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- EMDB-36206: Human sodium-dependent vitamin C transporter 1 in an apo occluded... -

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Basic information

Entry
Database: EMDB / ID: EMD-36206
TitleHuman sodium-dependent vitamin C transporter 1 in an apo occluded state
Map dataFSC-weighted, sharpened and masked map by PostProcess
Sample
  • Complex: Human SVCT1 dimer in an apo occluded state
    • Protein or peptide: Solute carrier family 23 member 1
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • 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 / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.85 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_36206.png

Downloads & links

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Map

FileDownload / File: emd_36206.map.gz / Format: CCP4 / Size: 6.6 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 120 pix.
= 119.52 Å		1 Å/pix.
x 120 pix.
= 119.52 Å		1 Å/pix.
x 120 pix.
= 119.52 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-0.12590112 - 0.20593718
Average (Standard dev.)0.0013546743 (±0.013803948)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin909090
Dimensions120120120
Spacing120120120
CellA=B=C: 119.52 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_36206_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_36206_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_36206_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 apo occluded state

EntireName: Human SVCT1 dimer in an apo occluded state
Components
  • Complex: Human SVCT1 dimer in an apo occluded state
    • Protein or peptide: Solute carrier family 23 member 1
  • Ligand: Lauryl Maltose Neopentyl Glycol
  • Ligand: CHOLESTEROL HEMISUCCINATE
  • 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 an apo occluded state

SupramoleculeName: Human SVCT1 dimer in an apo occluded 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: Lauryl Maltose Neopentyl Glycol

MacromoleculeName: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 2 / Number of copies: 3 / Formula: AV0
Molecular weightTheoretical: 1.005188 KDa
Chemical component information

ChemComp-AV0:
Lauryl Maltose Neopentyl Glycol

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Macromolecule #3: CHOLESTEROL HEMISUCCINATE

MacromoleculeName: CHOLESTEROL HEMISUCCINATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: Y01
Molecular weightTheoretical: 486.726 Da
Chemical component information

ChemComp-Y01:
CHOLESTEROL HEMISUCCINATE

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Macromolecule #4: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 4 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL / Cholesterol

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Macromolecule #5: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 5 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

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Macromolecule #6: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 6 / Number of copies: 1 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID / Palmitic acid

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / 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: 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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 25 eV
Sample stageCooling holder cryogen: NITROGEN
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3699304
Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.1) / Number images used: 116307
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

8jew


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

PDB-8jf1:
Human sodium-dependent vitamin C transporter 1 in an apo occluded state

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