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- EMDB-62423: Cryo-EM structure of Xenopus tropicalis glycine transporter 2 in ... -

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Basic information

Entry
Database: EMDB / ID: EMD-62423
TitleCryo-EM structure of Xenopus tropicalis glycine transporter 2 in complex with ALX1393
Map data
Sample
  • Complex: Cryo-EM structure of glycine transporter 2 in complex with ALX1393
    • Protein or peptide: Transporter
  • Ligand: (2~{S})-2-azanyl-3-[(~{R})-(3-fluorophenyl)-(2-phenylmethoxyphenyl)methoxy]propanoic acid
  • Ligand: CHOLESTEROL
KeywordsGLYT2 / PROTEIN STRUCTURE / MEMBRANE PROTEIN
Function / homology
Function and homology information


SLC-mediated transport of neurotransmitters / glycine:sodium symporter activity / synaptic transmission, glycinergic / glycine import across plasma membrane / sodium ion transmembrane transport / synapse / metal ion binding / plasma membrane
Similarity search - Function
Sodium:neurotransmitter symporter family signature 2. / Sodium:neurotransmitter symporter family signature 1. / Sodium:neurotransmitter symporter / Sodium:neurotransmitter symporter superfamily / Sodium:neurotransmitter symporter family / Sodium:neurotransmitter symporter family profile.
Similarity search - Domain/homology
Biological speciesXenopus tropicalis (tropical clawed frog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsWang Y / Zhao Y
Funding support China, 1 items
OrganizationGrant numberCountry
Chinese Academy of Sciences China
CitationJournal: To Be Published
Title: Transport mechanism and pharmacology of the Xenopus tropicalis GlyT2
Authors: Zhao Y / Wang Y
History
DepositionNov 15, 2024-
Header (metadata) releaseNov 19, 2025-
Map releaseNov 19, 2025-
UpdateNov 19, 2025-
Current statusNov 19, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62423.png

Downloads & links

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Map

FileDownload / File: emd_62423.map.gz / Format: CCP4 / Size: 64 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 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å		0.85 Å/pix.
x 256 pix.
= 217.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.175
Minimum - Maximum-0.918754 - 1.3208433
Average (Standard dev.)-0.0007059634 (±0.028698102)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_62423_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_62423_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM structure of glycine transporter 2 in complex with ALX1393

EntireName: Cryo-EM structure of glycine transporter 2 in complex with ALX1393
Components
  • Complex: Cryo-EM structure of glycine transporter 2 in complex with ALX1393
    • Protein or peptide: Transporter
  • Ligand: (2~{S})-2-azanyl-3-[(~{R})-(3-fluorophenyl)-(2-phenylmethoxyphenyl)methoxy]propanoic acid
  • Ligand: CHOLESTEROL

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Supramolecule #1: Cryo-EM structure of glycine transporter 2 in complex with ALX1393

SupramoleculeName: Cryo-EM structure of glycine transporter 2 in complex with ALX1393
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Xenopus tropicalis (tropical clawed frog)

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Macromolecule #1: Transporter

MacromoleculeName: Transporter / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus tropicalis (tropical clawed frog)
Molecular weightTheoretical: 87.269273 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MDYVNVMDGT KKTMNSPEGA APGPIGAAGI TSHTPDNDLP LQASSKLARL SQSTSNDSKF AAAEEPKACD LERSRIGGSC KMTTPGHSN FVLKRDSVEG CPAKNTSMAD SNGQTNPLHC RIVPLQSAEG ETNQGFGKNS LEQNNAKGGW VPSQSTVVLG T DGNTSVFP ...String:
MDYVNVMDGT KKTMNSPEGA APGPIGAAGI TSHTPDNDLP LQASSKLARL SQSTSNDSKF AAAEEPKACD LERSRIGGSC KMTTPGHSN FVLKRDSVEG CPAKNTSMAD SNGQTNPLHC RIVPLQSAEG ETNQGFGKNS LEQNNAKGGW VPSQSTVVLG T DGNTSVFP GTLNGDEEGD ENKARGNWSS KLDFILSMVG YAVGLGNVWR FPYLAFKNGG GAFLIPYLTM LALAGLPIFY ME VALGQFA SQGPISVWKA IPALQGCGIA MLIISVLIAI YYNIIMCYTI FYLFASLVSV LPWASCTNPW NTPDCKDKDR LML DSCIIG SQPNIHIKNS TFCMTAYPNL TLVNFTSHAN KSFVSGSEEY FKYNMLKISA GIEYPGEIRW PLAICLFLAW TIVY ASLAK GIKSSGKVVY FTATFPYVVL VILLIRGVTL PGAGDGIWWF IMPKWEKLMD AMVWKDAATQ IFFSLSAAWG GLITL SSYN KFHNNVYRDT LIVTCTNSAT SIFAGFVIFS VIGFMAHILN VDIEKVADQG PGIAFVVYPE ALTRLPLSPF WAIIFF LML LTLGLDTMFA TIETIVTSVS DEFPKLLRPH KPLFTLICCV AFFIMGFPMI TQGGIYMLQL VDNYAASYSL VIIAIFE LV GISYVYGLQR FCEDIEMMIG FQPSRFWKVC WAFVTPTILT FILCFSFYQW EPMTYGSYHY PTWSMVMGWL MLACSVIW I PVMFVIKMYL APGTFIERLK LVCSPQPDWG PFLAKHRGER YKNMIDPLGT SSLGLKLPPK DFELGTQC

UniProtKB: Transporter

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Macromolecule #2: (2~{S})-2-azanyl-3-[(~{R})-(3-fluorophenyl)-(2-phenylmethoxypheny...

MacromoleculeName: (2~{S})-2-azanyl-3-[(~{R})-(3-fluorophenyl)-(2-phenylmethoxyphenyl)methoxy]propanoic acid
type: ligand / ID: 2 / Number of copies: 1 / Formula: A1EZ0
Molecular weightTheoretical: 395.423 Da

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Macromolecule #3: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 3 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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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: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 168213
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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