[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleStructural basis of allosteric and bitopic ligands binding in sphingosine-1-phosphate receptors 2 and 3.
Journal, issue, pagesProtein Cell, Year 2025
Publish dateAug 20, 2025
AuthorsYanhong Wu / Qiuru Chen / Hongyu Wang / Kezhen Liu / Jiaxin Wei / Mu Wang / Kun Chen / Ya Zhu / Shuo Han / Cuiying Yi / Limin Ma / Gisela Schnapp / Alexander Pautsch / Christian Gnamm / Matthias Grauert / Esther Schmidt / Qiuxiang Tan / Beili Wu / Qiang Zhao /
External linksProtein Cell / PubMed:40851516
MethodsEM (single particle) / X-ray diffraction
Resolution3.0 - 3.8 Å
Structure data

65508

9w0m

EMDB-65508, PDB-9w0m:
Cryo-EM structure of S1P2 in complex with heterotrimeric G protein
Method: EM (single particle) / Resolution: 3.8 Å

65510

9w0o

EMDB-65510, PDB-9w0o:
cryoEM structure of S1P3 in complex with heterotrimeric G protein
Method: EM (single particle) / Resolution: 3.0 Å

PDB-9w0h:
S1P3 in complex with cpd-32 and spm242
Method: X-RAY DIFFRACTION / Resolution: 3 Å

PDB-9w0l:
S1P3 in complex with CYM52581 and spm242
Method: X-RAY DIFFRACTION / Resolution: 3.6 Å

Chemicals

PDB-1euh:
APO FORM OF A NADP DEPENDENT ALDEHYDE DEHYDROGENASE FROM STREPTOCOCCUS MUTANS

PDB-1euc:
CRYSTAL STRUCTURE OF DEPHOSPHORYLATED PIG HEART, GTP-SPECIFIC SUCCINYL-COA SYNTHETASE

PDB-1eud:
CRYSTAL STRUCTURE OF PHOSPHORYLATED PIG HEART, GTP-SPECIFIC SUCCINYL-COA SYNTHETASE

Source
  • homo sapiens (human)
  • niallia circulans (bacteria)
KeywordsMEMBRANE PROTEIN / S1P3 / G protein-coupled receptor / Bitter taste receptor 14 / Bitter taste receptor 46 / ligand binding / signal transduction

+
About Yorodumi Papers

-
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 Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more