8JUL | pdb_00008jul

Cryo-EM structure of SIDT1 in complex with phosphatidic acid

PDB DOI: https://doi.org/10.2210/pdb8JUL/pdb
EM Map EMD-36661: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTM mpstruc

Deposited: 2023-06-26 Released: 2023-11-15
Deposition Author(s): Sun, C.R., Xu, D., Li, Q., Zhou, C.Z., Chen, Y.
Funding Organization(s): Chinese Academy of Sciences

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.92 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Human SIDT1 mediates dsRNA uptake via its phospholipase activity.

Sun, C.R., Xu, D., Yang, F., Hou, Z., Luo, Y., Zhang, C.Y., Shan, G., Huang, G., Yao, X., Chen, Y., Li, Q., Zhou, C.Z.

(2024) Cell Res 34: 84-87

PubMed: 37932444 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41422-023-00889-x
Primary Citation Related Structures:
8JUL, 8JUN

Organizational Affiliation

School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China.

Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, China.

MOE Key Laboratory for Cellular Dynamics, University of Science and Technology of China, Hefei, Anhui, China.

School of Chemistry and Materials Science, National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui, China.

Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, the CAS Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui, China.

Nanjing Drum Tower Hospital Center of Molecular Diagnostic and Therapy, State Key Laboratory of Pharmaceutical Biotechnology, Jiangsu Engineering Research Center for MicroRNA Biology and Biotechnology, NJU Advanced Institute of Life Sciences (NAILS), School of Life Sciences, Nanjing University, Nanjing, Jiangsu, China.

MOE Key Laboratory for Cellular Dynamics, University of Science and Technology of China, Hefei, Anhui, China. yaoxb@ustc.edu.cn.

School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China. cyxing@ustc.edu.cn.

Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, China. cyxing@ustc.edu.cn.

School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China. liqiong@ustc.edu.cn.

Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, China. liqiong@ustc.edu.cn.

School of Life Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, China. zcz@ustc.edu.cn.

Biomedical Sciences and Health Laboratory of Anhui Province, University of Science and Technology of China, Hefei, Anhui, China. zcz@ustc.edu.cn.

Macromolecule Content

Total Structure Weight: 189.05 kDa
Atom Count: 9,690
Modeled Residue Count: 1,246
Deposited Residue Count: 1,654
Unique protein chains: 1

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SID1 transmembrane family member 1	A, B	827	Homo sapiens	Mutation(s): 0 Gene Names: SIDT1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXL6 (Homo sapiens) Explore Q9NXL6 Go to UniProtKB: Q9NXL6
PHAROS: Q9NXL6 GTEx: ENSG00000072858
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NXL6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PX2 (Subject of Investigation/LOI) Query on PX2 Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	1,2-DILAUROYL-SN-GLYCERO-3-PHOSPHATE C₂₇ H₅₂ O₈ P OKLASJZQBDJAPH-RUZDIDTESA-M		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]