8JUN

Cryo-EM structure of SIDT1 E555Q mutant

• PDB DOI: https://doi.org/10.2210/pdb8JUN/pdb
• EM Map EMD-36662: EMDB EMDataResource

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 
• Membrane Protein: Yes  PDBTM


• 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

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.38 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

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 
• DOI: https://doi.org/10.1038/s41422-023-00889-x
• Primary Citation of Related Structures:  
  8JUL, 8JUN

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 189.5 kDa 
• Atom Count: 11,098 
• Modelled Residue Count: 1,356 
• Deposited Residue Count: 1,654 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SID1 transmembrane family member 1	A, B	827	Homo sapiens	Mutation(s): 1  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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
POV (Subject of Investigation/LOI)	D [auth A], F [auth B]	(2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate C42 H82 N O8 P WTJKGGKOPKCXLL-PFDVCBLKSA-N
ZN (Subject of Investigation/LOI)	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.38 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.16-3549

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-15 
Deposition Author(s): Sun, C.R., Xu, D., Li, Q., Zhou, C.Z., Chen, Y.

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Funding Organization	Location	Grant Number
Chinese Academy of Sciences	China	XDB37020202

Revision History  

• Version 1.0: 2023-11-15
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Database references