[English] 日本語
Yorodumi
- EMDB-34095: Mouse SVCT1 in an apo state -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-34095
TitleMouse SVCT1 in an apo state
Map data
Sample
  • Complex: SVCT1
    • Protein or peptide: Solute carrier family 23 member 1
Keywordstransporter / membrane protein / Vitamin C / sodium / STRUCTURAL PROTEIN
Function / homology
Function and homology information


Vitamin C (ascorbate) metabolism / L-ascorbate:sodium symporter activity / L-ascorbic acid transmembrane transporter activity / L-ascorbic acid transmembrane transport / dehydroascorbic acid transmembrane transporter activity / intracellular organelle / sodium ion transmembrane transporter activity / dehydroascorbic acid transport / urate transmembrane transporter activity / sodium ion transport ...Vitamin C (ascorbate) metabolism / L-ascorbate:sodium symporter activity / L-ascorbic acid transmembrane transporter activity / L-ascorbic acid transmembrane transport / dehydroascorbic acid transmembrane transporter activity / intracellular organelle / sodium ion transmembrane transporter activity / dehydroascorbic acid transport / urate transmembrane transporter activity / sodium ion transport / lung development / basal plasma membrane / brain development / response to toxic substance / apical plasma membrane / 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 speciesMus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsShe J / Wang M / He J / Zhang K / Li S
Funding support China, 5 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)GG2070000569 China
Ministry of Science and Technology (MoST, China)2021YFF0600801 China
Other governmentKY9100000032
Other governmentWK2070000183
Other governmentWK9100000044
CitationJournal: Nat Commun / Year: 2023
Title: Structural basis of vitamin C recognition and transport by mammalian SVCT1 transporter.
Authors: Mingxing Wang / Jin He / Shanshan Li / Qianwen Cai / Kaiming Zhang / Ji She /
Abstract: Vitamin C (L-ascorbic acid) is an essential nutrient for human health, and its deficiency has long been known to cause scurvy. Sodium-dependent vitamin C transporters (SVCTs) are responsible for ...Vitamin C (L-ascorbic acid) is an essential nutrient for human health, and its deficiency has long been known to cause scurvy. Sodium-dependent vitamin C transporters (SVCTs) are responsible for vitamin C uptake and tissue distribution in mammals. Here, we present cryogenic electron microscopy structures of mouse SVCT1 in both the apo and substrate-bound states. Mouse SVCT1 forms a homodimer with each protomer containing a core domain and a gate domain. The tightly packed extracellular interfaces between the core domain and gate domain stabilize the protein in an inward-open conformation for both the apo and substrate-bound structures. Vitamin C binds at the core domain of each subunit, and two potential sodium ions are identified near the binding site. The coordination of sodium ions by vitamin C explains their coupling transport. SVCTs probably deliver substrate through an elevator mechanism in combination with local structural arrangements. Altogether, our results reveal the molecular mechanism by which SVCTs recognize vitamin C and lay a foundation for further mechanistic studies on SVCT substrate transport.
History
DepositionAug 16, 2022-
Header (metadata) releaseMay 3, 2023-
Map releaseMay 3, 2023-
UpdateOct 9, 2024-
Current statusOct 9, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_34095.png

Downloads & links

-
Map

FileDownload / File: emd_34095.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å		0.82 Å/pix.
x 384 pix.
= 314.88 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-1.5096493 - 2.1824026
Average (Standard dev.)-0.0000368696 (±0.032321364)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 314.88 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_34095_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_34095_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : SVCT1

EntireName: SVCT1
Components
  • Complex: SVCT1
    • Protein or peptide: Solute carrier family 23 member 1

-
Supramolecule #1: SVCT1

SupramoleculeName: SVCT1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Mus musculus (house mouse)

-
Macromolecule #1: Solute carrier family 23 member 1

MacromoleculeName: Solute carrier family 23 member 1 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 65.600438 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MKTPEDPGSP KQHEVVDSAG TSTRDRQAPL PTEPKFDMLY KIEDVPPWYL CILLGFQHYL TCFSGTIAVP FLLAEALCVG RDQHMVSQL IGTIFTCVGI TTLIQTTVGI RLPLFQASAF AFLVPAKSIL ALERWKCPSE EEIYGNWSMP LNTSHIWHPR I REVQGAIM ...String:
MKTPEDPGSP KQHEVVDSAG TSTRDRQAPL PTEPKFDMLY KIEDVPPWYL CILLGFQHYL TCFSGTIAVP FLLAEALCVG RDQHMVSQL IGTIFTCVGI TTLIQTTVGI RLPLFQASAF AFLVPAKSIL ALERWKCPSE EEIYGNWSMP LNTSHIWHPR I REVQGAIM VSSMVEVVIG LMGLPGALLS YIGPLTVTPT VSLIGLSVFQ AAGDRAGSHW GISACSILLI VLFSQYLRNL TF LLPVYRW GKGLTLFRVQ IFKMFPIVLA IMTVWLLCYV LTLTDVLPAD PTVYGFQART DARGDIMAIS PWIRIPYPCQ WGL PTVTVA AVLGMFSATL AGIIESIGDY YACARLAGAP PPPVHAINRG IFTEGICCII AGLLGTGNGS TSSSPNIGVL GITK VGSRR VVQYGAGIML ILGAIGKFTA LFASLPDPIL GGMFCTLFGM ITAVGLSNLQ FVDMNSSRNL FVLGFSMFFG LTLPN YLDS NPGAINTGIP EVDQILTVLL TTEMFVGGCL AFILDNTVPG SPEERGLIQW KAGAHANSET SASLKSYDFP FGMGMV KRT TFFRYIPICP VFRGFSKKTQ NQPPVLEDTP DNIETGSVCT KV

UniProtKB: Solute carrier family 23 member 1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.5 µm

-
Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2464213
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more