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- EMDB-52616: Cryo-EM structure of the AGR2 dimer in complex with the monomeric... -

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Basic information

Entry
Database: EMDB / ID: EMD-52616
TitleCryo-EM structure of the AGR2 dimer in complex with the monomeric IRE1beta luminal domain
Map data
Sample
  • Complex: The complex of AGR2 and IRE1beta luminal domain
    • Protein or peptide: Anterior gradient protein 2 homolog
    • Protein or peptide: Serine/threonine-protein kinase/endoribonuclease IRE2
Keywordsendoplasmic reticulum (ER) / molecular chaperones/ protein multimerisation/ unfolded protein response (UPR) / CHAPERONE
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsYan Y / Hardwick S / Tung J / Ron D
Funding support United Kingdom, 1 items
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, 2025-
Header (metadata) releaseOct 22, 2025-
Map releaseOct 22, 2025-
UpdateOct 22, 2025-
Current statusOct 22, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_52616.png

Downloads & links

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Map

FileDownload / File: emd_52616.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 416 pix.
= 303.264 Å		0.73 Å/pix.
x 416 pix.
= 303.264 Å		0.73 Å/pix.
x 416 pix.
= 303.264 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.729 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.11571237 - 0.38634348
Average (Standard dev.)0.00006561396 (±0.006317754)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 303.26398 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_52616_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_52616_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : The complex of AGR2 and IRE1beta luminal domain

EntireName: The complex of AGR2 and IRE1beta luminal domain
Components
  • Complex: The complex of AGR2 and IRE1beta luminal domain
    • Protein or peptide: Anterior gradient protein 2 homolog
    • Protein or peptide: Serine/threonine-protein kinase/endoribonuclease IRE2

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Supramolecule #1: The complex of AGR2 and IRE1beta luminal domain

SupramoleculeName: The complex of AGR2 and IRE1beta luminal domain / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Co-expressed in E.coli.
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Anterior gradient protein 2 homolog

MacromoleculeName: Anterior gradient protein 2 homolog / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 17.845541 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
RDTTVKPGAK KDTKDSRPKL PQTLSRGWGD QLIWTQTYEE ALYKSKTSNK PLMIIHHLDE CPHSQALKKV FAENKEIQKL AEQFVLLNL VYETTDKHLS PDGQYVPRIM FVDPSLTVRA DITGRYSNRL YAYEPADTAL LLDNMKKALK LLKTEL

UniProtKB: Anterior gradient protein 2 homolog

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Macromolecule #2: Serine/threonine-protein kinase/endoribonuclease IRE2

MacromoleculeName: Serine/threonine-protein kinase/endoribonuclease IRE2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO / EC number: non-specific serine/threonine protein kinase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 43.393164 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: LRPENLLLVS TLDGSLHALS KQTGDLKWTL RDDPVIEGPM YVTEMAFLSD PADGSLYILG TQKQQGLMKL PFTIPELVHA SPCRSSDGV FYTGRKQDAW FVVDPESGET QMTLTTEGPS TPRLYIGRTQ YTVTMHDPRA PALRWNTTYR RYSAPPMDGS P GKYMSHLA ...String:
LRPENLLLVS TLDGSLHALS KQTGDLKWTL RDDPVIEGPM YVTEMAFLSD PADGSLYILG TQKQQGLMKL PFTIPELVHA SPCRSSDGV FYTGRKQDAW FVVDPESGET QMTLTTEGPS TPRLYIGRTQ YTVTMHDPRA PALRWNTTYR RYSAPPMDGS P GKYMSHLA SCGMGLLLTV DPGSGTVLWT QDLGVPVMGV YTWHQDGLRQ LPHLTLARDT LHFLALRWGH IRLPASGPRD TA TLFSTLD TQLLMTLYVG KDETGFYVSK ALVHTGVALV PRGLTLAPAD GPTTDEVTLQ VSGEREGSPS TAVRYPSGSV ALP SQWLLI GHHELPPVLH TTMLRVHPTL GSGTAETRPP ENTQAPAFFL ELLSLSREKL WDSELHPEEK TPDSYLGLG

UniProtKB: Serine/threonine-protein kinase/endoribonuclease IRE2

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration3.2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
150.0 mMNaClsodium chloride
200.0 mMTristris(hydroxymethyl)aminomethane
0.2 mMTCEPtris(2-carboxyethyl)phosphine
GridModel: UltrAuFoil R0./1
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 281.15 K / Instrument: FEI VITROBOT MARK IV
DetailsThe complex elutes as a peak cooresponding to a complex containing two copies of AGR2 and one copy of IRE1beta luminal domain.

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 11.95 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 313426
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 4.6.0)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

5-f1

residue_range: 35-429, source_name: AlphaFold, initial_model_type: in silico model

9i3f

chain_id: A, source_name: PDB, initial_model_type: experimental model

9i3f

chain_id: C, source_name: PDB, initial_model_type: experimental model
RefinementProtocol: RIGID BODY FIT
Output model

PDB-9i3u:
Cryo-EM structure of the AGR2 dimer in complex with the monomeric IRE1beta luminal domain

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