9IKM

Cryo-EM structure of TLP-4

This is a non-PDB format compatible entry.

Summary for 9IKM

• Entry DOI: 10.2210/pdb9ikm/pdb
• EMDB information: 60659
• Descriptor: TLP-4, alpha-L-arabinofuranose-(1-2)-beta-D-galactopyranose-(1-2)-beta-L-arabinofuranose-(1-2)-[alpha-L-arabinofuranose-(1-2)-beta-L-arabinofuranose-(1-3)]beta-L-arabinofuranose-(1-3)-alpha-L-arabinofuranose, alpha-L-arabinofuranose-(1-3)-alpha-L-arabinofuranose-(1-3)-alpha-D-mannopyranose-(1-2)-[alpha-L-arabinofuranose-(1-2)-alpha-L-arabinofuranose-(1-4)][alpha-L-arabinofuranose-(1-6)]beta-D-galactopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-[alpha-L-arabinofuranose-(1-4)-alpha-D-mannopyranose-(1-3)-[alpha-L-arabinofuranose-(1-3)-[alpha-L-arabinofuranose-(1-6)]beta-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-[alpha-L-arabinofuranose-(1-2)][alpha-L-arabinofuranose-(1-6)]beta-D-mannopyranose-(1-6)][beta-L-arabinofuranose-(1-2)]alpha-D-mannopyranose-(1-6)-[alpha-L-arabinofuranose-(1-3)]2-acetamido-2-deoxy-beta-D-galactopyranose-(1-4)-[alpha-L-arabinofuranose-(1-3)-beta-L-arabinofuranose-(1-2)]beta-D-mannopyranose-(1-4)-beta-D-mannopyranose-(1-2)-[alpha-L-arabinofuranose-(1-5)]beta-L-arabinofuranose, ... (4 entities in total)
• Functional Keywords: fibril, protein fibril
• Biological source: algae metagenome
• Total number of polymer chains: 1
• Total formula weight: 143729.74

Authors

Yan, N.,Yan, C.,Li, Z.,Wang, T. (deposition date: 2024-06-27, release date: 2025-01-08)

Primary citation

Wang, T.,Huang, W.,Xu, K.,Sun, Y.,Zhang, Q.C.,Yan, C.,Li, Z.,Yan, N.
CryoSeek II: Cryo-EM analysis of glycofibrils from freshwater reveals well-structured glycans coating linear tetrapeptide repeats.
Proc.Natl.Acad.Sci.USA, 122:e2423943122-e2423943122, 2025

PubMed Abstract: 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 >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.

PubMed: 39739783
DOI: 10.1073/pnas.2423943122

Experimental method

ELECTRON MICROSCOPY (3.5 Å)