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- PDB-8jf0: Human sodium-dependent vitamin C transporter 1 in an intermediate... -

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Basic information

Entry
Database: PDB / ID: 8jf0
TitleHuman sodium-dependent vitamin C transporter 1 in an intermediate state
ComponentsSolute carrier family 23 member 1
KeywordsTRANSPORT PROTEIN / Transporter / Solute carrier / 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
Solute carrier family 23 member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 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 sodium-dependent vitamin C transporter 1
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


Theoretical massNumber of molelcules
Total (without water)64,8611
Polymers64,8611
Non-polymers00
Water0
1
A: Solute carrier family 23 member 1

A: Solute carrier family 23 member 1


Theoretical massNumber of molelcules
Total (without water)129,7212
Polymers129,7212
Non-polymers00
Water0
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)298.8009, 298.8009

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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 / 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- cells / Production host: Homo sapiens (human) / References: UniProt: Q9UHI7

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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 an intermediate state / Type: COMPLEX / Entity ID: all / 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: 50.9 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5907
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 25 eV

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Processing

EM software
IDNameVersionCategory
1RELION3.1.1particle selection
2EPU1.24.2image acquisition
4RELION3.1.1CTF correction
7Coot0.9.6model fitting
9RELION3.1.1initial Euler assignment
10RELION3.1.1final Euler assignment
12RELION3.1.13D reconstruction
13Servalcat0.2.115model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 3699304
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 149304 / Symmetry type: POINT
Atomic model buildingPDB-ID: 8JEZ

8jez
PDB Unreleased entry


Accession code: 8JEZ / Source name: PDB / Type: experimental model
RefinementResolution: 3.5→106.24 Å / Cor.coef. Fo:Fc: 0.838 / SU B: 34.105 / SU ML: 0.54 / ESU R: 0.529
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rwork0.4283 --
obs0.4283 39613 100 %
Solvent computationSolvent model: PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 141.873 Å2
Refinement stepCycle: 1 / Total: 3289
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
ELECTRON MICROSCOPYr_bond_refined_d0.0090.0133364
ELECTRON MICROSCOPYr_bond_other_d0.0060.0173295
ELECTRON MICROSCOPYr_angle_refined_deg1.3291.6234589
ELECTRON MICROSCOPYr_angle_other_deg1.6291.5577553
ELECTRON MICROSCOPYr_dihedral_angle_1_deg3.385432
ELECTRON MICROSCOPYr_dihedral_angle_2_deg34.81921.615130
ELECTRON MICROSCOPYr_dihedral_angle_3_deg11.76515527
ELECTRON MICROSCOPYr_dihedral_angle_4_deg17.7141515
ELECTRON MICROSCOPYr_chiral_restr0.080.2465
ELECTRON MICROSCOPYr_gen_planes_refined0.0140.023746
ELECTRON MICROSCOPYr_gen_planes_other0.010.02756
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_it14.6713.9231740
ELECTRON MICROSCOPYr_mcbond_other14.67213.9241739
ELECTRON MICROSCOPYr_mcangle_it24.41420.7812168
ELECTRON MICROSCOPYr_mcangle_other24.40920.7792169
ELECTRON MICROSCOPYr_scbond_it15.04716.1021624
ELECTRON MICROSCOPYr_scbond_other15.04316.0991625
ELECTRON MICROSCOPYr_scangle_it
ELECTRON MICROSCOPYr_scangle_other25.48623.3982422
ELECTRON MICROSCOPYr_long_range_B_refined49.92414704
ELECTRON MICROSCOPYr_long_range_B_other49.92314705
ELECTRON MICROSCOPYr_rigid_bond_restr
ELECTRON MICROSCOPYr_sphericity_free
ELECTRON MICROSCOPYr_sphericity_bonded
LS refinement shellResolution: 3.5→3.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork1.843 2906 -
obs--100 %

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