{"entity": "researcher", "timestamp": "2026-08-20T20:58:00.364Z", "family": "Beckmann", "given": "Roland", "initials": "R", "orcid": "0000-0003-4291-3898", "affiliations": [], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/db3a9ba195ec4b5385f2c415ce1f4720.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/db3a9ba195ec4b5385f2c415ce1f4720"}}, "publications": [{"entity": "publication", "iuid": "c8fdfd804f98430294ec82fcf9f251df", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/c8fdfd804f98430294ec82fcf9f251df.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/c8fdfd804f98430294ec82fcf9f251df"}}, "title": "Structural and mutational analysis of the ribosome-arresting human XBP1u.", "authors": [{"family": "Shanmuganathan", "given": "Vivekanandan", "initials": "V"}, {"family": "Schiller", "given": "Nina", "initials": "N"}, {"family": "Magoulopoulou", "given": "Anastasia", "initials": "A"}, {"family": "Cheng", "given": "Jingdong", "initials": "J"}, {"family": "Braunger", "given": "Katharina", "initials": "K", "orcid": "0000-0002-9067-2155", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2b39fb3443274977a68d01fa57862b6d.json"}}, {"family": "Cymer", "given": "Florian", "initials": "F"}, {"family": "Berninghausen", "given": "Otto", "initials": "O"}, {"family": "Beatrix", "given": "Birgitta", "initials": "B"}, {"family": "Kohno", "given": "Kenji", "initials": "K", "orcid": "0000-0002-3503-6551", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e2a1db1d762d47e48ad86f25b7ae5962.json"}}, {"family": "von Heijne", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-4490-8569", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/529a460e668a479ca7d9b9271375ef9f.json"}}, {"family": "Beckmann", "given": "Roland", "initials": "R", "orcid": "0000-0003-4291-3898", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db3a9ba195ec4b5385f2c415ce1f4720.json"}}], "type": "journal article", "published": "2019-06-27", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "8", "issn-l": "2050-084X"}, "abstract": "XBP1u, a central component of the unfolded protein response (UPR), is a mammalian protein containing a functionally critical translational arrest peptide (AP). Here, we present a 3 \u00c5 cryo-EM structure of the stalled human XBP1u AP. It forms a unique turn in the ribosomal exit tunnel proximal to the peptidyl transferase center where it causes a subtle distortion, thereby explaining the temporary translational arrest induced by XBP1u. During ribosomal pausing the hydrophobic region 2 (HR2) of XBP1u is recognized by SRP, but fails to efficiently gate the Sec61 translocon. An exhaustive mutagenesis scan of the XBP1u AP revealed that only 8 out of 20 mutagenized positions are optimal; in the remaining 12 positions, we identify 55 different mutations increase the level of translational arrest. Thus, the wildtype XBP1u AP induces only an intermediate level of translational arrest, allowing efficient targeting by SRP without activating the Sec61 channel.", "doi": "10.7554/eLife.46267", "pmid": "31246176", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC6624018"}, {"db": "pii", "key": "46267"}], "notes": [], "created": "2026-08-20T13:52:46.645Z", "modified": "2026-08-20T13:52:46.685Z"}, {"entity": "publication", "iuid": "0c727bba3fcb4a39be867a4a424af099", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/0c727bba3fcb4a39be867a4a424af099.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/0c727bba3fcb4a39be867a4a424af099"}}, "title": "Author response: Structural and mutational analysis of the ribosome-arresting human XBP1u", "authors": [{"family": "Shanmuganathan", "given": "Vivekanandan", "initials": "V"}, {"family": "Schiller", "given": "Nina", "initials": "N"}, {"family": "Magoulopoulou", "given": "Anastasia", "initials": "A"}, {"family": "Cheng", "given": "Jingdong", "initials": "J"}, {"family": "Braunger", "given": "Katharina", "initials": "K", "orcid": "0000-0002-9067-2155", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2b39fb3443274977a68d01fa57862b6d.json"}}, {"family": "Cymer", "given": "Florian", "initials": "F"}, {"family": "Berninghausen", "given": "Otto", "initials": "O"}, {"family": "Beatrix", "given": "Birgitta", "initials": "B"}, {"family": "Kohno", "given": "Kenji", "initials": "K", "orcid": "0000-0002-3503-6551", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e2a1db1d762d47e48ad86f25b7ae5962.json"}}, {"family": "von Heijne", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-4490-8569", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/529a460e668a479ca7d9b9271375ef9f.json"}}, {"family": "Beckmann", "given": "Roland", "initials": "R", "orcid": "0000-0003-4291-3898", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db3a9ba195ec4b5385f2c415ce1f4720.json"}}], "type": "peer-review", "published": "2019-06-19", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.46267.038", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:52:48.660Z", "modified": "2026-08-20T13:52:48.720Z"}, {"entity": "publication", "iuid": "7f4bc7efed704d009c25b5cf03a0831e", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/7f4bc7efed704d009c25b5cf03a0831e.