[English] 日本語
Yorodumi
- PDB-7p4i: Structure of human ASCT1 transporter -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7p4i
TitleStructure of human ASCT1 transporter
ComponentsNeutral amino acid transporter A
KeywordsTRANSPORT PROTEIN / Solute carrier / membrane protein / amino acid transport
Function / homology
Function and homology information


L-threonine transmembrane transporter activity / L-alanine transport / L-serine transport / threonine transport / hydroxyproline transport / L-hydroxyproline transmembrane transporter activity / L-serine import across plasma membrane / L-proline transmembrane transporter activity / L-cystine transmembrane transporter activity / L-cystine transport ...L-threonine transmembrane transporter activity / L-alanine transport / L-serine transport / threonine transport / hydroxyproline transport / L-hydroxyproline transmembrane transporter activity / L-serine import across plasma membrane / L-proline transmembrane transporter activity / L-cystine transmembrane transporter activity / L-cystine transport / L-glutamine transmembrane transporter activity / glutamine transport / L-serine transmembrane transporter activity / L-alanine transmembrane transporter activity / L-alanine import across plasma membrane / proline transport / L-glutamate transmembrane transport / L-aspartate transmembrane transporter activity / L-aspartate import across plasma membrane / amino acid transmembrane transporter activity / Amino acid transport across the plasma membrane / symporter activity / intermediate filament / chloride channel activity / amino acid transport / transport across blood-brain barrier / synaptic transmission, glutamatergic / cognition / melanosome / neuronal cell body / centrosome / dendrite / synapse / cell surface / extracellular exosome / membrane / plasma membrane
Similarity search - Function
: / Sodium:dicarboxylate symporter family signature 2. / Sodium:dicarboxylate symporter / Sodium:dicarboxylate symporter, conserved site / Sodium:dicarboxylate symporter superfamily / Sodium:dicarboxylate symporter family / Sodium:dicarboxylate symporter family signature 1.
Similarity search - Domain/homology
Neutral amino acid transporter A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsStetsenko, A. / Stehantsev, P. / Gati, C. / Guskov, A.
CitationJournal: Comput Struct Biotechnol J / Year: 2021
Title: A structural view onto disease-linked mutations in the human neutral amino acid exchanger ASCT1.
Authors: Pavlo Stehantsev / Artem Stetsenko / Mariia Nemchinova / Nanda Gowtham Aduri / Siewert J Marrink / Cornelius Gati / Albert Guskov /
Abstract: The ASCT1 transporter of the SLC1 family is largely involved in equilibration of neutral amino acids' pools across the plasma membrane and plays a prominent role in the transport of both L- and D- ...The ASCT1 transporter of the SLC1 family is largely involved in equilibration of neutral amino acids' pools across the plasma membrane and plays a prominent role in the transport of both L- and D-isomers of serine, essential for the normal functioning of the central nervous system in mammals. A number of mutations in ASCT1 (E256K, G381R, R457W) have been linked to severe neurodevelopmental disorders, however in the absence of ASCT1 structure it is hard to understand their impact on substrate transport. To ameliorate that we have determined a cryo-EM structure of human ASCT1 at 4.2 Å resolution and performed functional transport assays and molecular dynamics simulations, which revealed that given mutations lead to the diminished transport capability of ASCT1 caused by instability of transporter and impeded transport cycle.
History
DepositionJul 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-13193
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Neutral amino acid transporter A
B: Neutral amino acid transporter A
C: Neutral amino acid transporter A


Theoretical massNumber of molelcules
Total (without water)167,3003
Polymers167,3003
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area6350 Å2
ΔGint-59 kcal/mol
Surface area69270 Å2

-
Components

#1: Protein Neutral amino acid transporter A / Alanine/serine/cysteine/threonine transporter 1 / ASCT-1 / SATT / Solute carrier family 1 member 4


Mass: 55766.660 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLC1A4, ASCT1, SATT / Production host: Komagataella pastoris (fungus) / References: UniProt: P43007

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

-
Sample preparation

ComponentName: trimeric ASCT1 transporter / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.167 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Komagataella pastoris (fungus)
Buffer solutionpH: 7
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

-
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: OTHER
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

-
Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: NONE
3D reconstructionResolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 134344 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0029672
ELECTRON MICROSCOPYf_angle_d0.69113158
ELECTRON MICROSCOPYf_dihedral_angle_d4.4081344
ELECTRON MICROSCOPYf_chiral_restr0.0391659
ELECTRON MICROSCOPYf_plane_restr0.0041626

+
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