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- PDB-9i3f: Crystal structure of the AGR2 and IRE1beta_loop complex -

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Basic information

Entry
Database: PDB / ID: 9i3f
TitleCrystal structure of the AGR2 and IRE1beta_loop complex
Components
  • Anterior gradient protein 2 homolog
  • Serine/threonine-protein kinase/endoribonuclease IRE2
KeywordsCHAPERONE / molecular chaperones / unfolded protein response (UPR) / endoplasmic reticulum (ER) / protein multimerisation
Function / homology
Function and homology information


lung goblet cell differentiation / positive regulation of PERK-mediated unfolded protein response / apoptotic chromosome condensation / IRE1-TRAF2-ASK1 complex / endoplasmic reticulum quality control compartment / mucus secretion / dystroglycan binding / rRNA catabolic process / positive regulation of developmental growth / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters ...lung goblet cell differentiation / positive regulation of PERK-mediated unfolded protein response / apoptotic chromosome condensation / IRE1-TRAF2-ASK1 complex / endoplasmic reticulum quality control compartment / mucus secretion / dystroglycan binding / rRNA catabolic process / positive regulation of developmental growth / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / positive regulation of cell-substrate adhesion / epidermal growth factor receptor binding / positive regulation of epidermal growth factor receptor signaling pathway / IRE1-mediated unfolded protein response / digestive tract morphogenesis / positive regulation of IRE1-mediated unfolded protein response / intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress / RNA endonuclease activity / response to endoplasmic reticulum stress / positive regulation of protein localization to plasma membrane / mRNA processing / unfolded protein binding / endonuclease activity / protein phosphorylation / non-specific serine/threonine protein kinase / inflammatory response / protein serine kinase activity / negative regulation of DNA-templated transcription / protein serine/threonine kinase activity / positive regulation of gene expression / magnesium ion binding / endoplasmic reticulum / extracellular space / extracellular region / ATP binding / identical protein binding / cytosol
Similarity search - Function
: / Thioredoxin-like / 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 ...: / Thioredoxin-like / 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 / Thioredoxin-like superfamily / 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
Similarity search - Domain/homology
Anterior gradient protein 2 homolog / Serine/threonine-protein kinase/endoribonuclease IRE2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsYan, Y. / Ron, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome TrustSGAG/182 United Kingdom
CitationJournal: To Be Published
Title: A structural basis for chaperone repression of stress signalling from the endoplasmic reticulum
Authors: Neidhardt, L. / Ron, D. / Yan, Y.
History
DepositionJan 22, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
I: Serine/threonine-protein kinase/endoribonuclease IRE2
A: Anterior gradient protein 2 homolog
B: Anterior gradient protein 2 homolog
C: Anterior gradient protein 2 homolog
D: Anterior gradient protein 2 homolog
F: Serine/threonine-protein kinase/endoribonuclease IRE2
G: Serine/threonine-protein kinase/endoribonuclease IRE2
H: Serine/threonine-protein kinase/endoribonuclease IRE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,81911
Polymers82,7468
Non-polymers733
Water6,648369
1
I: Serine/threonine-protein kinase/endoribonuclease IRE2
B: Anterior gradient protein 2 homolog
D: Anterior gradient protein 2 homolog
F: Serine/threonine-protein kinase/endoribonuclease IRE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,3975
Polymers41,3734
Non-polymers241
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Anterior gradient protein 2 homolog
C: Anterior gradient protein 2 homolog
G: Serine/threonine-protein kinase/endoribonuclease IRE2
H: Serine/threonine-protein kinase/endoribonuclease IRE2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,4226
Polymers41,3734
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.199, 81.820, 120.871
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Serine/threonine-protein kinase/endoribonuclease IRE2 / Endoplasmic reticulum-to-nucleus signaling 2 / Inositol-requiring protein 2 / hIRE2p / Ire1-beta / IRE1b


Mass: 5544.084 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERN2, IRE2 / Production host: Escherichia (bacteria)
References: UniProt: Q76MJ5, non-specific serine/threonine protein kinase, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
#2: Protein
Anterior gradient protein 2 homolog / AG-2 / hAG-2 / HPC8 / Secreted cement gland protein XAG-2 homolog


Mass: 15142.388 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGR2, AG2, UNQ515/PRO1030 / Production host: Escherichia (bacteria) / References: UniProt: O95994
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.2M Magnesium chloride, 0.1M TRIS PH8.5 and 24% PEG8000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Feb 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.9→67.76 Å / Num. obs: 57731 / % possible obs: 99.6 % / Redundancy: 6.4 % / CC1/2: 0.992 / Rmerge(I) obs: 0.198 / Net I/σ(I): 6
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 1.234 / Num. unique obs: 17355 / CC1/2: 0.707

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→67.76 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.957 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 2862 5 %RANDOM
Rwork0.19948 ---
obs0.20116 54791 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.997 Å2
Baniso -1Baniso -2Baniso -3
1--1.86 Å2-0 Å20 Å2
2--3.72 Å2-0 Å2
3----1.85 Å2
Refinement stepCycle: 1 / Resolution: 1.9→67.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4789 0 3 369 5161
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0124939
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164751
X-RAY DIFFRACTIONr_angle_refined_deg1.2461.8456714
X-RAY DIFFRACTIONr_angle_other_deg0.4541.77210974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7415597
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.928523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.42310885
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0610.2776
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025644
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021052
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2892.0712403
X-RAY DIFFRACTIONr_mcbond_other1.2892.0712403
X-RAY DIFFRACTIONr_mcangle_it2.1783.7012995
X-RAY DIFFRACTIONr_mcangle_other2.1783.7012996
X-RAY DIFFRACTIONr_scbond_it1.7432.2492536
X-RAY DIFFRACTIONr_scbond_other1.7432.2492537
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.914.0443720
X-RAY DIFFRACTIONr_long_range_B_refined4.24921.625470
X-RAY DIFFRACTIONr_long_range_B_other4.17520.795393
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 214 -
Rwork0.361 3785 -
obs--94.49 %

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