7Y63

ApoSIDT2-pH7.4

Summary for 7Y63

• Entry DOI: 10.2210/pdb7y63/pdb
• EMDB information: 33632
• Descriptor: SID1 transmembrane family member 2, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, ZINC ION, ... (4 entities in total)
• Functional Keywords: membrane protein
• Biological source: Homo sapiens (human)
• Total number of polymer chains: 2
• Total formula weight: 192235.55

Authors

Gong, D.S. (deposition date: 2022-06-18, release date: 2023-06-21, Last modification date: 2024-11-20)

Primary citation

Qian, D.,Cong, Y.,Wang, R.,Chen, Q.,Yan, C.,Gong, D.S.
Structural insight into the human SID1 transmembrane family member 2 reveals its lipid hydrolytic activity.
Nat Commun, 14:3568-3568, 2023

PubMed Abstract: The systemic RNAi-defective (SID) transmembrane family member 2 (SIDT2) is a putative nucleic acid channel or transporter that plays essential roles in nucleic acid transport and lipid metabolism. Here, we report the cryo-electron microscopy (EM) structures of human SIDT2, which forms a tightly packed dimer with extensive interactions mediated by two previously uncharacterized extracellular/luminal β-strand-rich domains and the unique transmembrane domain (TMD). The TMD of each SIDT2 protomer contains eleven transmembrane helices (TMs), and no discernible nucleic acid conduction pathway has been identified within the TMD, suggesting that it may act as a transporter. Intriguingly, TM3-6 and TM9-11 form a large cavity with a putative catalytic zinc atom coordinated by three conserved histidine residues and one aspartate residue lying approximately 6 Å from the extracellular/luminal surface of the membrane. Notably, SIDT2 can hydrolyze C18 ceramide into sphingosine and fatty acid with a slow rate. The information presented advances the understanding of the structure-function relationships in the SID1 family proteins.

PubMed: 37322007
DOI: 10.1038/s41467-023-39335-2

Experimental method

ELECTRON MICROSCOPY (3.16 Å)