8JEZ | pdb_00008jez

Human sodium-dependent vitamin C transporter 1 in an apo inward-open state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8JEZ

This is version 1.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 69.09 kDa 
  • Atom Count: 4,141 
  • Modeled Residue Count: 513 
  • Deposited Residue Count: 598 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q9UHI7-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

Help  
Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AV0
(Subject of Investigation/LOI)

Query on AV0



Download:Ideal Coordinates CCD File
C [auth A],
E [auth A]
Lauryl Maltose Neopentyl Glycol
C47 H88 O22
MADJBYLAYPCCOO-VWHTXWAPSA-N
LBN
(Subject of Investigation/LOI)

Query on LBN



Download:Ideal Coordinates CCD File
D [auth A]1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
C42 H82 N O8 P
WTJKGGKOPKCXLL-VYOBOKEXSA-N
CLR
(Subject of Investigation/LOI)

Query on CLR



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A]
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
PLM
(Subject of Investigation/LOI)

Query on PLM



Download:Ideal Coordinates CCD File
H [auth A]PALMITIC ACID
C16 H32 O2
IPCSVZSSVZVIGE-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.60 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: 2024-06-19
    Type: Initial release
  • Version 1.1: 2024-11-13
    Changes: Data collection, Structure summary
  • Version 1.2: 2024-12-04
    Changes: Data collection, Database references