8Y5U | pdb_00008y5u

human NaS1 intermediate state 1

• PDB DOI: https://doi.org/10.2210/pdb8Y5U/pdb
• EM Map EMD-38953: EMDB EMDataResource

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


• Deposited: 2024-02-01 Released: 2025-01-22 
• Deposition Author(s): Zhang, S.S.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.04 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

human NaS1 intermediate state 1

Zhang, S.S.

(2024) Sci Adv 10: eado6778

• PubMed: 39576865 
• DOI: https://doi.org/10.1126/sciadv.ado6778
• Primary Citation Related Structures: 
  8Y5U, 8Y5W, 8Y5X, 8Y5Y, 8Y5Z


• PubMed Abstract: 
  

  Sulfate (SO ₄ ^2- ) is a pivotal inorganic anion with essential roles in mammalian physiology. NaS1, a member of solute carrier 13 family and divalent anion/sodium symporter family, functions as a Na ⁺ -sulfate cotransporter, facilitating sulfate (re)absorption across renal proximal tubule and small intestine epithelia. While previous studies have linked several human disorders to mutations in the NaS1 gene, its transport mechanism remains unclear. Here, we report the cryo-electron microscopy structures of five distinct conformations of the human NaS1 at resolutions of 2.7 to 3.3 angstroms, revealing the substrates recognition mechanism and the conformational change of NaS1 during the Na ⁺ -sulfate cotransport cycle. Our studies delineate the molecular basis of the detailed dynamic transport cycle of NaS1. These findings advance the current understanding of the Na ⁺ -sulfate cotransport mechanism, human sulfate (re)absorption, and the implications of disease-associated NaS1 mutations.

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Organizational Affiliation: 
• Ministry of Education Key Laboratory of Protein Science, Tsinghua-Peking Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
Department of Nephrology, First Medical Center of Chinese PLA General Hospital, State Key Laboratory of Kidney Diseases, National Clinical Research Center for Kidney Diseases, Beijing Key Laboratory of Kidney Diseases Research, Beijing 100853, China.
Beijing Life Science Academy, Beijing 102209, China.
Department of Cardiology, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing 102218, China.
Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Hangzhou Normal University, Hangzhou 311121, China.
Radioisotope Laboratory of Center of Biomedical Analysis, Tsinghua University, Beijing 100084, China.
Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.
Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.
Cryo-EM Facility Center, Southern University of Science and Technology, Shenzhen, 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: 132.63 kDa 
• Atom Count: 7,961 
• Modeled Residue Count: 1,016 
• Deposited Residue Count: 1,190 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Solute carrier family 13 member 1	A, B	595	Homo sapiens	Mutation(s): 0  Gene Names: SLC13A1, NAS1, NASI1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZW2 (Homo sapiens) Explore Q9BZW2  Go to UniProtKB:  Q9BZW2
PHAROS:  Q9BZW2 GTEx:  ENSG00000081800

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	D [auth A], G [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
NA	C [auth A], E [auth B], F [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.04 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-01-22 
Deposition Author(s): Zhang, S.S.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	32030056

Revision History  

• Version 1.0: 2025-01-22
  Type: Initial release