[English] 日本語
Yorodumi
- EMDB-62422: Cryo-EM structure of glycine transporter 2 in complex with oleoyl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-62422
TitleCryo-EM structure of glycine transporter 2 in complex with oleoyl-D-lysine
Map data
Sample
  • Complex: Cryo-EM structure of glycine transporter 2 in complex with oleoyl-D-lysine
    • Protein or peptide: Transporter
  • Ligand: CHOLESTEROL
  • Ligand: D-LYSINE
  • Ligand: OLEIC ACID
  • 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: 3.2 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 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

-
Structure visualization

Supplemental images

emd_62422.png

Downloads & links

-
Map

FileDownload / File: emd_62422.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: 0.276
Minimum - Maximum-1.2079558 - 1.5624933
Average (Standard dev.)0.00012077971 (±0.047150496)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #2

Fileemd_62422_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_62422_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

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

EntireName: Cryo-EM structure of glycine transporter 2 in complex with oleoyl-D-lysine
Components
  • Complex: Cryo-EM structure of glycine transporter 2 in complex with oleoyl-D-lysine
    • Protein or peptide: Transporter
  • Ligand: CHOLESTEROL
  • Ligand: D-LYSINE
  • Ligand: OLEIC ACID
  • Ligand: water

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

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

-
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: 66.681391 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: GDENKARGNW SSKLDFILSM VGYAVGLGNV WRFPYLAFKN GGGAFLIPYL TMLALAGLPI FYMEVALGQF ASQGPISVWK AIPALQGCG IAMLIISVLI AIYYNVIICY TIFYLFASLV SVLPWASCTN PWNTPDCKDK DRLMLDSCII GSQPNIHIKN S TFCMTAYP ...String:
GDENKARGNW SSKLDFILSM VGYAVGLGNV WRFPYLAFKN GGGAFLIPYL TMLALAGLPI FYMEVALGQF ASQGPISVWK AIPALQGCG IAMLIISVLI AIYYNVIICY TIFYLFASLV SVLPWASCTN PWNTPDCKDK DRLMLDSCII GSQPNIHIKN S TFCMTAYP NLTLVNFTSH ANKSFVSGSE EYFKYNMLKI SAGIEYPGEI RWPLAICLFL AWTIVYASLA KGIKSSGKVV YF TATFPYV VLVILLIRGV TLPGAGDGIW WFIMPKWEKL MDAMVWKDAA TQIFFSLSAA WGGLITLSSY NKFHNNVYRD TLI VTCTNS ATSIFAGFVI FSVIGFMANE RKVNIENVAD QGPGIAFVVY PEALTRLPLS PFWAIIFFLM LLTLGLDTMF ATIE TIVTS VSDEFPKLLR PHKPLFTLIC CVAFFIMGFP MITQGGIYMF QLVDNYAASY SLVIIAIFEL VGISYVYGLQ RFCED IEMM IGFQPSRFWK VCWAFVTPTI LTFILCFSFY QWEPMTYGSY HYPTWSMVMG WLMLACSVIW IPVMFVIKMY LAPGTF IER LKLVCSPQPD WGPFLAKHRG ERYKNMID

UniProtKB: Transporter

-
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

-
Macromolecule #3: D-LYSINE

MacromoleculeName: D-LYSINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: DLY
Molecular weightTheoretical: 146.188 Da
Chemical component information

ChemComp-DLY:
D-LYSINE

-
Macromolecule #4: OLEIC ACID

MacromoleculeName: OLEIC ACID / type: ligand / ID: 4 / Number of copies: 1 / Formula: OLA
Molecular weightTheoretical: 282.461 Da
Chemical component information

ChemComp-OLA:
OLEIC ACID

-
Macromolecule #5: water

MacromoleculeName: water / type: ligand / ID: 5 / Number of copies: 4 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
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

+
Image processing

CTF correctionType: PHASE FLIPPING ONLY
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 35621
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more