8K13 | pdb_00008k13

SID1 transmembrane family member 1

• PDB DOI: https://doi.org/10.2210/pdb8K13/pdb
• EM Map EMD-36785: EMDB EMDataResource

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2023-07-10 Released: 2024-07-10 
• Deposition Author(s): Guo, H., Qi, C., Lu, Y., Yang, H., Zhu, Y., Sun, F., Ji, X.
• Funding Organization(s): Other government

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.33 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-EM structures of human SID-1 transmembrane family proteins and implications for their low-pH-dependent RNA transport activity.

Zheng, L., Yang, T., Guo, H., Qi, C., Lu, Y., Xiao, H., Gao, Y., Liu, Y., Yang, Y., Zhou, M., Nguyen, H.C., Zhu, Y., Sun, F., Zhang, C.Y., Ji, X.

(2024) Cell Res 34: 80-83

• PubMed: 37932445 
• DOI: https://doi.org/10.1038/s41422-023-00893-1
• Primary Citation Related Structures: 
  8K10, 8K11, 8K12, 8K13, 8K1B, 8K1D

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Organizational Affiliation: 
• National Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, Jiangsu, China.
National Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, Jiangsu, China. [e-mail].
National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.
University of Chinese Academy of Sciences, Beijing, China.
Shanghai Institute for Advanced Immunochemical Studies and School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
Lingang Laboratory, Shanghai, China.
Shanghai Clinical Research and Trial Center, Shanghai, China.
National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. [e-mail].
National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China. [e-mail].
University of Chinese Academy of Sciences, Beijing, China. [e-mail].
National Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, Jiangsu, China. [e-mail].
National Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Institute of Artificial Intelligence Biomedicine, Nanjing University, Nanjing, Jiangsu, China. [e-mail].
Engineering Research Center of Protein and Peptide Medicine, Ministry of Education, Nanjing, Jiangsu, China. [e-mail].

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: 184.87 kDa 
• Atom Count: 9,078 
• Modeled Residue Count: 1,118 
• Deposited Residue Count: 1,606 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SID1 transmembrane family member 1	A, B	803	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
Glycosylation
Glycosylation Sites: 3		Go to GlyGen: Q9NXL6-1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG (Subject of Investigation/LOI)	C [auth A], D [auth A], E [auth A], F [auth B], G [auth B], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.33 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-07-10 
Deposition Author(s): Guo, H., Qi, C., Lu, Y., Yang, H., Zhu, Y., Sun, F., Ji, X.

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Funding Organization	Location	Grant Number
Other government	China	--

Revision History  

• Version 1.0: 2024-07-10
  Type: Initial release
  
• Version 1.1: 2024-10-23
  Changes: Data collection, Structure summary
• Version 1.2: 2025-07-16
  Changes: Data collection