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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | Heterotrimeric Complex of Human ASCT2 with Syncytin-1 | |||||||||
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![]() | Small neutral amino acid transporter / ASCT2 / Syncytin-1 / ![]() ![]() | |||||||||
Function / homology | ![]() syncytium formation by plasma membrane fusion / glutamine secretion / syncytium formation / L-glutamine import across plasma membrane / glutamine transport / L-glutamine transmembrane transporter activity / L-serine transmembrane transporter activity / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Khare S / Reyes N | |||||||||
Funding support | European Union, 1 items
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![]() | ![]() Title: Receptor-recognition and antiviral mechanisms of retrovirus-derived human proteins. Authors: Shashank Khare / Miryam I Villalba / Juan C Canul-Tec / Arantza Balsebre Cajiao / Anand Kumar / Marija Backovic / Felix A Rey / Els Pardon / Jan Steyaert / Camilo Perez / Nicolas Reyes / ![]() ![]() ![]() ![]() Abstract: Human syncytin-1 and suppressyn are cellular proteins of retroviral origin involved in cell-cell fusion events to establish the maternal-fetal interface in the placenta. In cell culture, they ...Human syncytin-1 and suppressyn are cellular proteins of retroviral origin involved in cell-cell fusion events to establish the maternal-fetal interface in the placenta. In cell culture, they restrict infections from members of the largest interference group of vertebrate retroviruses, and are regarded as host immunity factors expressed during development. At the core of the syncytin-1 and suppressyn functions are poorly understood mechanisms to recognize a common cellular receptor, the membrane transporter ASCT2. Here, we present cryo-electron microscopy structures of human ASCT2 in complexes with the receptor-binding domains of syncytin-1 and suppressyn. Despite their evolutionary divergence, the two placental proteins occupy similar positions in ASCT2, and are stabilized by the formation of a hybrid β-sheet or 'clamp' with the receptor. Structural predictions of the receptor-binding domains of extant retroviruses indicate overlapping binding interfaces and clamping sites with ASCT2, revealing a competition mechanism between the placental proteins and the retroviruses. Our work uncovers a common ASCT2 recognition mechanism by a large group of endogenous and disease-causing retroviruses, and provides high-resolution views on how placental human proteins exert morphological and immunological functions. | |||||||||
History |
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | 217 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.7 KB 21.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 13.3 KB | Display | ![]() |
Images | ![]() | 86.2 KB | ||
Filedesc metadata | ![]() | 7 KB | ||
Others | ![]() ![]() | 226.3 MB 226.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8oujMC ![]() 8oudC ![]() 8ouhC ![]() 8ouiC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 0.731 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_17194_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_17194_half_map_2.map | ||||||||||||
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Density Histograms |
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Sample components
-Entire : Complex ASCT2 with Syncytin-1
Entire | Name: Complex ASCT2 with Syncytin-1 |
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Components |
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-Supramolecule #1: Complex ASCT2 with Syncytin-1
Supramolecule | Name: Complex ASCT2 with Syncytin-1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2 |
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Molecular weight | Theoretical: 180 kDa/nm |
-Supramolecule #2: Alanine Serine Cysteine Transporter 2
Supramolecule | Name: Alanine Serine Cysteine Transporter 2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: Syncytin-1
Supramolecule | Name: Syncytin-1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: ![]() ![]() |
-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: ![]() ![]() |
Molecular weight | Theoretical: 58.984566 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MWSHPQFEKS SGGLEVLFQG PMVADPPRDS KGLAAAEPTA NGGLALASIE DQGAAAGGYC GSRDQVRRCL RANLLVLLTV VAVVAGVAL GLGVSGAGGA LALGPERLSA FVFPGELLLR LLRMIILPLV VCSLIGGAAS LDPGALGRLG AWALLFFLVT T LLASALGV ...String: MWSHPQFEKS SGGLEVLFQG PMVADPPRDS KGLAAAEPTA NGGLALASIE DQGAAAGGYC GSRDQVRRCL RANLLVLLTV VAVVAGVAL GLGVSGAGGA LALGPERLSA FVFPGELLLR LLRMIILPLV VCSLIGGAAS LDPGALGRLG AWALLFFLVT T LLASALGV GLALALQPGA ASAAINASVG AAGSAENAPS KEVLDSFLDL ARNIFPSNLV SAAFRSYSTT YEERNITGTR VK VPVGQEV EGMNILGLVV FAIVFGVALR KLGPEGELLI RFFNSFNEAT MVLVSWIMWY APVGIMFLVA GKIVEMEDVG LLF ARLGKY ILCCLLGHAI HGLLVLPLIY FLFTRKNPYR FLWGIVTPLA TAFGTSSSSA TLPLMMKCVE ENNGVAKHIS RFIL PIGAT VNMDGAALFQ CVAAVFIAQL SQQSLDFVKI ITILVTATAS SVGAAGIPAG GVLTLAIILE AVNLPVDHIS LILAV DWLV DRSCTVLNVE GDALGAGLLQ NYVDRTESRS TEPELIQVKS ELPLDPLPVP TEEGNPLLKH YRGPAGDATV ASEKES VM UniProtKB: Neutral amino acid transporter B(0) |
-Macromolecule #2: Syncytin-1
Macromolecule | Name: Syncytin-1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 49.24593 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: AVVAFVGLSL GAPPPCRCMT SSSPYQEFLW RMQRPGNIDA PSYRSLSKGT PTFTAHTHMP RNCYHSATLC MHANTHYWTG KMINPSCPG GLGVTVCWTY FTQTGMSDGG GVQDQAREKH VKEVISQLTR VHGTSSPYKG LDLSKLHETL RTHTRLVSLF N TTLTGLHE ...String: AVVAFVGLSL GAPPPCRCMT SSSPYQEFLW RMQRPGNIDA PSYRSLSKGT PTFTAHTHMP RNCYHSATLC MHANTHYWTG KMINPSCPG GLGVTVCWTY FTQTGMSDGG GVQDQAREKH VKEVISQLTR VHGTSSPYKG LDLSKLHETL RTHTRLVSLF N TTLTGLHE VSAQNPTNSW ICLPLNFRPY VSIPVPEQWN NFSTEINTTS VLVGPLVSNL EITHTSNLTC VKFSNTTYTT NS QCIRWVT PPTQIVCLPS GIFFVCGTSA YRCLNGSSES MCFLSFLVPP MTIYTEQDLY NYVISKPRNK RVPILPFVIG AGV LGALGT GIGGITTSTQ FYYKLSQELN GDMERVADSL VTLQDQLNSL AAVVLQNRRA LDLLTAERGG TCLFLGEECC YYVN QSGIV TEKVKEIRDR IQRRAEELRN TGPWGSGLEV LFQGPGPEPE A UniProtKB: Syncytin-1 |
-Macromolecule #3: ALANINE
Macromolecule | Name: ALANINE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ALA |
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Molecular weight | Theoretical: 89.093 Da |
Chemical component information | ![]() ChemComp-ALA: |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Concentration | 9 mg/mL | ||||||||||||||||||
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Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 10 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 40 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.003 kPa | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Name: TFS Selectris X / Energy filter - Slit width: 10 eV |
Sample stage | Cooling holder cryogen: NITROGEN |
Software | Name: EPU (ver. 2) |
Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 15376 / Average exposure time: 6.0 sec. / Average electron dose: 53.4 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Initial model |
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Software | Name: ![]() | |||||||||
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 82.2 | |||||||||
Output model | ![]() PDB-8ouj: |