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- EMDB-36205: Human sodium-dependent vitamin C transporter 1 in an intermediate... -

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Basic information

Entry
Database: EMDB / ID: EMD-36205
TitleHuman sodium-dependent vitamin C transporter 1 in an intermediate state
Map dataUnsharpened map by Refine3D
Sample
  • Complex: Human SVCT1 dimer in an intermediate state
    • Protein or peptide: Solute carrier family 23 member 1
KeywordsTransporter / Solute carrier / 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 / dehydroascorbic acid transport / sodium ion transmembrane transporter activity / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process ...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 / dehydroascorbic acid transport / sodium ion transmembrane transporter activity / Vitamin C (ascorbate) metabolism / L-ascorbic acid metabolic process / intracellular organelle / 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: 3.5 Å
AuthorsKobayashi TA / Kusakizako T / Nureki O
Funding support Japan, 1 items
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 TA / Kusakizako T / Nureki O
History
DepositionMay 16, 2023-
Header (metadata) releaseMay 22, 2024-
Map releaseMay 22, 2024-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_36205.png

Downloads & links

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Map

FileDownload / File: emd_36205.map.gz / Format: CCP4 / Size: 5.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationUnsharpened map by Refine3D
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.11 Å/pix.
x 114 pix.
= 126.16 Å		1.11 Å/pix.
x 114 pix.
= 126.16 Å		1.11 Å/pix.
x 114 pix.
= 126.16 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.10667 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.043850586 - 0.08660102
Average (Standard dev.)-0.00001902413 (±0.0053410027)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin787878
Dimensions114114114
Spacing114114114
CellA=B=C: 126.160385 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_36205_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36205_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_36205_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 an intermediate state

EntireName: Human SVCT1 dimer in an intermediate state
Components
  • Complex: Human SVCT1 dimer in an intermediate state
    • Protein or peptide: Solute carrier family 23 member 1

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Supramolecule #1: Human SVCT1 dimer in an intermediate state

SupramoleculeName: Human SVCT1 dimer in an intermediate state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
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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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: 5907 / Average electron dose: 50.9 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: 3699304
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 149304
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:

8jez


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

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

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