21NR

Cryo-EM structure of TLP-IPT

Summary for 21NR

• Entry DOI: 10.2210/pdb21nr/pdb
• EMDB information: 67848
• Descriptor: TLP-IPT, alpha-D-mannopyranose-(1-3)-beta-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-[beta-D-xylopyranose-(1-2)][alpha-D-mannopyranose-(1-4)]beta-D-galactopyranose-(1-3)-[beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)-[beta-D-xylopyranose-(1-2)][beta-D-glucopyranose-(1-4)]beta-D-galactopyranose-(1-3)-beta-D-xylopyranose-(1-2)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-beta-D-glucopyranose-(1-4)]beta-D-xylopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-mannopyranose-(1-6)-beta-D-glucopyranose-(1-2)-[beta-D-glucopyranose-(1-2)-beta-D-xylopyranose-(1-3)-alpha-L-arabinofuranose-(1-3)]alpha-D-galactopyranose-(1-3)-[beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]beta-D-mannopyranose-(1-4)-[beta-D-xylopyranose-(1-2)-[beta-D-xylopyranose-(1-4)]beta-D-glucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]beta-D-mannopyranose-(1-3)-beta-D-xylopyranose-(1-6)][beta-D-glucopyranose-(1-2)-[beta-D-glucopyranose-(1-4)]beta-D-xylopyranose-(1-3)-alpha-D-mannopyranose-(1-2)][beta-D-xylopyranose-(1-3)]beta-D-glucopyranose-(1-6)-beta-D-glucopyranose-(1-2)-beta-L-arabinofuranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)-beta-D-xylopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)]beta-D-glucopyranose-(1-3)][beta-D-xylopyranose-(1-4)]beta-D-mannopyranose-(1-2)-[beta-D-glucopyranose-(1-4)-beta-D-xylopyranose-(1-4)]beta-D-xylopyranose-(1-3)-[beta-D-xylopyranose-(1-3)-[beta-D-glucopyranose-(1-4)][beta-D-glucopyranose-(1-6)]beta-D-glucopyranose-(1-3)-alpha-D-mannopyranose-(1-4)]beta-D-glucopyranose-(1-6)-[beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose, ... (14 entities in total)
• Functional Keywords: glycofibril, carbohydrate
• Biological source: algae metagenome
• Total number of polymer chains: 1
• Total formula weight: 188630.62

Authors

Yan, N.,Li, Z.,Wang, T. (deposition date: 2025-12-21, release date: 2026-06-24)

Primary citation

Li, Z.,Wang, T.,Sun, Y.,Xu, K.,Huang, W.,Zhang, Q.C.,Yan, C.,Hu, M.,Yan, N.
CryoSeek identification of glycofibrils with diverse compositions and structural assemblies.
Cell Chem Biol, 33:699-710.e2, 2026

PubMed Abstract: CryoSeek is a research strategy that employs cryo-electron microscopy (cryo-EM) to discover bio-entities from accessible sources, supplemented with AI-facilitated data processing and bioinformatic analyses. Here we report CryoSeek-based characterization of more glycofibrils isolated from the Tsinghua Lotus Pond (TLP), named TLP-0/2/3/4b/IPT, with resolutions ranging from 3.0-3.5 Å. These glycofibrils, all covered with dense glycoshells, have various mass percentiles of the central protein components. TLP-0 has no protein at all, TLP-2 and TLP-4b each only have a linear chain of di- or tetra-peptide repeats, respectively; the central stem of TLP-3 is a trimer of linear tripeptide repeats, and IPT (immunoglobulin-like, plexins, and transcription factors) refers to the tandem domain that constitutes the central stem of TLP-IPT. Glycan-mediated interactions determine the structural assembly of the glycofibrils that lack folded protein component. Our previous and current studies reveal the diversity of the structural folds of glycans, advance our understanding of glycan architecture, and further demonstrate CryoSeek as a structure-first paradigm for discovery.

PubMed: 42013841
DOI: 10.1016/j.chembiol.2026.03.008

Experimental method

ELECTRON MICROSCOPY (3.3 Å)