9ikm: Difference between revisions
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==Cryo-EM structure of TLP-4== | |||
<StructureSection load='9ikm' size='340' side='right'caption='[[9ikm]], [[Resolution|resolution]] 3.50Å' scene=''> | |||
== Structural highlights == | |||
<table><tr><td colspan='2'>[[9ikm]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Algae_metagenome Algae metagenome]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9IKM OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9IKM FirstGlance]. <br> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.5Å</td></tr> | |||
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=A1D9O:(2~{S},3~{S},4~{S})-3,4-bis(oxidanyl)pyrrolidine-2-carboxylic+acid'>A1D9O</scene>, <scene name='pdbligand=AHR:ALPHA-L-ARABINOFURANOSE'>AHR</scene>, <scene name='pdbligand=BGC:BETA-D-GLUCOSE'>BGC</scene>, <scene name='pdbligand=BMA:BETA-D-MANNOSE'>BMA</scene>, <scene name='pdbligand=FUB:BETA-L-ARABINOFURANOSE'>FUB</scene>, <scene name='pdbligand=GAL:BETA-D-GALACTOSE'>GAL</scene>, <scene name='pdbligand=MAN:ALPHA-D-MANNOSE'>MAN</scene>, <scene name='pdbligand=NGA:N-ACETYL-D-GALACTOSAMINE'>NGA</scene></td></tr> | |||
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=9ikm FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9ikm OCA], [https://pdbe.org/9ikm PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9ikm RCSB], [https://www.ebi.ac.uk/pdbsum/9ikm PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9ikm ProSAT]</span></td></tr> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
CryoSeek II: Cryo-EM analysis of glycofibrils from freshwater reveals well-structured glycans coating linear tetrapeptide repeats.,Wang T, Huang W, Xu K, Sun Y, Zhang QC, Yan C, Li Z, Yan N Proc Natl Acad Sci U S A. 2025 Jan 7;122(1):e2423943122. doi: , 10.1073/pnas.2423943122. Epub 2024 Dec 31. PMID:39739783<ref>PMID:39739783</ref> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
[[Category: | </div> | ||
<div class="pdbe-citations 9ikm" style="background-color:#fffaf0;"></div> | |||
== References == | |||
<references/> | |||
__TOC__ | |||
</StructureSection> | |||
[[Category: Algae metagenome]] | |||
[[Category: Large Structures]] | |||
[[Category: Li Z]] | |||
[[Category: Wang T]] | |||
[[Category: Yan C]] | |||
[[Category: Yan N]] | |||
