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- PDB-2hz6: The crystal structure of human IRE1-alpha luminal domain -

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Basic information

Entry
Database: PDB / ID: 2hz6
TitleThe crystal structure of human IRE1-alpha luminal domain
ComponentsEndoplasmic reticulum to nucleus signalling 1 isoform 1 variant
KeywordsSIGNALING PROTEIN / triangular beta-sheet cluster
Function / homology
Function and homology information


: / : / : / regulation of cell cycle => GO:0051726 / peptidyl-serine trans-autophosphorylation / mRNA splicing, via endonucleolytic cleavage and ligation / AIP1-IRE1 complex / Ire1 complex / : / IRE1alpha activates chaperones ...: / : / : / regulation of cell cycle => GO:0051726 / 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 / endoplasmic reticulum unfolded protein response / 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 kinase activity / protein phosphorylation / 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
Serine/threonine-protein kinase/endoribonuclease IRE1/2-like / KEN domain / KEN domain superfamily / Ribonuclease 2-5A / KEN domain profile. / PUB domain / domain in protein kinases, N-glycanases and other nuclear proteins / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily ...Serine/threonine-protein kinase/endoribonuclease IRE1/2-like / KEN domain / KEN domain superfamily / Ribonuclease 2-5A / KEN domain profile. / PUB domain / domain in protein kinases, N-glycanases and other nuclear proteins / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / Quinoprotein alcohol dehydrogenase-like superfamily / 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
Similarity search - Domain/homology
Serine/threonine-protein kinase/endoribonuclease IRE1 / Serine/threonine-protein kinase/endoribonuclease IRE1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 3.1 Å
AuthorsKaufman, R.J. / Xu, Z. / Zhou, J.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2006
Title: The crystal structure of human IRE1 luminal domain reveals a conserved dimerization interface required for activation of the unfolded protein response.
Authors: Zhou, J. / Liu, C.Y. / Back, S.H. / Clark, R.L. / Peisach, D. / Xu, Z. / Kaufman, R.J.
History
DepositionAug 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Category: database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Endoplasmic reticulum to nucleus signalling 1 isoform 1 variant


Theoretical massNumber of molelcules
Total (without water)41,1921
Polymers41,1921
Non-polymers00
Water0
1
A: Endoplasmic reticulum to nucleus signalling 1 isoform 1 variant

A: Endoplasmic reticulum to nucleus signalling 1 isoform 1 variant


Theoretical massNumber of molelcules
Total (without water)82,3832
Polymers82,3832
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Unit cell
Length a, b, c (Å)185.010, 185.010, 67.690
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsThe second part of the biological assembly is generated by the rotation: -1 0 0 0 1 0 0 0 -1 followed with the translation: ( 0, 0, 33.84).

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Components

#1: Protein Endoplasmic reticulum to nucleus signalling 1 isoform 1 variant


Mass: 41191.547 Da / Num. of mol.: 1 / Fragment: N-terminal domain / Mutation: C148S, C332S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q59EE2, UniProt: O75460*PLUS

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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: 4.06 Å3/Da / Density % sol: 69.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 3-3.5% PEG 20000, 0.1M PIPES, 3% MPD, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1.0023, 0.9785, 0.9795, 0.9567
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 30, 2002
RadiationMonochromator: Graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.00231
20.97851
30.97951
40.95671
ReflectionResolution: 3.1→200 Å / Num. all: 12847 / Num. obs: 12651 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3
Reflection shellResolution: 3.1→3.21 Å / % possible all: 98.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 3.1→8 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 583891.59 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.316 1185 10.3 %RANDOM
Rwork0.268 ---
obs0.268 11471 95.6 %-
all-12651 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 138.617 Å2 / ksol: 0.377078 e/Å3
Displacement parametersBiso mean: 100.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.46 Å2-0.32 Å20 Å2
2---6.46 Å20 Å2
3---12.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.56 Å0.47 Å
Luzzati d res low-5 Å
Luzzati sigma a0.69 Å0.6 Å
Refinement stepCycle: LAST / Resolution: 3.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1812 0 0 0 1812
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.94
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it10.181.5
X-RAY DIFFRACTIONc_mcangle_it15.832
X-RAY DIFFRACTIONc_scbond_it21.642
X-RAY DIFFRACTIONc_scangle_it25.712.5
LS refinement shellResolution: 3.1→3.28 Å / Rfactor Rfree error: 0.031 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.406 175 10.4 %
Rwork0.383 1511 -
obs--86 %
Xplor fileSerial no: 1 / Param file: protein_rep.param / Topol file: protein.top

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