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- EMDB-36204: Human sodium-dependent vitamin C transporter 1 in an apo inward-o... -
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Basic information
Entry | ![]() | |||||||||
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Title | Human sodium-dependent vitamin C transporter 1 in an apo inward-open state | |||||||||
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![]() | Transporter / Membrane protein / Ascorbic acid / Vitamin C / Sodium / TRANSPORT PROTEIN | |||||||||
Function / homology | ![]() 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 / 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 | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.6 Å | |||||||||
![]() | Kobayashi TA / Kusakizako T / Nureki O | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Cryo-EM structures of human sodium-dependent vitamin C transporter 1 Authors: Kobayashi TA / Kusakizako T / Nureki O | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.6 KB 16.6 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 10.6 KB | Display | ![]() |
Images | ![]() | 114.2 KB | ||
Masks | ![]() | 7.6 MB | ![]() | |
Filedesc metadata | ![]() | 6.6 KB | ||
Others | ![]() ![]() | 6.4 MB 6.4 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8jezMC ![]() 8jf0C ![]() 8jf1C M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.996 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_36204_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_36204_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Human SVCT1 dimer in an apo inward-open state
Entire | Name: Human SVCT1 dimer in an apo inward-open state |
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Components |
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-Supramolecule #1: Human SVCT1 dimer in an apo inward-open state
Supramolecule | Name: Human SVCT1 dimer in an apo inward-open state / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Solute carrier family 23 member 1
Macromolecule | Name: Solute carrier family 23 member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 64.860707 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: 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 |
-Macromolecule #3: Lauryl Maltose Neopentyl Glycol
Macromolecule | Name: Lauryl Maltose Neopentyl Glycol / type: ligand / ID: 3 / Number of copies: 2 / Formula: AV0 |
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Molecular weight | Theoretical: 1.005188 KDa |
Chemical component information | ![]() ChemComp-AV0: |
-Macromolecule #4: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine
Macromolecule | Name: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine / type: ligand / ID: 4 / Number of copies: 1 / Formula: LBN |
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Molecular weight | Theoretical: 760.076 Da |
Chemical component information | ![]() ChemComp-LBN: |
-Macromolecule #5: CHOLESTEROL
Macromolecule | Name: CHOLESTEROL / type: ligand / ID: 5 / Number of copies: 2 / Formula: CLR |
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Molecular weight | Theoretical: 386.654 Da |
Chemical component information | ![]() ChemComp-CLR: |
-Macromolecule #6: PALMITIC ACID
Macromolecule | Name: PALMITIC ACID / type: ligand / ID: 6 / Number of copies: 1 / Formula: PLM |
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Molecular weight | Theoretical: 256.424 Da |
Chemical component information | ![]() ChemComp-PLM: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7 |
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 25 eV |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 3474 / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000 |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |