8JF0 | pdb_00008jf0

Human sodium-dependent vitamin C transporter 1 in an intermediate state

• PDB DOI: https://doi.org/10.2210/pdb8JF0/pdb
• EM Map EMD-36205: EMDB EMDataResource

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


• Deposited: 2023-05-16 Released: 2024-05-22 
• Deposition Author(s): Kobayashi, T.A., Kusakizako, T., Nureki, O.
• Funding Organization(s): Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Dimeric transport mechanism of human vitamin C transporter SVCT1.

Kobayashi, T.A., Shimada, H., Sano, F.K., Itoh, Y., Enoki, S., Okada, Y., Kusakizako, T., Nureki, O.

(2024) Nat Commun 15: 5569-5569

• PubMed: 38956111 
• DOI: https://doi.org/10.1038/s41467-024-49899-2
• Primary Citation Related Structures: 
  8JEW, 8JEZ, 8JF0, 8JF1


• PubMed Abstract: 
  

  Vitamin C plays important roles as a cofactor in many enzymatic reactions and as an antioxidant against oxidative stress. As some mammals including humans cannot synthesize vitamin C de novo from glucose, its uptake from dietary sources is essential, and is mediated by the sodium-dependent vitamin C transporter 1 (SVCT1). Despite its physiological significance in maintaining vitamin C homeostasis, the structural basis of the substrate transport mechanism remained unclear. Here, we report the cryo-EM structures of human SVCT1 in different states at 2.5-3.5 Å resolutions. The binding manner of vitamin C together with two sodium ions reveals the counter ion-dependent substrate recognition mechanism. Furthermore, comparisons of the inward-open and occluded structures support a transport mechanism combining elevator and distinct rotational motions. Our results demonstrate the molecular mechanism of vitamin C transport with its underlying conformational cycle, potentially leading to future industrial and medical applications.

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Organizational Affiliation: 
• Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
Research Division, Chugai Pharmaceutical Co., Ltd., Kanagawa, Japan.
Department of Physics, and Universal Biology Institute (UBI), Graduate School of Science, The University of Tokyo, Tokyo, Japan.
Department of Cell Biology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
Laboratory for Cell Polarity Regulation, RIKEN Center for Biosystems Dynamics Research (BDR), Osaka, Japan.
International Research Center for Neurointelligence (WPI-IRCN), The University of Tokyo, Tokyo, Japan.
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan. [e-mail].
Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan. [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 64.86 kDa 
• Atom Count: 3,289 
• Modeled Residue Count: 436 
• Deposited Residue Count: 598 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Solute carrier family 23 member 1	A	598	Homo sapiens	Mutation(s): 0  Gene Names: SLC23A1, SVCT1, YSPL3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHI7 (Homo sapiens) Explore Q9UHI7  Go to UniProtKB:  Q9UHI7
PHAROS:  Q9UHI7 GTEx:  ENSG00000170482

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	3.1.1
MODEL REFINEMENT	Servalcat	0.2.115

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-05-22 
Deposition Author(s): Kobayashi, T.A., Kusakizako, T., Nureki, O.

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Funding Organization	Location	Grant Number
Japan Society for the Promotion of Science (JSPS)	Japan	--

Revision History  

• Version 1.0: 2024-05-22
  Type: Initial release
  
• Version 1.1: 2024-12-04
  Changes: Data collection, Database references, Structure summary