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- EMDB-13193: Structure of human ASCT1 transporter -

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Basic information

Entry
Database: EMDB / ID: EMD-13193
TitleStructure of human ASCT1 transporter
Map data
Sample
  • Complex: trimeric ASCT1 transporter
    • Protein or peptide: Neutral amino acid transporter A
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 / glutamine transport / L-glutamine transmembrane transporter activity / L-serine transmembrane transporter activity / L-alanine transmembrane transporter activity / L-alanine import across plasma membrane / proline transport / L-glutamate transmembrane transport / amino acid transmembrane transporter activity / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity / L-aspartate transmembrane transporter activity / L-aspartate import across plasma membrane / symporter activity / amino acid transport / intermediate filament / chloride channel activity / plasma membrane => GO:0005886 / transport across blood-brain barrier / synaptic transmission, glutamatergic / cognition / melanosome / membrane => GO:0016020 / centrosome / neuronal cell body / synapse / dendrite / 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)
Methodsingle 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, 2021-
Header (metadata) releaseOct 6, 2021-
Map releaseOct 6, 2021-
UpdateOct 6, 2021-
Current statusOct 6, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.417
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.417
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7p4i
  • Surface level: 0.417
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13193.png

Downloads & links

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Map

FileDownload / File: emd_13193.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 320 pix.
= 272.672 Å		0.85 Å/pix.
x 320 pix.
= 272.672 Å		0.85 Å/pix.
x 320 pix.
= 272.672 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8521 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.417 / Movie #1: 0.417
Minimum - Maximum-0.02743699 - 0.88789356
Average (Standard dev.)0.023190068 (±0.07316704)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 272.672 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.85210.85210.8521
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z272.672272.672272.672
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0270.8880.023

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Supplemental data

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Sample components

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Entire : trimeric ASCT1 transporter

EntireName: trimeric ASCT1 transporter
Components
  • Complex: trimeric ASCT1 transporter
    • Protein or peptide: Neutral amino acid transporter A

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Supramolecule #1: trimeric ASCT1 transporter

SupramoleculeName: trimeric ASCT1 transporter / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Komagataella pastoris (fungus)
Molecular weightExperimental: 167 KDa

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Macromolecule #1: Neutral amino acid transporter A

MacromoleculeName: Neutral amino acid transporter A / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 55.76666 KDa
Recombinant expressionOrganism: Komagataella pastoris (fungus)
SequenceString: MEKSNETNGY LDSAQAGPAA GPGAPGTAAG RARRCAGFLR RQALVLLTVS GVLAGAGLGA ALRGLSLSRT QVTYLAFPGE MLLRMLRMI ILPLVVCSLV SGAASLDASC LGRLGGIAVA YFGLTTLSAS ALAVALAFII KPGSGAQTLQ SSDLGLEDSG P PPVPKETV ...String:
MEKSNETNGY LDSAQAGPAA GPGAPGTAAG RARRCAGFLR RQALVLLTVS GVLAGAGLGA ALRGLSLSRT QVTYLAFPGE MLLRMLRMI ILPLVVCSLV SGAASLDASC LGRLGGIAVA YFGLTTLSAS ALAVALAFII KPGSGAQTLQ SSDLGLEDSG P PPVPKETV DSFLDLARNL FPSNLVVAAF RTYATDYKVV TQNSSSGNVT HEKIPIGTEI EGMNILGLVL FALVLGVALK KL GSEGEDL IRFFNSLNEA TMVLVSWIMW YVPVGIMFLV GSKIVEMKDI IVLVTSLGKY IFASILGHVI HGGIVLPLIY FVF TRKNPF RFLLGLLAPF ATAFATCSSS ATLPSMMKCI EENNGVDKRI SRFILPIGAT VNMDGAAIFQ CVAAVFIAQL NNVE LNAGQ IFTILVTATA SSVGAAGVPA GGVLTIAIIL EAIGLPTHDL PLILAVDWIV DRTTTVVNVE GDALGAGILH HLNQK ATKK GEQELAEVKV EAIPNCKSEE ETSPLVTHQN PAGPVASAPE LESKESVL

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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
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: OTHER
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6gct

Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 134344

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