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- PDB-3sdm: Structure of oligomeric kinase/RNase Ire1 in complex with an olig... -

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Basic information

Entry
Database: PDB / ID: 3sdm
TitleStructure of oligomeric kinase/RNase Ire1 in complex with an oligonucleotide
ComponentsSerine/threonine-protein kinase/endoribonuclease IRE1
KeywordsTRANSFERASE / HYDROLASE / kinase / RNase / ribonuclease / Hac1 / XBP1 / splicing / RNA / UPR / unfolded protein response / oligomer / complex / oligonucleotide
Function / homology
Function and homology information


IRE1alpha activates chaperones / Ire1 complex / IRE1-TRAF2-ASK1 complex / fungal-type cell wall organization / protein localization to Golgi apparatus / inositol metabolic process / 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 / protein localization to Golgi apparatus / inositol metabolic process / 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 / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / endoplasmic reticulum membrane / endoplasmic reticulum / ATP binding / identical protein binding / nucleus / metal ion binding
Similarity search - Function
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 / Quinoprotein alcohol dehydrogenase-like superfamily / Serine/threonine-protein kinase, active site ...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 / 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
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 6.6 Å
AuthorsKorennykh, A. / Korostelev, A. / Egea, P. / Finer-Moore, J. / Zhang, C. / Stroud, R. / Shokat, K. / Walter, P.
Citation
Journal: Bmc Biol. / Year: 2011
Title: Cofactor-mediated conformational control in the bifunctional kinase/RNase Ire1.
Authors: Korennykh, A.V. / Egea, P.F. / Korostelev, A.A. / Finer-Moore, J. / Stroud, R.M. / Zhang, C. / Shokat, K.M. / Walter, P.
#1: Journal: Bmc Biol. / Year: 2011
Title: Structural and functional basis for RNA cleavage by Ire1.
Authors: Korennykh, A.V. / Korostelev, A.A. / Egea, P.F. / Finer-Moore, J. / Stroud, R.M. / Zhang, C. / Shokat, K.M. / Walter, P.
History
DepositionJun 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 13, 2011Provider: repository / Type: Initial release

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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
D: Serine/threonine-protein kinase/endoribonuclease IRE1
E: Serine/threonine-protein kinase/endoribonuclease IRE1
F: Serine/threonine-protein kinase/endoribonuclease IRE1
G: Serine/threonine-protein kinase/endoribonuclease IRE1


Theoretical massNumber of molelcules
Total (without water)363,1847
Polymers363,1847
Non-polymers00
Water00
1
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
E: Serine/threonine-protein kinase/endoribonuclease IRE1
F: Serine/threonine-protein kinase/endoribonuclease IRE1
G: Serine/threonine-protein kinase/endoribonuclease IRE1

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
E: Serine/threonine-protein kinase/endoribonuclease IRE1
F: Serine/threonine-protein kinase/endoribonuclease IRE1
G: Serine/threonine-protein kinase/endoribonuclease IRE1


Theoretical massNumber of molelcules
Total (without water)726,36714
Polymers726,36714
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
2
A: Serine/threonine-protein kinase/endoribonuclease IRE1
B: Serine/threonine-protein kinase/endoribonuclease IRE1


Theoretical massNumber of molelcules
Total (without water)103,7672
Polymers103,7672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-6 kcal/mol
Surface area37570 Å2
MethodPISA
3
C: Serine/threonine-protein kinase/endoribonuclease IRE1
D: Serine/threonine-protein kinase/endoribonuclease IRE1


Theoretical massNumber of molelcules
Total (without water)103,7672
Polymers103,7672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3730 Å2
ΔGint-7 kcal/mol
Surface area37490 Å2
MethodPISA
4
E: Serine/threonine-protein kinase/endoribonuclease IRE1

E: Serine/threonine-protein kinase/endoribonuclease IRE1


Theoretical massNumber of molelcules
Total (without water)103,7672
Polymers103,7672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area3590 Å2
ΔGint-5 kcal/mol
Surface area37680 Å2
MethodPISA
5
F: Serine/threonine-protein kinase/endoribonuclease IRE1
G: Serine/threonine-protein kinase/endoribonuclease IRE1


Theoretical massNumber of molelcules
Total (without water)103,7672
Polymers103,7672
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3770 Å2
ΔGint-6 kcal/mol
Surface area37470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.650, 580.670, 177.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222

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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: 51883.391 Da / Num. of mol.: 7 / Fragment: kinase/RNase domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: IRE1, ERN1, YHR079C / Production host: Escherichia coli (E. coli)
References: UniProt: P32361, non-specific serine/threonine protein kinase, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters

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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: 3.26 Å3/Da / Density % sol: 62.26 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: SODIUM CITRATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.115879 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 9, 2008
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.115879 Å / Relative weight: 1
ReflectionResolution: 6.6→96.778 Å / Num. all: 9403 / Num. obs: 9380 / % possible obs: 99.76 % / Observed criterion σ(F): 1.99 / Observed criterion σ(I): 1.99

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.5_2)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 6.6→96.778 Å / SU ML: 1.33 / σ(F): 1.99 / Phase error: 31.47 / Stereochemistry target values: ML
Details: Side chains are not resolved at the resolution of this data set. All side chains in this file are inherited from chain C of PDB entry 3fbv. They are an approximation and should be interpreted with caution.
RfactorNum. reflection% reflection
Rfree0.317 469 5 %
Rwork0.2863 --
obs0.2875 9380 99.76 %
all-9406 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 80 Å2 / ksol: 0.288 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-406.0384 Å20 Å20 Å2
2--148.1242 Å2-0 Å2
3---313.6178 Å2
Refinement stepCycle: LAST / Resolution: 6.6→96.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms23793 0 0 0 23793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00624269
X-RAY DIFFRACTIONf_angle_d0.92532725
X-RAY DIFFRACTIONf_dihedral_angle_d17.8129226
X-RAY DIFFRACTIONf_chiral_restr0.0623598
X-RAY DIFFRACTIONf_plane_restr0.0044158
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
6.6-7.55470.3611520.36652892X-RAY DIFFRACTION100
7.5547-9.51690.2471550.24522947X-RAY DIFFRACTION100
9.5169-96.78870.33351620.28563072X-RAY DIFFRACTION99

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