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- EMDB-62421: Cryo-EM structure of glycine transporter 2 in complex with substr... -

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Basic information

Entry
Database: EMDB / ID: EMD-62421
TitleCryo-EM structure of glycine transporter 2 in complex with substrate glycine
Map data
Sample
  • Complex: Cryo-EM structure of Xenopus tropicalis glycine transporter 2 in complex with GLYCINE
    • Protein or peptide: Transporter
  • Ligand: CHOLESTEROL
  • Ligand: GLYCINE
  • Ligand: SODIUM ION
  • Ligand: CHLORIDE ION
  • Ligand: water
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: 2.9 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_62421.png

Downloads & links

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Map

FileDownload / File: emd_62421.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: 0.25
Minimum - Maximum-1.1318583 - 1.5785859
Average (Standard dev.)0.00013523905 (±0.041402053)
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_62421_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_62421_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 Xenopus tropicalis glycine transporter 2 in ...

EntireName: Cryo-EM structure of Xenopus tropicalis glycine transporter 2 in complex with GLYCINE
Components
  • Complex: Cryo-EM structure of Xenopus tropicalis glycine transporter 2 in complex with GLYCINE
    • Protein or peptide: Transporter
  • Ligand: CHOLESTEROL
  • Ligand: GLYCINE
  • Ligand: SODIUM ION
  • Ligand: CHLORIDE ION
  • Ligand: water

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Supramolecule #1: Cryo-EM structure of Xenopus tropicalis glycine transporter 2 in ...

SupramoleculeName: Cryo-EM structure of Xenopus tropicalis glycine transporter 2 in complex with GLYCINE
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: CHOLESTEROL

MacromoleculeName: CHOLESTEROL / type: ligand / ID: 2 / Number of copies: 1 / Formula: CLR
Molecular weightTheoretical: 386.654 Da
Chemical component information

ChemComp-CLR:
CHOLESTEROL

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Macromolecule #3: GLYCINE

MacromoleculeName: GLYCINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: GLY
Molecular weightTheoretical: 75.067 Da
Chemical component information

ChemComp-GLY:
GLYCINE

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Macromolecule #4: SODIUM ION

MacromoleculeName: SODIUM ION / type: ligand / ID: 4 / Number of copies: 3
Molecular weightTheoretical: 22.99 Da

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Macromolecule #5: CHLORIDE ION

MacromoleculeName: CHLORIDE ION / type: ligand / ID: 5 / Number of copies: 1 / Formula: CL
Molecular weightTheoretical: 35.453 Da

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Macromolecule #6: water

MacromoleculeName: water / type: ligand / ID: 6 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 54731
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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