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/7f4bc7efed704d009c25b5cf03a0831e"}}, "title": "Structural and mutational analysis of the ribosome-arresting human XBP1u", "authors": [{"family": "Shanmuganathan", "given": "Vivekanandan", "initials": "V"}, {"family": "Schiller", "given": "Nina", "initials": "N"}, {"family": "Magoulopoulou", "given": "Anastasia", "initials": "A"}, {"family": "Cheng", "given": "Jingdong", "initials": "J"}, {"family": "Braunger", "given": "Katharina", "initials": "K", "orcid": "0000-0002-9067-2155", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/2b39fb3443274977a68d01fa57862b6d.json"}}, {"family": "Cymer", "given": "Florian", "initials": "F"}, {"family": "Berninghausen", "given": "Otto", "initials": "O"}, {"family": "Beatrix", "given": "Birgitta", "initials": "B"}, {"family": "Kohno", "given": "Kenji", "initials": "K", "orcid": "0000-0002-3503-6551", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/e2a1db1d762d47e48ad86f25b7ae5962.json"}}, {"family": "von Heijne", "given": "Gunnar", "initials": "G"}, {"family": "Beckmann", "given": "Roland", "initials": "R", "orcid": "0000-0003-4291-3898", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db3a9ba195ec4b5385f2c415ce1f4720.json"}}], "type": "posted-content", "published": "2019-03-25", "journal": {"issn-l": null}, "abstract": null, "doi": "10.1101/588681", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T11:13:24.825Z", "modified": "2026-08-20T11:13:24.944Z"}, {"entity": "publication", "iuid": "9e3d9eb161254546b2717d84a66f73fe", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9e3d9eb161254546b2717d84a66f73fe.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9e3d9eb161254546b2717d84a66f73fe"}}, "title": "The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling.", "authors": [{"family": "Su", "given": "Ting", "initials": "T", "orcid": "0000-0002-3185-8144", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d496e2bc5d34090a8454c553a7f21ea.json"}}, {"family": "Cheng", "given": "Jingdong", "initials": "J", "orcid": "0000-0003-4442-377X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5d20d179bb3b4727a94304aab9401e84.json"}}, {"family": "Sohmen", "given": "Daniel", "initials": "D"}, {"family": "Hedman", "given": "Rickard", "initials": "R"}, {"family": "Berninghausen", "given": "Otto", "initials": "O"}, {"family": "von Heijne", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-4490-8569", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/529a460e668a479ca7d9b9271375ef9f.json"}}, {"family": "Wilson", "given": "Daniel N", "initials": "DN", "orcid": "0000-0003-3816-3828", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c2d78750ccb42239a7363f99f58dcc5.json"}}, {"family": "Beckmann", "given": "Roland", "initials": "R", "orcid": "0000-0003-4291-3898", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db3a9ba195ec4b5385f2c415ce1f4720.json"}}], "type": "journal article", "published": "2017-05-30", "journal": {"title": "Elife", "issn": "2050-084X", "volume": "6", "issue": null, "issn-l": "2050-084X"}, "abstract": "Interaction between the nascent polypeptide chain and the ribosomal exit tunnel can modulate the rate of translation and induce translational arrest to regulate expression of downstream genes. The ribosomal tunnel also provides a protected environment for initial protein folding events. Here, we present a 2.9 \u00c5 cryo-electron microscopy structure of a ribosome stalled during translation of the extremely compacted VemP nascent chain. The nascent chain forms two \u03b1-helices connected by an \u03b1-turn and a loop, enabling a total of 37 amino acids to be observed within the first 50-55 \u00c5 of the exit tunnel. The structure reveals how \u03b1-helix formation directly within the peptidyltransferase center of the ribosome interferes with aminoacyl-tRNA accommodation, suggesting that during canonical translation, a major role of the exit tunnel is to prevent excessive secondary structure formation that can interfere with the peptidyltransferase activity of the ribosome.", "doi": "10.7554/eLife.25642", "pmid": "28556777", "labels": {"Affiliated researcher": null}, "xrefs": [{"db": "pmc", "key": "PMC5449182"}, {"db": "pii", "key": "e25642"}], "notes": [], "created": "2018-12-05T11:26:11.770Z", "modified": "2026-08-20T13:52:08.671Z"}, {"entity": "publication", "iuid": "9a237cc1cea04e4db61963c8b08b68de", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/9a237cc1cea04e4db61963c8b08b68de.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/9a237cc1cea04e4db61963c8b08b68de"}}, "title": "Author response: The force-sensing peptide VemP employs extreme compaction and secondary structure formation to induce ribosomal stalling", "authors": [{"family": "Su", "given": "Ting", "initials": "T", "orcid": "0000-0002-3185-8144", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/8d496e2bc5d34090a8454c553a7f21ea.json"}}, {"family": "Cheng", "given": "Jingdong", "initials": "J", "orcid": "0000-0003-4442-377X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5d20d179bb3b4727a94304aab9401e84.json"}}, {"family": "Sohmen", "given": "Daniel", "initials": "D"}, {"family": "Hedman", "given": "Rickard", "initials": "R"}, {"family": "Berninghausen", "given": "Otto", "initials": "O"}, {"family": "von Heijne", "given": "Gunnar", "initials": "G", "orcid": "0000-0002-4490-8569", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/529a460e668a479ca7d9b9271375ef9f.json"}}, {"family": "Wilson", "given": "Daniel N", "initials": "DN", "orcid": "0000-0003-3816-3828", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/7c2d78750ccb42239a7363f99f58dcc5.json"}}, {"family": "Beckmann", "given": "Roland", "initials": "R", "orcid": "0000-0003-4291-3898", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/db3a9ba195ec4b5385f2c415ce1f4720.json"}}], "type": "peer-review", "published": "2017-05-17", "journal": {"issn-l": null}, "abstract": null, "doi": "10.7554/elife.25642.017", "pmid": null, "labels": [], "xrefs": [], "notes": [], "created": "2026-08-20T13:52:10.571Z", "modified": "2026-08-20T13:52:10.616Z"}]}