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The stress-sensing domain of activated IRE1α forms helical filaments in narrow ER membrane tubes

Carter, Stephen D. and Tran, Ngoc-Han and De Maziere, Ann and Ashkenazi, Avi and Klumperman, Judith and Jensen, Grant J. and Walter, Peter (2021) The stress-sensing domain of activated IRE1α forms helical filaments in narrow ER membrane tubes. . (Unpublished)

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The signaling network of the unfolded protein response (UPR) adjusts the protein folding capacity of the endoplasmic reticulum (ER) according to need. The most conserved UPR sensor, IRE1α, spans the ER membrane and activates through oligomerization. IRE1α oligomers accumulate in dynamic foci. We determined the in-situ structure of IRE1α foci by cryogenic correlated light and electron microscopy (cryo-CLEM), combined with electron cryo-tomography (cryo-ET) and complementary immuno-electron microscopy. IRE1α oligomers localize to a network of narrow anastomosing ER tubes (diameter ~28 nm) with complex branching. The lumen of the tubes contains protein filaments, likely composed of linear arrays of IRE1α lumenal domain dimers, arranged in two intertwined, left-handed helices. Our findings define a previously unrecognized ER subdomain and suggest positive feedback in IRE1 signaling.

Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription Paper ItemCode
Carter, Stephen D.0000-0002-4237-4276
Tran, Ngoc-Han0000-0003-0638-2583
De Maziere, Ann0000-0001-8070-5104
Ashkenazi, Avi0000-0002-6890-4589
Klumperman, Judith0000-0003-4835-6228
Jensen, Grant J.0000-0003-1556-4864
Walter, Peter0000-0002-6849-708X
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. This version posted February 24, 2021. In the spirit of equal contribution, the order of co-first and co-corresponding authors will be switched for publication. Author order was determined by coin flip. We thank Margaret Elvekrog, Ariane Briegel, Diego Acosta-Alvear, Richard Fetter, Suzanne van Dijk, Stefan Niekamp and Vladislav Belyy for their advice and technical assistance. We thank Greg Huber, Robert Ernst, Adam Frost and Jodi Nunnari for insightful discussions. This work was supported in parts by NIH grants P50 AI150464 and R35 GM122588 to GJJ and NIH R01-GM032384 to PW. NHT is supported by the National Science Foundation Graduate Research Fellowship. JK is supported by the Dutch Research Council NEMI research program project number 184.034.014. ADM received salary from Genentech, Inc. PW is an Investigator of the Howard Hughes Medical Institute. Author contributions: AA, JK, PW and GJ, conceived of the study. NHT, SDC, PW and GJ designed cryo-CLEM experiments. NHT and SDC generated and screened grids. SDC performed the cryo-CLEM/cryo-ET and subtomogram averaging and generated IRE1α subdomain models, neural network-derived segmentations and movies. NHT performed manual segmentation, quantification of IRE1α subdomain dimension and calculations. ADM performed Epon-embedded electron microscopy and immunogold labeling experiments. NHT and SDC prepared figures. NHT, SDC, PW and GJ wrote the manuscript. The authors declare no competing interests. Data and materials availability: The codes used for data quantification and plots in this paper are freely available at The final sub-tomogram averaged maps and representative tomograms can be accessed at EMDB entry ID EMD-23058. All raw and processed data are available upon request. All cell lines and plasmids used in this paper are in the Walter lab depository and are available upon request.
Funding AgencyGrant Number
NIHP50 AI150464
NIHR35 GM122588
NSF Graduate Research FellowshipUNSPECIFIED
Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)184.034.014
Genentech, Inc.UNSPECIFIED
Howard Hughes Medical Institute (HHMI)UNSPECIFIED
Record Number:CaltechAUTHORS:20210225-141123693
Persistent URL:
Official Citation:The stress-sensing domain of activated IRE1α forms helical filaments in narrow ER membrane tubes. Stephen D Carter, Ngoc-Han Tran, Ann De Maziere, Avi Ashkenazi, Judith Klumperman, Grant J Jensen, Peter Walter. bioRxiv 2021.02.24.432779; doi:
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:108215
Deposited By: Tony Diaz
Deposited On:26 Feb 2021 00:29
Last Modified:26 Feb 2021 00:29

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