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Yorodumi- EMDB-10016: Inward-open structure of the ASCT2 (SLC1A5) mutant C467R in prese... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10016 | ||||||||||||||||||
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Title | Inward-open structure of the ASCT2 (SLC1A5) mutant C467R in presence of TBOA | ||||||||||||||||||
Map data | ASCT2-C467R in the presence of TBOA at 3.6 %u212B resolution sharpened at -204 %u212B^2 | ||||||||||||||||||
Sample |
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Keywords | solute carrier family 1 (SLC1A) one-gate elevator mechanism neutral amino acid exchange membrane protein cryo-EM / MEMBRANE PROTEIN | ||||||||||||||||||
Function / homology | Function and homology information glutamine secretion / L-glutamine import across plasma membrane / glutamine transport / L-glutamine transmembrane transporter activity / L-serine transmembrane transporter activity / ligand-gated channel activity / neutral amino acid transport / amino acid transmembrane transporter activity / L-aspartate transmembrane transporter activity / Amino acid transport across the plasma membrane ...glutamine secretion / L-glutamine import across plasma membrane / glutamine transport / L-glutamine transmembrane transporter activity / L-serine transmembrane transporter activity / ligand-gated channel activity / neutral amino acid transport / amino acid transmembrane transporter activity / L-aspartate transmembrane transporter activity / Amino acid transport across the plasma membrane / L-aspartate import across plasma membrane / neutral L-amino acid transmembrane transporter activity / symporter activity / antiporter activity / amino acid transport / RHOJ GTPase cycle / RHOQ GTPase cycle / protein homotrimerization / RHOH GTPase cycle / transport across blood-brain barrier / RAC3 GTPase cycle / basal plasma membrane / RAC1 GTPase cycle / erythrocyte differentiation / virus receptor activity / melanosome / signaling receptor activity / extracellular exosome / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.61 Å | ||||||||||||||||||
Authors | Garaeva AA / Guskov A | ||||||||||||||||||
Funding support | Netherlands, 5 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10016.map.gz | 28.5 MB | EMDB map data format | |
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Header (meta data) | emd-10016-v30.xml emd-10016.xml | 19.7 KB 19.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_10016_fsc.xml | 7.2 KB | Display | FSC data file |
Images | emd_10016.png | 130.6 KB | ||
Masks | emd_10016_msk_1.map | 30.5 MB | Mask map | |
Filedesc metadata | emd-10016.cif.gz | 6.4 KB | ||
Others | emd_10016_half_map_1.map.gz emd_10016_half_map_2.map.gz | 23.3 MB 23.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10016 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10016 | HTTPS FTP |
-Validation report
Summary document | emd_10016_validation.pdf.gz | 764.5 KB | Display | EMDB validaton report |
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Full document | emd_10016_full_validation.pdf.gz | 764 KB | Display | |
Data in XML | emd_10016_validation.xml.gz | 12.7 KB | Display | |
Data in CIF | emd_10016_validation.cif.gz | 17.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10016 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10016 | HTTPS FTP |
-Related structure data
Related structure data | 6rvxMC 6rvyC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10016.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | ASCT2-C467R in the presence of TBOA at 3.6 %u212B resolution sharpened at -204 %u212B^2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.012 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_10016_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: None
File | emd_10016_half_map_1.map | ||||||||||||
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Annotation | None | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: None
File | emd_10016_half_map_2.map | ||||||||||||
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Annotation | None | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : C467R mutant of ASCT2 (Alanine Serine Cysteine Transporter 2, SLC1A)
Entire | Name: C467R mutant of ASCT2 (Alanine Serine Cysteine Transporter 2, SLC1A) |
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Components |
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-Supramolecule #1: C467R mutant of ASCT2 (Alanine Serine Cysteine Transporter 2, SLC1A)
Supramolecule | Name: C467R mutant of ASCT2 (Alanine Serine Cysteine Transporter 2, SLC1A) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 172 KDa |
-Macromolecule #1: Neutral amino acid transporter B(0)
Macromolecule | Name: Neutral amino acid transporter B(0) / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 57.521848 KDa |
Recombinant expression | Organism: Komagataella pastoris (fungus) |
Sequence | String: MVADPPRDSK GLAAAEPTAN GGLALASIED QGAAAGGYCG SRDQVRRCLR ANLLVLLTVV AVVAGVALGL GVSGAGGALA LGPERLSAF VFPGELLLRL LRMIILPLVV CSLIGGAASL DPGALGRLGA WALLFFLVTT LLASALGVGL ALALQPGAAS A AINASVGA ...String: MVADPPRDSK GLAAAEPTAN GGLALASIED QGAAAGGYCG SRDQVRRCLR ANLLVLLTVV AVVAGVALGL GVSGAGGALA LGPERLSAF VFPGELLLRL LRMIILPLVV CSLIGGAASL DPGALGRLGA WALLFFLVTT LLASALGVGL ALALQPGAAS A AINASVGA AGSAENAPSK EVLDSFLDLA RNIFPSNLVS AAFRSYSTTY EERNITGTRV KVPVGQEVEG MNILGLVVFA IV FGVALRK LGPEGELLIR FFNSFNEATM VLVSWIMWYA PVGIMFLVAG KIVEMEDVGL LFARLGKYIL CCLLGHAIHG LLV LPLIYF LFTRKNPYRF LWGIVTPLAT AFGTSSSSAT LPLMMKCVEE NNGVAKHISR FILPIGATVN MDGAALFQCV AAVF IAQLS QQSLDFVKII TILVTATASS VGAAGIPAGG VLTLAIILEA VNLPVDHISL ILAVDWLVDR SRTVLNVEGD ALGAG LLQN YVDRTESRST EPELIQVKSE LPLDPLPVPT EEGNPLLKHY RGPAGDATVA SEKESVMHHH HHH UniProtKB: Neutral amino acid transporter B(0) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 5 mg/mL |
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Buffer | pH: 7.4 Details: 20 mM Tris pH 7.4, 300 mM NaCl, 0.05% DDM, 0.005% CHS |
Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 288 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Temperature | Min: 90.0 K / Max: 105.0 K |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film 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: 7327 / Average exposure time: 9.0 sec. / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 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 FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 49407 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |