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- PDB-7ytw: Structural basis of vitamin C recognition and transport by mammal... -

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Basic information

Entry
Database: PDB / ID: 7ytw
TitleStructural basis of vitamin C recognition and transport by mammalian SVCT1 transporter
ComponentsSolute carrier family 23 member 1
KeywordsSTRUCTURAL PROTEIN / transporter / membrane protein / Vitamin C / sodium
Function / homology
Function and homology information


Vitamin C (ascorbate) metabolism / L-ascorbate:sodium symporter activity / L-ascorbic acid transmembrane transporter activity / L-ascorbic acid transmembrane transport / dehydroascorbic acid transmembrane transporter activity / intracellular organelle / sodium ion transmembrane transporter activity / dehydroascorbic acid transport / urate transmembrane transporter activity / sodium ion transport ...Vitamin C (ascorbate) metabolism / L-ascorbate:sodium symporter activity / L-ascorbic acid transmembrane transporter activity / L-ascorbic acid transmembrane transport / dehydroascorbic acid transmembrane transporter activity / intracellular organelle / sodium ion transmembrane transporter activity / dehydroascorbic acid transport / urate transmembrane transporter activity / sodium ion transport / lung development / basal plasma membrane / brain development / response to toxic substance / apical plasma membrane / plasma membrane / cytoplasm
Similarity search - Function
Nucleobase cation symporter 2 family / Permease family
Similarity search - Domain/homology
ASCORBIC ACID / Solute carrier family 23 member 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsShe, J. / Wang, M. / He, J. / Zhang, K. / Li, S.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)GG2070000569 China
Ministry of Science and Technology (MoST, China)2021YFF0600801 China
Other governmentKY9100000032
Other governmentWK2070000183
Other governmentWK9100000044
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis of vitamin C recognition and transport by mammalian SVCT1 transporter.
Authors: Mingxing Wang / Jin He / Shanshan Li / Qianwen Cai / Kaiming Zhang / Ji She /
Abstract: Vitamin C (L-ascorbic acid) is an essential nutrient for human health, and its deficiency has long been known to cause scurvy. Sodium-dependent vitamin C transporters (SVCTs) are responsible for ...Vitamin C (L-ascorbic acid) is an essential nutrient for human health, and its deficiency has long been known to cause scurvy. Sodium-dependent vitamin C transporters (SVCTs) are responsible for vitamin C uptake and tissue distribution in mammals. Here, we present cryogenic electron microscopy structures of mouse SVCT1 in both the apo and substrate-bound states. Mouse SVCT1 forms a homodimer with each protomer containing a core domain and a gate domain. The tightly packed extracellular interfaces between the core domain and gate domain stabilize the protein in an inward-open conformation for both the apo and substrate-bound structures. Vitamin C binds at the core domain of each subunit, and two potential sodium ions are identified near the binding site. The coordination of sodium ions by vitamin C explains their coupling transport. SVCTs probably deliver substrate through an elevator mechanism in combination with local structural arrangements. Altogether, our results reveal the molecular mechanism by which SVCTs recognize vitamin C and lay a foundation for further mechanistic studies on SVCT substrate transport.
History
DepositionAug 16, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
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Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _pdbx_entry_details.has_protein_modification
Revision 1.2Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Solute carrier family 23 member 1
B: Solute carrier family 23 member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,6458
Polymers131,2012
Non-polymers4446
Water362
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Solute carrier family 23 member 1 / Na(+)/L-ascorbic acid transporter 1 / Sodium-dependent vitamin C transporter 1 / Yolk sac permease- ...Na(+)/L-ascorbic acid transporter 1 / Sodium-dependent vitamin C transporter 1 / Yolk sac permease-like molecule 3


Mass: 65600.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Slc23a1, Svct1, Yspl3 / Production host: Homo sapiens (human) / References: UniProt: Q9Z2J0
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#3: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H8O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SVCT1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Mus musculus (house mouse)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI TITAN
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 2370225 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0087964
ELECTRON MICROSCOPYf_angle_d1.08910870
ELECTRON MICROSCOPYf_dihedral_angle_d16.1741088
ELECTRON MICROSCOPYf_chiral_restr0.0651290
ELECTRON MICROSCOPYf_plane_restr0.011348

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