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Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2025,1,7]]},"abstract":"<jats:p>Despite the recent breakthrough in structure determination and prediction of proteins, the structural investigation of carbohydrates remains a challenge. Here, we report the cryo-EM analysis of a glycofibril found in the freshwater in the Tsinghua Lotus Pond. The fibril, which we name TLP-4, is made of a linear chain of tetrapeptide repeats coated with &gt;4 nm thick glycans. In each repeat, two glycans are O-linked to a 3,4-dihydroxyproline and another glycan attaches to the adjacent Ser or Thr. The fibril structure is entirely maintained through glycan packing. Bioinformatic analysis confirms the conservation of the TLP-4 repeats across species, suggesting the existence of a large number of glycofibrils to be discovered. Our findings not only provide valuable insights into the structural roles of glycans in bio-assemblies but also demonstrate the potential of our recently formulated research strategy of CryoSeek to find bioentities and establish prototypes for structural studies of carbohydrates.<\/jats:p>","DOI":"10.1073\/pnas.2423943122","type":"journal-article","created":{"date-parts":[[2024,12,31]],"date-time":"2024-12-31T13:42:02Z","timestamp":1735652522000},"update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":11,"title":["CryoSeek II: Cryo-EM analysis of glycofibrils from freshwater reveals well-structured glycans coating linear tetrapeptide repeats"],"prefix":"10.1073","volume":"122","author":[{"given":"Tongtong","family":"Wang","sequence":"first","affiliation":[{"name":"Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenze","family":"Huang","sequence":"additional","affiliation":[{"name":"Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7226-5479","authenticated-orcid":false,"given":"Kui","family":"Xu","sequence":"additional","affiliation":[{"name":"Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yitong","family":"Sun","sequence":"additional","affiliation":[{"name":"Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qiangfeng Cliff","family":"Zhang","sequence":"additional","affiliation":[{"name":"Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9338-8048","authenticated-orcid":false,"given":"Chuangye","family":"Yan","sequence":"additional","affiliation":[{"name":"Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3296-2293","authenticated-orcid":false,"given":"Zhangqiang","family":"Li","sequence":"additional","affiliation":[{"name":"Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University","place":["Beijing, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4829-7416","authenticated-orcid":false,"given":"Nieng","family":"Yan","sequence":"additional","affiliation":[{"name":"Beijing Frontier Research Center for Biological Structures, State Key Laboratory of Membrane Biology, Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University","place":["Beijing, China"]},{"name":"Institute of Bio-Architecture and Bio-Interactions, Shenzhen Medical Academy of Research and Translation","place":["Shenzhen, China"]},{"name":"Institute of Chemical Biology, Shenzhen Bay Laboratory","place":["Shenzhen, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2024,12,31]]},"reference":[{"key":"e_1_3_4_1_2","doi-asserted-by":"publisher","DOI":"10.1093\/glycob\/cww086"},{"key":"e_1_3_4_2_2","first-page":"77","volume-title":"Essentials of Glycobiology","author":"Varki A.","year":"2015","unstructured":"A. Varki, P. Gagneux, \u201cBiological functions of glycans\u201d in Essentials of Glycobiology, A. Varki , Eds. (Cold Spring Harbor, New York, NY, 2015), pp. 77\u201388, 10.1101\/glycobiology.3e.007."},{"key":"e_1_3_4_3_2","doi-asserted-by":"publisher","DOI":"10.1093\/glycob\/3.2.97"},{"key":"e_1_3_4_4_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrm1746"},{"key":"e_1_3_4_5_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-981-13-2158-0_1"},{"key":"e_1_3_4_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.sbi.2009.06.001"},{"key":"e_1_3_4_7_2","doi-asserted-by":"publisher","DOI":"10.1038\/ni.f.203"},{"key":"e_1_3_4_8_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1749-6632.2012.06492.x"},{"key":"e_1_3_4_9_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1432-1033.1993.tb18347.x"},{"key":"e_1_3_4_10_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrm3383"},{"key":"e_1_3_4_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/0304-4157(87)90008-6"},{"key":"e_1_3_4_12_2","doi-asserted-by":"publisher","DOI":"10.1002\/(SICI)1521-1878(199905)21:5<412::AID-BIES8>3.0.CO;2-5"},{"key":"e_1_3_4_13_2","doi-asserted-by":"publisher","DOI":"10.1146\/annurev-pathol-012414-040438"},{"key":"e_1_3_4_14_2","doi-asserted-by":"publisher","DOI":"10.1111\/imr.12431"},{"key":"e_1_3_4_15_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2362-1"},{"key":"e_1_3_4_16_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.adh3856"},{"key":"e_1_3_4_17_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41589-021-00896-2"},{"key":"e_1_3_4_18_2","volume-title":"Essentials of Glycobiology","author":"Mulloy B.","year":"2009","unstructured":"B. Mulloy, G. Hart, P. Stanley, \u201cStructural analysis of glycans\u201d in Essentials of Glycobiology, A. Varki , Eds. (Cold Spring Harbor, New York, NY, 2009)."},{"key":"e_1_3_4_19_2","volume-title":"Essentials of Glycobiology","author":"Stanley P.","year":"2009","unstructured":"P. Stanley, R. Cummings, \u201cStructures common to different glycans\u201d in Essentials of Glycobiology, A. Varki , Eds. 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Wang The cryo-EM map of TLP-4. EMDB. https:\/\/www.ebi.ac.uk\/emdb\/EMD-60659. Deposited 27 June 2024."},{"key":"e_1_3_4_55_2","unstructured":"T. Wang The atomic coordinates of TLP-4. PDB. https:\/\/www.rcsb.org\/structure\/9IKM. Deposited 27 June 2024."},{"key":"e_1_3_4_56_2","unstructured":"T. Wang The metagenomic sequencing dataset of Tsinghua Lotus Pond. SRA. https:\/\/www.ncbi.nlm.nih.gov\/sra\/SRR31369693. Deposited 17 November 2024."}],"container-title":["Proceedings of the National Academy of Sciences"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pnas.org\/doi\/pdf\/10.1073\/pnas.2423943122","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,12,31]],"date-time":"2024-12-31T13:42:07Z","timestamp":1735652527000},"score":1,"resource":{"primary":{"URL":"https:\/\/pnas.org\/doi\/10.1073\/pnas.2423943122"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,12,31]]},"references-count":56,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2025,1,7]]}},"alternative-id":["10.1073\/pnas.2423943122"],"URL":"https:\/\/doi.org\/10.1073\/pnas.2423943122","relation":{},"ISSN":["0027-8424","1091-6490"],"issn-type":[{"value":"0027-8424","type":"print"},{"value":"1091-6490","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,12,31]]},"assertion":[{"value":"2024-11-17","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-12-02","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-12-31","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e2423943122"}}