{"entity": "researcher", "timestamp": "2026-08-20T21:13:16.866Z", "family": "Cheng", "given": "Jingdong", "initials": "J", "orcid": "0000-0003-4442-377X", "affiliations": ["Gene Center Munich, Department of Biochemistry, University of Munich, Munich 81377, Germany."], "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/researcher/5d20d179bb3b4727a94304aab9401e84.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/researcher/5d20d179bb3b4727a94304aab9401e84"}}, "publications": [{"entity": "publication", "iuid": "67ef952b33644de3bf92e8209d553778", "links": {"self": {"href": "https://publications-affiliated.scilifelab.se/publication/67ef952b33644de3bf92e8209d553778.json"}, "display": {"href": "https://publications-affiliated.scilifelab.se/publication/67ef952b33644de3bf92e8209d553778"}}, "title": "Structural basis of l-tryptophan-dependent inhibition of release factor 2 by the TnaC arrest peptide.", "authors": [{"family": "Su", "given": "Ting", "initials": "T"}, {"family": "Kudva", "given": "Renuka", "initials": "R"}, {"family": "Becker", "given": "Thomas", "initials": "T"}, {"family": "Buschauer", "given": "Robert", "initials": "R"}, {"family": "Komar", "given": "Tobias", "initials": "T"}, {"family": "Berninghausen", "given": "Otto", "initials": "O"}, {"family": "von Heijne", "given": "Gunnar", "initials": "G"}, {"family": "Cheng", "given": "Jingdong", "initials": "J", "orcid": "0000-0003-4442-377X", "researcher": {"href": "https://publications-affiliated.scilifelab.se/researcher/5d20d179bb3b4727a94304aab9401e84.json"}}, {"family": "Beckmann", "given": "Roland", "initials": "R"}], "type": "journal article", "published": "2021-09-20", "journal": {"title": "Nucleic Acids Res.", "issn": "1362-4962", "volume": "49", "issue": "16", "pages": "9539-9547", "issn-l": "0305-1048"}, "abstract": "In Escherichia coli, elevated levels of free l-tryptophan (l-Trp) promote translational arrest of the TnaC peptide by inhibiting its termination. However, the mechanism by which translation-termination by the UGA-specific decoding release factor 2 (RF2) is inhibited at the UGA stop codon of stalled TnaC-ribosome-nascent chain complexes has so far been ambiguous. This study presents cryo-EM structures for ribosomes stalled by TnaC in the absence and presence of RF2 at average resolutions of 2.9 and 3.5 \u00c5, respectively. Stalled TnaC assumes a distinct conformation composed of two small \u03b1-helices that act together with residues in the peptide exit tunnel (PET) to coordinate a single L-Trp molecule. In addition, while the peptidyl-transferase center (PTC) is locked in a conformation that allows RF2 to adopt its canonical position in the ribosome, it prevents the conserved and catalytically essential GGQ motif of RF2 from adopting its active conformation in the PTC. This explains how translation of the TnaC peptide effectively allows the ribosome to function as a L-Trp-specific small-molecule sensor that regulates the tnaCAB operon.", "doi": "10.1093/nar/gkab665", "pmid": "34403461", "labels": [], "xrefs": [{"db": "pmc", "key": "PMC8450073"}, {"db": "pii", "key": "6353806"}], "notes": [], "created": "2026-08-20T09:49:41.150Z", "modified": "2026-08-20T09:49:41.220Z"}, {"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"}]}