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- EMDB-34094: Structural basis of vitamin C recognition and transport by mammal... -

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Basic information

Entry
Database: EMDB / ID: EMD-34094
TitleStructural basis of vitamin C recognition and transport by mammalian SVCT1 transporter
Map data
Sample
  • Complex: SVCT1
    • Protein or peptide: Solute carrier family 23 member 1
  • Ligand: SODIUM IONSodium
  • Ligand: ASCORBIC ACIDVitamin C
  • Ligand: water
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 / dehydroascorbic acid transport / sodium ion transmembrane transporter activity / intracellular organelle / sodium ion transport / brush border ...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 / dehydroascorbic acid transport / sodium ion transmembrane transporter activity / intracellular organelle / sodium ion transport / brush border / basal plasma membrane / lung development / 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
Solute carrier family 23 member 1
Similarity search - Component
Biological speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsShe J / Wang M / He J / Zhang K / Li S
Funding support China, 5 items
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, 2022-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateMay 3, 2023-
Current statusMay 3, 2023Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_34094.png

Downloads & links

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Map

FileDownload / File: emd_34094.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.82 Å
Density
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.6302977 - 2.463076
Average (Standard dev.)0.00030071463 (±0.03446542)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #1

Fileemd_34094_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_34094_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_34094_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : SVCT1

EntireName: SVCT1
Components
  • Complex: SVCT1
    • Protein or peptide: Solute carrier family 23 member 1
  • Ligand: SODIUM IONSodium
  • Ligand: ASCORBIC ACIDVitamin C
  • Ligand: water

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Supramolecule #1: SVCT1

SupramoleculeName: SVCT1 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mus musculus (house mouse)

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Macromolecule #1: Solute carrier family 23 member 1

MacromoleculeName: Solute carrier family 23 member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 65.600438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKTPEDPGSP KQHEVVDSAG TSTRDRQAPL PTEPKFDMLY KIEDVPPWYL CILLGFQHYL TCFSGTIAVP FLLAEALCVG RDQHMVSQL IGTIFTCVGI TTLIQTTVGI RLPLFQASAF AFLVPAKSIL ALERWKCPSE EEIYGNWSMP LNTSHIWHPR I REVQGAIM ...String:
MKTPEDPGSP KQHEVVDSAG TSTRDRQAPL PTEPKFDMLY KIEDVPPWYL CILLGFQHYL TCFSGTIAVP FLLAEALCVG RDQHMVSQL IGTIFTCVGI TTLIQTTVGI RLPLFQASAF AFLVPAKSIL ALERWKCPSE EEIYGNWSMP LNTSHIWHPR I REVQGAIM VSSMVEVVIG LMGLPGALLS YIGPLTVTPT VSLIGLSVFQ AAGDRAGSHW GISACSILLI VLFSQYLRNL TF LLPVYRW GKGLTLFRVQ IFKMFPIVLA IMTVWLLCYV LTLTDVLPAD PTVYGFQART DARGDIMAIS PWIRIPYPCQ WGL PTVTVA AVLGMFSATL AGIIESIGDY YACARLAGAP PPPVHAINRG IFTEGICCII AGLLGTGNGS TSSSPNIGVL GITK VGSRR VVQYGAGIML ILGAIGKFTA LFASLPDPIL GGMFCTLFGM ITAVGLSNLQ FVDMNSSRNL FVLGFSMFFG LTLPN YLDS NPGAINTGIP EVDQILTVLL TTEMFVGGCL AFILDNTVPG SPEERGLIQW KAGAHANSET SASLKSYDFP FGMGMV KRT TFFRYIPICP VFRGFSKKTQ NQPPVLEDTP DNIETGSVCT KV

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Macromolecule #2: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 2 / Number of copies: 4
Molecular weightTheoretical: 22.99 Da

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Macromolecule #3: ASCORBIC ACID

MacromoleculeName: ASCORBIC ACID / type: ligand / ID: 3 / Number of copies: 2 / Formula: ASC
Molecular weightTheoretical: 176.124 Da
Chemical component information

ChemComp-ASC:
ASCORBIC ACID / medication*YM / Vitamin C

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER / Water

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.5 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2370225

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