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- EMDB-36201: Human sodium-dependent vitamin C transporter 1 bound to L-ascorbi... -

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Basic information

Entry
Database: EMDB / ID: EMD-36201
TitleHuman sodium-dependent vitamin C transporter 1 bound to L-ascorbic acid in an inward-open state
Map dataFSC-weighted, sharpened and masked map by PostProcess
Sample
  • Complex: Human SVCT1 dimer in a substrate-bound inward-open state
    • Protein or peptide: Solute carrier family 23 member 1
  • Ligand: ASCORBIC ACID
  • Ligand: SODIUM ION
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: CHOLESTEROL
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PALMITIC ACID
  • Ligand: water
KeywordsTransporter / Membrane protein / Ascorbic acid / Vitamin C / Sodium / TRANSPORT PROTEIN
Function / homology
Function and homology information


nucleobase transport / L-ascorbate:sodium symporter activity / L-ascorbic acid transmembrane transporter activity / L-ascorbic acid transmembrane transport / nucleobase transmembrane transporter activity / dehydroascorbic acid transmembrane transporter activity / intracellular organelle / sodium ion transmembrane transporter activity / dehydroascorbic acid transport / Vitamin C (ascorbate) metabolism ...nucleobase transport / L-ascorbate:sodium symporter activity / L-ascorbic acid transmembrane transporter activity / L-ascorbic acid transmembrane transport / nucleobase transmembrane transporter activity / dehydroascorbic acid transmembrane transporter activity / intracellular organelle / sodium ion transmembrane transporter activity / dehydroascorbic acid transport / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process / urate transmembrane transporter activity / sodium ion transport / basal plasma membrane / lung development / brain development / response to toxic substance / apical plasma membrane / extracellular exosome / 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 speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.49 Å
AuthorsKobayashi TA / Kusakizako T / Nureki O
Funding support Japan, 1 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: Nat Commun / Year: 2024
Title: Dimeric transport mechanism of human vitamin C transporter SVCT1.
Authors: Takaaki A Kobayashi / Hiroto Shimada / Fumiya K Sano / Yuzuru Itoh / Sawako Enoki / Yasushi Okada / Tsukasa Kusakizako / Osamu Nureki /
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 ...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.
History
DepositionMay 16, 2023-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateDec 4, 2024-
Current statusDec 4, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36201.png

Downloads & links

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Map

FileDownload / File: emd_36201.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFSC-weighted, sharpened and masked map by PostProcess
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 128 pix.
= 127.488 Å		1 Å/pix.
x 128 pix.
= 127.488 Å		1 Å/pix.
x 128 pix.
= 127.488 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.996 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.16140743 - 0.2568061
Average (Standard dev.)0.0011767556 (±0.014041576)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin868686
Dimensions128128128
Spacing128128128
CellA=B=C: 127.488 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_36201_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36201_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_36201_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human SVCT1 dimer in a substrate-bound inward-open state

EntireName: Human SVCT1 dimer in a substrate-bound inward-open state
Components
  • Complex: Human SVCT1 dimer in a substrate-bound inward-open state
    • Protein or peptide: Solute carrier family 23 member 1
  • Ligand: ASCORBIC ACID
  • Ligand: SODIUM ION
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
  • Ligand: CHOLESTEROL
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
  • Ligand: PALMITIC ACID
  • Ligand: water

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Supramolecule #1: Human SVCT1 dimer in a substrate-bound inward-open state

SupramoleculeName: Human SVCT1 dimer in a substrate-bound inward-open state
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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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: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 64.860707 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MRAQEDLEGR TQHETTRDPS TPLPTEPKFD MLYKIEDVPP WYLCILLGFQ HYLTCFSGTI AVPFLLAEAL CVGHDQHMVS QLIGTIFTC VGITTLIQTT VGIRLPLFQA SAFAFLVPAK AILALERWKC PPEEEIYGNW SLPLNTSHIW HPRIREVQGA I MVSSVVEV ...String:
MRAQEDLEGR TQHETTRDPS TPLPTEPKFD MLYKIEDVPP WYLCILLGFQ HYLTCFSGTI AVPFLLAEAL CVGHDQHMVS QLIGTIFTC VGITTLIQTT VGIRLPLFQA SAFAFLVPAK AILALERWKC PPEEEIYGNW SLPLNTSHIW HPRIREVQGA I MVSSVVEV VIGLLGLPGA LLNYIGPLTV TPTVSLIGLS VFQAAGDRAG SHWGISACSI LLIILFSQYL RNLTFLLPVY RW GKGLTLL RIQIFKMFPI MLAIMTVWLL CYVLTLTDVL PTDPKAYGFQ ARTDARGDIM AIAPWIRIPY PCQWGLPTVT AAA VLGMFS ATLAGIIESI GDYYACARLA GAPPPPVHAI NRGIFTEGIC CIIAGLLGTG NGSTSSSPNI GVLGITKVGS RRVV QYGAA IMLVLGTIGK FTALFASLPD PILGGMFCTL FGMITAVGLS NLQFVDMNSS RNLFVLGFSM FFGLTLPNYL ESNPG AINT GILEVDQILI VLLTTEMFVG GCLAFILDNT VPGSPEERGL IQWKAGAHAN SDMSSSLKSY DFPIGMGIVK RITFLK YIP ICPVFKGFSS SSKDQIAIPE DTPENTETAS VCTKV

UniProtKB: Solute carrier family 23 member 1

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Macromolecule #2: ASCORBIC ACID

MacromoleculeName: ASCORBIC ACID / type: ligand / ID: 2 / Number of copies: 1 / Formula: ASC
Molecular weightTheoretical: 176.124 Da
Chemical component information

ChemComp-ASC:
ASCORBIC ACID / medication*YM

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Macromolecule #3: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 3 / Number of copies: 2
Molecular weightTheoretical: 22.99 Da

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Macromolecule #4: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 4 / Number of copies: 2 / Formula: AV0
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

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Macromolecule #5: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine

MacromoleculeName: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 5 / Number of copies: 1 / Formula: LBN
Molecular weightTheoretical: 760.076 Da
Chemical component information

ChemComp-LBN:
1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / phospholipid*YM

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Macromolecule #6: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 6 / Number of copies: 2 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #7: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 7 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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Macromolecule #8: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 8 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #9: water

MacromoleculeName: water / type: ligand / ID: 9 / Number of copies: 3 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
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: 7
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 25 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 3753 / Average electron dose: 49.7 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2852953
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 147401
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

uhi7


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-8jew:
Human sodium-dependent vitamin C transporter 1 bound to L-ascorbic acid in an inward-open state

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