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- PDB-9i3u: Cryo-EM structure of the AGR2 dimer in complex with the monomeric... -

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Basic information

Entry
Database: PDB / ID: 9i3u
TitleCryo-EM structure of the AGR2 dimer in complex with the monomeric IRE1beta luminal domain
Components
  • Anterior gradient protein 2 homolog
  • Serine/threonine-protein kinase/endoribonuclease IRE2
KeywordsCHAPERONE / endoplasmic reticulum (ER) / molecular chaperones/ protein multimerisation/ unfolded protein response (UPR)
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)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsYan, Y. / Hardwick, S. / Tung, J. / 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. / Tung, J. / Ron, D. / Yan, Y.
History
DepositionJan 24, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 22, 2025Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Oct 22, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Anterior gradient protein 2 homolog
D: Anterior gradient protein 2 homolog
A: Serine/threonine-protein kinase/endoribonuclease IRE2


Theoretical massNumber of molelcules
Total (without water)79,0843
Polymers79,0843
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Both gel filtration and mass spectrometry confirm a 2:1 stoichiometry for the complex.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein Anterior gradient protein 2 homolog / AG-2 / hAG-2 / HPC8 / Secreted cement gland protein XAG-2 homolog


Mass: 17845.541 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGR2, AG2, UNQ515/PRO1030 / Production host: Escherichia coli (E. coli) / References: UniProt: O95994
#2: Protein Serine/threonine-protein kinase/endoribonuclease IRE2 / Endoplasmic reticulum-to-nucleus signaling 2 / Inositol-requiring protein 2 / hIRE2p / Ire1-beta / ...Endoplasmic reticulum-to-nucleus signaling 2 / Inositol-requiring protein 2 / hIRE2p / Ire1-beta / IRE1b / IRE1beta luminal domain


Mass: 43393.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ERN2, IRE2 / Production host: Escherichia coli (E. coli)
References: UniProt: Q76MJ5, non-specific serine/threonine protein kinase, Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: The complex of AGR2 and IRE1beta luminal domain / Type: COMPLEX / Details: Co-expressed in E.coli. / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia (bacteria)
Buffer solutionpH: 7.4
Buffer component
IDConc.NameFormulaBuffer-ID
1150 mMsodium chlorideNaCl1
2200 mMtris(hydroxymethyl)aminomethaneTris1
30.2 mMtris(2-carboxyethyl)phosphineTCEP1
SpecimenConc.: 3.2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The complex elutes as a peak cooresponding to a complex containing two copies of AGR2 and one copy of IRE1beta luminal domain.
Specimen supportGrid type: UltrAuFoil R0./1
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 281.15 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 11.95 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails
7UCSF ChimeraX1.9model fittinglocal EM fitting
9cryoSPARC4.6.0initial Euler assignment
10cryoSPARC4.6.0final Euler assignment
11cryoSPARC4.6.0classification
12cryoSPARC4.6.03D reconstruction
19PHENIX1.21.2_5419model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 313426 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT
Atomic model building

3D fitting-ID: 1

IDPDB-IDPdb chain-IDAccession codeChain residue rangeInitial refinement model-IDSource nameTypeChain-ID
1AF-Q76MJ5-F135-4291AlphaFoldin silico model
29I3F

9i3f

A9I3FPDBexperimental modelA
39I3F

9i3f

C9I3FPDBexperimental modelC
RefinementHighest resolution: 2.9 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0034554
ELECTRON MICROSCOPYf_angle_d0.576198
ELECTRON MICROSCOPYf_dihedral_angle_d4.894609
ELECTRON MICROSCOPYf_chiral_restr0.04712
ELECTRON MICROSCOPYf_plane_restr0.006776

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