[English] 日本語
Yorodumi
- EMDB-10017: Inward-open structure of the ASCT2 (SLC1A5) in absence of substrate -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-10017
TitleInward-open structure of the ASCT2 (SLC1A5) in absence of substrate
Map dataNone
Sample
  • Complex: ASCT2 (Alanine Serine Cysteine Transporter 2, SLC1A)
    • Protein or peptide: ASCT2
Function / homology
Function and homology information


glutamine secretion / L-glutamine import across plasma membrane / L-serine transmembrane transporter activity / glutamine transport / L-glutamine transmembrane transporter activity / ligand-gated channel activity / neutral amino acid transport / amino acid transmembrane transporter activity / Amino acid transport across the plasma membrane / neutral L-amino acid transmembrane transporter activity ...glutamine secretion / L-glutamine import across plasma membrane / L-serine transmembrane transporter activity / glutamine transport / L-glutamine transmembrane transporter activity / ligand-gated channel activity / neutral amino acid 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 / antiporter activity / RHOJ GTPase cycle / RHOQ GTPase cycle / protein homotrimerization / RHOH GTPase cycle / transport across blood-brain barrier / RAC3 GTPase cycle / RAC1 GTPase cycle / basal plasma membrane / erythrocyte differentiation / melanosome / virus receptor activity / signaling receptor activity / extracellular exosome / membrane / metal ion binding / 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 B(0)
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.98 Å
AuthorsGaraeva AA / Guskov A / Slotboom DJ / Paulino C
Funding support Netherlands, 5 items
OrganizationGrant numberCountry
Netherlands Organisation for Scientific Research723.014.002 Netherlands
European Research Council282083 Netherlands
Netherlands Organisation for Scientific Research865.11.001 Netherlands
Netherlands Organisation for Scientific Research740.018.016 Netherlands
Netherlands Organisation for Scientific Research722.017.001 Netherlands
CitationJournal: Nat Commun / Year: 2019
Title: A one-gate elevator mechanism for the human neutral amino acid transporter ASCT2.
Authors: Alisa A Garaeva / Albert Guskov / Dirk J Slotboom / Cristina Paulino /
Abstract: The human Alanine Serine Cysteine Transporter 2 (ASCT2) is a neutral amino acid exchanger that belongs to the solute carrier family 1 (SLC1A). SLC1A structures have revealed an elevator-type ...The human Alanine Serine Cysteine Transporter 2 (ASCT2) is a neutral amino acid exchanger that belongs to the solute carrier family 1 (SLC1A). SLC1A structures have revealed an elevator-type mechanism, in which the substrate is translocated across the cell membrane by a large displacement of the transport domain, whereas a small movement of hairpin 2 (HP2) gates the extracellular access to the substrate-binding site. However, it has remained unclear how substrate binding and release is gated on the cytoplasmic side. Here, we present an inward-open structure of the human ASCT2, revealing a hitherto elusive SLC1A conformation. Strikingly, the same structural element (HP2) serves as a gate in the inward-facing as in the outward-facing state. The structures reveal that SLC1A transporters work as one-gate elevators. Unassigned densities near the gate and surrounding the scaffold domain, may represent potential allosteric binding sites, which could guide the design of lipidic-inhibitors for anticancer therapy.
History
DepositionJun 3, 2019-
Header (metadata) releaseJun 12, 2019-
Map releaseAug 7, 2019-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0403
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.0403
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10017.png

Downloads & links

-
Map

FileDownload / File: emd_10017.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNone
Voxel sizeX=Y=Z: 1.012 Å
Density
Contour LevelBy AUTHOR: 0.0403 / Movie #1: 0.0403
Minimum - Maximum-0.07360207 - 0.14080314
Average (Standard dev.)0.0009318083 (±0.0060447273)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 202.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0121.0121.012
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z202.400202.400202.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0740.1410.001

-
Supplemental data

-
Mask #1

Fileemd_10017_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 2 used during refinement and for...

Fileemd_10017_half_map_1.map
Annotationhalf map 2 used during refinement and for FSC gold-standard resolution calculation of apo ASCT2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map 1 used during refinement and for...

Fileemd_10017_half_map_2.map
Annotationhalf map 1 used during refinement and for FSC gold-standard resolution calculation of apo ASCT2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ASCT2 (Alanine Serine Cysteine Transporter 2, SLC1A)

EntireName: ASCT2 (Alanine Serine Cysteine Transporter 2, SLC1A)
Components
  • Complex: ASCT2 (Alanine Serine Cysteine Transporter 2, SLC1A)
    • Protein or peptide: ASCT2

-
Supramolecule #1: ASCT2 (Alanine Serine Cysteine Transporter 2, SLC1A)

SupramoleculeName: ASCT2 (Alanine Serine Cysteine Transporter 2, SLC1A) / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: in absence of substrate
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Komagataella pastoris (fungus)
Molecular weightTheoretical: 172 KDa

-
Macromolecule #1: ASCT2

MacromoleculeName: ASCT2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
SequenceString: MVADPPRDSK GLAAAEPTAN GGLALASIED QGAAAGGYCG SRDQVRRCLR ANLLVLLTVV AVVAGVALG LGVSGAGGAL ALGPERLSAF VFPGELLLRL LRMIILPLVV CSLIGGAASL D PGALGRLG AWALLFFLVT TLLASALGVG LALALQPGAA SAAINASVGA ...String:
MVADPPRDSK GLAAAEPTAN GGLALASIED QGAAAGGYCG SRDQVRRCLR ANLLVLLTVV AVVAGVALG LGVSGAGGAL ALGPERLSAF VFPGELLLRL LRMIILPLVV CSLIGGAASL D PGALGRLG AWALLFFLVT TLLASALGVG LALALQPGAA SAAINASVGA AGSAENAPSK EV LDSFLDL ARNIFPSNLV SAAFRSYSTT YEERNITGTR VKVPVGQEVE GMNILGLVVF AIV FGVALR KLGPEGELLI RFFNSFNEAT MVLVSWIMWY APVGIMFLVA GKIVEMEDVG LLFA RLGKY ILCCLLGHAI HGLLVLPLIY FLFTRKNPYR FLWGIVTPLA TAFGTSSSSA TLPLM MKCV EENNGVAKHI SRFILPIGAT VNMDGAALFQ CVAAVFIAQL SQQSLDFVKI ITILVT ATA SSVGAAGIPA GGVLTLAIIL EAVNLPVDHI SLILAVDWLV DRSCTVLNVE GDALGAG LL QNYVDRTESR STEPELIQVK SELPLDPLPV PTEEGNPLLK HYRGPAGDAT VASEKESV M HHHHHH

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration8 mg/mL
BufferpH: 7.4
Details: 20 mM Tris pH 7.4, 300 mM NaCl, 0.05% DDM, 0.005% CHS
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.0 µm / Calibrated defocus min: 0.3 µm / Calibrated magnification: 49407 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 49407
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
TemperatureMin: 90.0 K / Max: 105.0 K
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-60 / Number grids imaged: 6 / Number real images: 4305 / Average exposure time: 9.0 sec. / Average electron dose: 52.0 e/Å2
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 452900
CTF correctionSoftware - Name: CTFFIND (ver. 4.1.8)
Startup modelType of model: EMDB MAP
EMDB ID:

4386

Initial angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0-beta-2)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0-beta-2)
Final reconstructionApplied symmetry - Point group: C3 (3 fold cyclic) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 6.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0-beta-2) / Number images used: 19651
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6gct

RefinementSpace: REAL

+
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