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- PDB-8jew: Human sodium-dependent vitamin C transporter 1 bound to L-ascorbi... -

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Basic information

Entry
Database: PDB / ID: 8jew
TitleHuman sodium-dependent vitamin C transporter 1 bound to L-ascorbic acid in an inward-open state
ComponentsSolute carrier family 23 member 1
KeywordsTRANSPORT PROTEIN / Transporter / Membrane protein / Ascorbic acid / Vitamin C / Sodium
Function / homology
Function and homology information


nucleobase transport / nucleobase transmembrane transporter activity / 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 / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process ...nucleobase transport / nucleobase transmembrane transporter activity / 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 / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process / urate transmembrane transporter activity / intracellular organelle / 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
ASCORBIC ACID / Lauryl Maltose Neopentyl Glycol / CHOLESTEROL / 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / PALMITIC ACID / Solute carrier family 23 member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.49 Å
AuthorsKobayashi, T.A. / Kusakizako, T. / Nureki, O.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS) Japan
CitationJournal: To Be Published
Title: Cryo-EM structures of human vitamin C transporter SVCT1
Authors: Kobayashi, T.A. / Kusakizako, T. / Nureki, O.
History
DepositionMay 16, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)69,10411
Polymers64,8611
Non-polymers4,24310
Water543
1
A: Solute carrier family 23 member 1
hetero molecules

A: Solute carrier family 23 member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)138,20822
Polymers129,7212
Non-polymers8,48720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(-1), (-1), (1)298.79999, 298.79999

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Solute carrier family 23 member 1 / Na(+)/L-ascorbic acid transporter 1 / Sodium-dependent vitamin C transporter 1 / hSVCT1 / Yolk sac ...Na(+)/L-ascorbic acid transporter 1 / Sodium-dependent vitamin C transporter 1 / hSVCT1 / Yolk sac permease-like molecule 3


Mass: 64860.707 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC23A1, SVCT1, YSPL3 / Plasmid: pEG BacMam / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q9UHI7

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Sugars , 2 types, 2 molecules

#2: Sugar ChemComp-ASC / ASCORBIC ACID / Vitamin C / Vitamin C


Type: L-saccharide / Mass: 176.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O6 / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 6 types, 11 molecules

#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-AV0 / Lauryl Maltose Neopentyl Glycol / 2,2-didecylpropane-1,3-bis-b-D-maltopyranoside / 2-decyl-2-{[(4-O-alpha-D-glucopyranosyl-beta-D-glucopyranosyl)oxy]methyl}dodecyl4-O-alpha-D-glucopyranosyl-beta-D-glucopyranoside


Mass: 1005.188 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C47H88O22 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-LBN / 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / (2R)-2-[(9Z)-9-Octadecenoyloxy]-3-(palmitoyloxy)propyl 2-(trimethylammonio)ethyl phosphate / POPC


Mass: 760.076 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H82NO8P / Feature type: SUBJECT OF INVESTIGATION / Comment: phospholipid*YM
#6: Chemical ChemComp-CLR / CHOLESTEROL / Cholesterol


Mass: 386.654 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H46O / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-PLM / PALMITIC ACID / Palmitic acid


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: Human SVCT1 dimer in a substrate-bound inward-open state
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 105000 X / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 49.7 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3753
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 25 eV

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Processing

EM software
IDNameVersionCategory
1RELION3.1.1particle selection
2SerialEM3.9.0image acquisition
4RELION3.1.1CTF correction
7Coot0.9.6model fitting
9Servalcat0.2.115model refinement
10RELION3.1.1initial Euler assignment
11RELION3.1.1final Euler assignment
12RELION3.1.1classification
13RELION3.1.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2852953
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 2.49 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 147401 / Symmetry type: POINT
Atomic model buildingAccession code: Q9UHI7 / Source name: AlphaFold / Type: in silico model
RefinementResolution: 2.49→2.49 Å / Cor.coef. Fo:Fc: 0.852 / SU B: 4.878 / SU ML: 0.105 / ESU R: 0.126
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.30797 --
obs0.30797 157995 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 70.175 Å2
Refinement stepCycle: 1 / Total: 4142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0110.0134246
ELECTRON MICROSCOPYr_bond_other_d0.0020.0174229
ELECTRON MICROSCOPYr_angle_refined_deg1.5451.6385794
ELECTRON MICROSCOPYr_angle_other_deg1.5021.5539766
ELECTRON MICROSCOPYr_dihedral_angle_1_deg5.145509
ELECTRON MICROSCOPYr_dihedral_angle_2_deg37.05421.192151
ELECTRON MICROSCOPYr_dihedral_angle_3_deg15.80115626
ELECTRON MICROSCOPYr_dihedral_angle_4_deg17.8451516
ELECTRON MICROSCOPYr_chiral_restr0.10.2614
ELECTRON MICROSCOPYr_gen_planes_refined0.0120.024443
ELECTRON MICROSCOPYr_gen_planes_other0.0090.02885
ELECTRON MICROSCOPYr_nbd_refined
ELECTRON MICROSCOPYr_nbd_other
ELECTRON MICROSCOPYr_nbtor_refined
ELECTRON MICROSCOPYr_nbtor_other
ELECTRON MICROSCOPYr_xyhbond_nbd_refined
ELECTRON MICROSCOPYr_xyhbond_nbd_other
ELECTRON MICROSCOPYr_metal_ion_refined
ELECTRON MICROSCOPYr_metal_ion_other
ELECTRON MICROSCOPYr_symmetry_vdw_refined
ELECTRON MICROSCOPYr_symmetry_vdw_other
ELECTRON MICROSCOPYr_symmetry_hbond_refined
ELECTRON MICROSCOPYr_symmetry_hbond_other
ELECTRON MICROSCOPYr_symmetry_metal_ion_refined
ELECTRON MICROSCOPYr_symmetry_metal_ion_other
ELECTRON MICROSCOPYr_mcbond_it6.1936.3742045
ELECTRON MICROSCOPYr_mcbond_other6.1916.372044
ELECTRON MICROSCOPYr_mcangle_it8.7669.5752551
ELECTRON MICROSCOPYr_mcangle_other8.7659.5812552
ELECTRON MICROSCOPYr_scbond_it7.7178.3552201
ELECTRON MICROSCOPYr_scbond_other7.7158.3572202
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other12.11112.1123244
ELECTRON MICROSCOPYr_long_range_B_refined21.49818353
ELECTRON MICROSCOPYr_long_range_B_other21.49718354
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.983 11676 -
obs--100 %

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