8JF0

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


Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/s41467-024-49899-2
  • Primary Citation of 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.


  • Organizational Affiliation

    Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Solute carrier family 23 member 1598Homo sapiensMutation(s): 0 
Gene Names: SLC23A1SVCT1YSPL3
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 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UHI7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1.1
MODEL REFINEMENTServalcat0.2.115

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Japan Society for the Promotion of Science (JSPS)Japan--

Revision History  (Full details and data files)

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