Density % sol: 60.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: The crystals of pIRE1a with Mg2+-ADP were grown by mixing 2 ul protein solution (10 mg/ml pIRE1a (547-977) in 50 mM Hepes, pH 7.5, 200 mM NaCl, 5 mM DTT, 1 mM EDTA, 1 mM ADP (100mM ADP stock ...Details: The crystals of pIRE1a with Mg2+-ADP were grown by mixing 2 ul protein solution (10 mg/ml pIRE1a (547-977) in 50 mM Hepes, pH 7.5, 200 mM NaCl, 5 mM DTT, 1 mM EDTA, 1 mM ADP (100mM ADP stock was ~ pH 7.0), 1 mM MgCl2) with 2 ul reservoir solution (16 % PEG 3350, 200 mM Na+ Malonate pH 6.0) in sitting drops at room temperature. Seeding was used to initiate crystal growth. Crystals appeared the next day and grew to full size in 3 weeks. For data collection, the crystals were frozen in a solution of 20% ethylene glycol, 22% PEG 3350, 200 mM Na+ Malonate pH 6.0 and added to the protein drop before mounting the crystals on the loop.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.97949 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 27, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 3.102→45.643 Å / Num. obs: 30914 / % possible obs: 100 % / Redundancy: 3.8 % / Biso Wilson estimate: 84.26 Å2 / Rmerge(I) obs: 0.087 / Χ2: 1.055 / Net I/av σ(I): 15.225 / Net I/σ(I): 9.9 / Num. measured all: 118513
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
3.14-3.253.80.56930631.048100
3.25-3.383.90.38630791.088100
3.38-3.543.80.27430841.052100
3.54-3.723.90.19630811.081100
3.72-3.963.80.15130891.057100
3.96-4.263.80.11430681.094100
4.26-4.693.80.08230931.041100
4.69-5.373.80.0730821.04100
5.37-6.763.80.06131211.045100
6.76-503.80.05231541.00899.9

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3P23

3p23


Resolution: 3.102→45.643 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 30.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2728 1561 5.04 %random
Rwork0.2315 ---
obs0.2335 30914 98.93 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.102→45.643 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8676 0 83 27 8786
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048982
X-RAY DIFFRACTIONf_angle_d0.83712228
X-RAY DIFFRACTIONf_dihedral_angle_d12.0873140
X-RAY DIFFRACTIONf_chiral_restr0.0411366
X-RAY DIFFRACTIONf_plane_restr0.0041579
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1022-3.15070.39261240.31542049X-RAY DIFFRACTION78
3.1507-3.20230.39011280.34462602X-RAY DIFFRACTION100
3.2023-3.25750.3311510.31832683X-RAY DIFFRACTION100
3.2575-3.31680.3771650.30682567X-RAY DIFFRACTION100
3.3168-3.38050.40251530.29472693X-RAY DIFFRACTION100
3.3805-3.44950.3711110.29562652X-RAY DIFFRACTION100
3.4495-3.52450.34971220.29672639X-RAY DIFFRACTION100
3.5245-3.60640.33931510.27422619X-RAY DIFFRACTION100
3.6064-3.69660.33481000.26992740X-RAY DIFFRACTION100
3.6966-3.79650.28681450.27622619X-RAY DIFFRACTION100
3.7965-3.90820.36981270.24352702X-RAY DIFFRACTION100
3.9082-4.03420.23641290.22922661X-RAY DIFFRACTION100
4.0342-4.17830.25491490.23052590X-RAY DIFFRACTION100
4.1783-4.34550.21041630.22512640X-RAY DIFFRACTION100
4.3455-4.54310.25931310.2022666X-RAY DIFFRACTION100
4.5431-4.78240.24761440.19352618X-RAY DIFFRACTION100
4.7824-5.08160.26281390.2142654X-RAY DIFFRACTION100
5.0816-5.47340.27981480.21252655X-RAY DIFFRACTION100
5.4734-6.02310.22711540.22262644X-RAY DIFFRACTION100
6.0231-6.89210.25371470.2152613X-RAY DIFFRACTION100
6.8921-8.67360.23251660.21472638X-RAY DIFFRACTION100
8.6736-45.64750.22931100.1912655X-RAY DIFFRACTION99

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