PROTAC-induced IRE1 ternary complex

2026-04-22 REL RCSB INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY INITIAL_RELEASE REPOSITORY DATABASE_REFERENCES citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update EXPERIMENTAL_SUMMARY citation citation_author em_admin _citation.country _citation.journal_abbrev _citation.journal_id_CSD _citation.journal_id_ISSN _citation.journal_volume _citation.page_first _citation.page_last _citation.pdbx_database_id_DOI _citation.pdbx_database_id_PubMed _citation.title _citation.year _em_admin.last_update RCSB RCSB 2025-02-07 2025-11-05 2025-11-05 2026-04-22 Other private United States PROTAC-induced IRE1 ternary complex Du J Johnson M Azumaya C Rohou A Hsu PL Ashkenazi A Complex, degrader, TRANSFERASE Du J Villemure E Johnson M Azumaya C Gaspar CJ Marsters S Lawrence D Foster S Rohou A Cheung TK Rose CM Garner T Ro S Clark K Beresini MH Braun MG Rudolph J Hsu P Ashkenazi A Chemically-induced degradation of the endoplasmic-reticulum stress sensor IRE1 by a VHL-recruiting chimera. Nat Commun UK 16 11445 11445 2025 41381506 doi:10.1038/s41467-025-66382-8 2041-1723 9n88 FULLOVERLAP EMDB EMD-49119 associated EM volume

IRE1:G6374:VHL:Eloc:Elob IRE1:G6374:VHL:Eloc:Elob 0 1 2 3

G6374 is the PROTAC that recruits VHL to IRE1. IRE1 is recombinantly expressed and purified from Sf9 cells, VHL is co-expressed and co-purified with Eloc and Elob in BL21 cells. The complex was formed by adding each component in vitro. Because the EloB density had insufficient quality for de novo modeling, we built only residues 68 to 73 into the structure.

Homo sapiens Serine/threonine-protein kinase/endoribonuclease IRE1 Homo sapiens 0.046329266 2 Spodoptera frugiperda LEVO VVIVGKISFCPKDVLGHGAEGTIVYRGMFDNRDVAVKRILPECFSFADREVQLLRESDEHPNVIRYFCTEKDRQFQYIAI ELCAATLQEYVEQKDFAHLGLEPITLLQQTTSGLAHLHSLNIVHRDLKPHNILISMPNAHGKIKAMISDFGLCKKLAVGR HSFSRRSGVPGTEGWIAPEMLSEDCKENPTYTVDIFSAGCVFYYVISEGSHPFGKSLQRQANILLGACSLDCLHPEKHED VIARELIEKMIAMDPQKRPSAKHVLKHPFFWSLEKQLQFFQDVSDRIEKESLDGPIVKQLERGGRAVVKMDWRENITVPL QTDLRKFRTYKGGSVRDLLRAMRNKKHHYRELPAEVRETLGSLPDDFVCYFTSRFPHLLAHTYRAMELCSHERLFQPYYF HE O75460 2.7.11.1 von Hippel-Lindau disease tumor suppressor Homo sapiens 0.017031412 2 Escherichia coli BL21(DE3) LEVO PVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSL NVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIA P40337 Elongin-C Homo sapiens 0.01062519 2 Escherichia coli BL21(DE3) LEVO MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIA PEIALELLMAANFL Q15369 Elongin-B peptide Homo sapiens 0.0006397229999999999 2 Escherichia coli BL21(DE3) LEVO RPQAPA Q15370 3-methyl-N-(5-{4-[(1r,4S)-4-{[7-oxo-8-(propan-2-yl)-7,8-dihydropyrido[2,3-d]pyrimidin-2-yl]amino}cyclohexyl]piperazin-1-yl}pentanoyl)-L-valyl-(4R)-4-hydroxy-N-{[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl}-L-prolinamide 0.000883156 2 A1BWF water 1.8015e-05 6 HOH singleParticle particle 0.15 7.2 20.0 HEPES 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid 150.0 NaCl sodium chloride 1.0 TCEP tris(2-carboxyethyl)phosphine 0.005 CTAB cetrimonium bromide

I used 0.5 mM BS3 for crosslinking the protein complex, then diluted it to 0.05 mM for grid preparation.

UltrAuFoil R1.2/1.3 GOLD 300 GOLD HOLEY 2.5

The grid was coated with a hydrophilic self-assembled PEG monolayer to improve particle distribution.

ETHANE 100 277.15 FEI VITROBOT MARK IV

7 force; 2 s blot time..

Got monodispersed particles on the grid.

TFS KRIOS FLOOD BEAM BRIGHT FIELD FIELD EMISSION GUN 300 0.6 3.5 TFS FALCON 4i (4k x 4k) 12400 45.0 1 5101645 cryoSPARC 4.6 PHASE FLIPPING ONLY 6W3B

I have used 2 PDB entries to build the model: 6W3B 5T35

C2 2.6 FSC 0.143 CUT-OFF cryoSPARC 4.6 400055 RANDOM ASSIGNMENT cryoSPARC 4.6 MAXIMUM LIKELIHOOD cryoSPARC 4.6 emd_49119.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 408 408 408 0 0 0 408 408 408 298.24802 298.24802 298.24802 90.0 90.0 90.0 X Y Z -0.0645948 0.1749696 -0.00004245554 0.0029520201 0.73100007 0.73100007 0.73100007 0.03 AUTHOR ::::EMDATABANK.org::::EMD-49119:::: emd_49119_half_map_2.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 408 408 408 0 0 0 408 408 408 298.24802 298.24802 298.24802 90.0 90.0 90.0 X Y Z -0.06592177 0.18506558 0.000024155135 0.004428384 0.73100007 0.73100007 0.73100007 AUTHOR ::::EMDATABANK.org::::EMD-49119:::: emd_49119_half_map_1.map.gz 1 IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) 408 408 408 0 0 0 408 408 408 298.24802 298.24802 298.24802 90.0 90.0 90.0 X Y Z -0.06868864 0.18035267 0.00002439023 0.0044297543 0.73100007 0.73100007 0.73100007 AUTHOR ::::EMDATABANK.org::::EMD-49119::::