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- EMDB-17193: Complex of ASCT2 with Suppressyn -

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Basic information

Entry
Database: EMDB / ID: EMD-17193
TitleComplex of ASCT2 with Suppressyn
Map dataMain map from 3D flex reconstruction in Cryosparc.
Sample
  • Complex: Complex of Alanine Serine Cysteine Transporter 2 with Suppressyn
    • Protein or peptide: Neutral amino acid transporter B(0)
    • Protein or peptide: Suppressyn
  • Ligand: ALANINE
KeywordsSmall neural amino acid transporter / ASCT2 / Receptor binding domain / Suppressyn / PROTEIN TRANSPORT
Function / homologysyncytium formation / extracellular space / Suppressyn
Function and homology information
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.39 Å
AuthorsKhare S / Kumar A / Reyes N
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)771965European Union
CitationJournal: Nat Struct Mol Biol / Year: 2024
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
DepositionApr 23, 2023-
Header (metadata) releaseMay 1, 2024-
Map releaseMay 1, 2024-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17193.png

Downloads & links

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Map

FileDownload / File: emd_17193.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map from 3D flex reconstruction in Cryosparc.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 256 pix.
= 208.384 Å		0.81 Å/pix.
x 256 pix.
= 208.384 Å		0.81 Å/pix.
x 256 pix.
= 208.384 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.814 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00491
Minimum - Maximum-0.013732714 - 0.023225188
Average (Standard dev.)0.00005816048 (±0.00077221094)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 208.384 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: This is the half-map A corresponding to the...

Fileemd_17193_additional_1.map
AnnotationThis is the half-map A corresponding to the main map from the 3D flex reconstruction job in Cryosparc.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: This is the half-map B corresponding to the...

Fileemd_17193_additional_2.map
AnnotationThis is the half-map B corresponding to the main map from the 3D flex reconstruction job in Cryosparc.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: This is the half-map A from the non-uniform...

Fileemd_17193_half_map_1.map
AnnotationThis is the half-map A from the non-uniform refinement job, the parent job for running 3D flex reconstruction.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: This is the half-map B from the non-uniform...

Fileemd_17193_half_map_2.map
AnnotationThis is the half-map B from the non-uniform refinement job, the parent job for running 3D flex reconstruction.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Complex of Alanine Serine Cysteine Transporter 2 with Suppressyn

EntireName: Complex of Alanine Serine Cysteine Transporter 2 with Suppressyn
Components
  • Complex: Complex of Alanine Serine Cysteine Transporter 2 with Suppressyn
    • Protein or peptide: Neutral amino acid transporter B(0)
    • Protein or peptide: Suppressyn
  • Ligand: ALANINE

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Supramolecule #1: Complex of Alanine Serine Cysteine Transporter 2 with Suppressyn

SupramoleculeName: Complex of Alanine Serine Cysteine Transporter 2 with Suppressyn
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Neutral amino acid transporter B(0)

MacromoleculeName: Neutral amino acid transporter B(0) / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 57.897273 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MWSHPQFEKV ADPPRDSKGL AAAEPTANGG LALASIEDQG AAAGGYCGSR DQVRRFLRRN LLVLLTVSGV LAGVALGLGV RGAGGGLAL SRAQLTYFAF PGELLLRLLR MIILPLVVCS LIGGAASLDP GALGRLGAWA LLFFLVTTLL ASALGVGLAL A LQPGAASA ...String:
MWSHPQFEKV ADPPRDSKGL AAAEPTANGG LALASIEDQG AAAGGYCGSR DQVRRFLRRN LLVLLTVSGV LAGVALGLGV RGAGGGLAL SRAQLTYFAF PGELLLRLLR MIILPLVVCS LIGGAASLDP GALGRLGAWA LLFFLVTTLL ASALGVGLAL A LQPGAASA AITASVGAAG SAENAPSKEV LDSFLDLARN IFPSNLVSAA FRSYSTTYEE RTITGTRVKV PVGQEVEGMN IL GLVVFAI VFGVALRKLG PEGEELIRFF NSFNEATMVL VSWIMWYAPV GIMFLVASKI VEMEDVVLLF TSLGKYIFCC ILG HAIHGL IVLPLIYFAF TRKNPYRFLL GLLTPLATAF GTSSSSATLP LMMKCVEENN GVDKRISRFI LPIGATVNMD GAAI FQCVA AVFIAQLNNV PLNFGQIITI LVTATASSVG AAGIPAGGVL TLAIILEAIG LPTHDLSLIL AVDWLVDRTT TVVNV EGDA LGAGILQHLN DKTMKKSEEQ ELIQVKSELP LDPLPVPTEE GNPLLKHYRG PAGDATVASE KESVM

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Macromolecule #2: Suppressyn

MacromoleculeName: Suppressyn / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 18.152035 KDa
Recombinant expressionOrganism: Drosophila melanogaster (fruit fly)
SequenceString:
MACIYPTTFY TSLPTKSLNM GISLTTILIL SVAVLLSTAA PPSCRECYQS LHYRGEMQQY FTYHTHIERS CYGNLIEECV ESGKSYYKV KNLGVCGSRN GAICPRGKQW LCFTKIGQWG VNTQVLEDIK REQIIAKAKA SKPTTPPENR PRHFHSFIQK L

UniProtKB: Suppressyn

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Macromolecule #3: ALANINE

MacromoleculeName: ALANINE / type: ligand / ID: 3 / Number of copies: 2 / Formula: ALA
Molecular weightTheoretical: 89.093 Da
Chemical component information

ChemComp-ALA:
ALANINE / Alanine

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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

Concentration0.9 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
100.0 mMNaClSodium chlorideSodium Chloride
5.0 mMC3H7NO2L-AlanineAlanine
25.0 mMC8H18N2O4SHepes
0.05 %C24H44O12Sucrose Monododecanoate
0.01 %C31H50O4.C4H11NO3Cholesteryl Hemisuccinate Tris Salt
GridModel: 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 - Atmosphere: AIR
VitrificationCryogen name: NITROGEN / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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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: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.8 µm
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 8400 / Average electron dose: 42.61 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: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3)
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.39 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.1.1) / Number images used: 125356
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6gct


Chain - Source name: PDB / Chain - Initial model type: experimental model
SoftwareName: Coot (ver. 0.9.8.3)
RefinementProtocol: AB INITIO MODEL / Overall B value: 90
Output model

PDB-8oui:
Complex of ASCT2 with Suppressyn

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