[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

TitleNative mass spectrometry prescreening of G protein-coupled receptor complexes for cryo-EM structure determination.
Journal, issue, pagesStructure, Vol. 32, Issue 12, Page 2206-22219.e4, Year 2024
Publish dateDec 5, 2024
AuthorsDonggyun Kim / Weijing Liu / Rosa Viner / Vadim Cherezov /
PubMed AbstractG protein-coupled receptors (GPCRs) are essential transmembrane proteins playing key roles in human health and disease. Understanding their atomic-level molecular structure and conformational states ...G protein-coupled receptors (GPCRs) are essential transmembrane proteins playing key roles in human health and disease. Understanding their atomic-level molecular structure and conformational states is imperative for advancing drug development. Recent breakthroughs in single-particle cryogenic electron microscopy (cryo-EM) have propelled the structural biology of GPCRs into a new era. Nevertheless, the preparation of suitable GPCR samples and their complexes for cryo-EM analysis remains challenging due to their poor stability and highly dynamic nature. Here, we present our online buffer exchange-native MS method combined with Direct Mass Technology (OBE-nMS+DMT) which facilitates high-throughput analysis and guides sample preparation. We applied this method to optimize the GPR119-G complex sample prior to cryo-EM analysis, leading to a 3.51 Å resolution structure from only 396 movies collected on a 200 kV Glacios. This study suggests that the OBE-nMS+DMT method emerges as a powerful tool for prescreening sample conditions in cryo-EM studies of GPCRs and other membrane protein complexes.
External linksStructure / PubMed:39471802 / PubMed Central
MethodsEM (single particle)
Resolution3.47 - 3.66 Å
Structure data

43236

8vhf

EMDB-43236, PDB-8vhf:
Cryo-EM structure of GPR119-Gs-Nb35 complex with small molecule agonist MBX-2982
Method: EM (single particle) / Resolution: 3.51 Å

EMDB-43252: Cryo-EM structure of GPR119-Gs-Nb35 complex with small molecule agonist MBX-2982 (consensus map)
Method: EM (single particle) / Resolution: 3.48 Å

EMDB-43253: Cryo-EM structure of GPR119-Gs-Nb35 complex with small molecule agonist MBX-2982 (Receptor-focused map)
Method: EM (single particle) / Resolution: 3.61 Å

EMDB-43254: Cryo-EM structure of GPR119-Gs-Nb35 complex with small molecule agonist MBX-2982 (G protein-focused map)
Method: EM (single particle) / Resolution: 3.47 Å

EMDB-47154: Cryo-EM structure of GPR119-Gs-Nb35 complex with endogenous agonist oleoylethanolamide (OEA) (consensus map)
Method: EM (single particle) / Resolution: 3.66 Å

Chemicals

ChemComp-8VP:
2-[1-(5-ethylpyrimidin-2-yl)piperidin-4-yl]-4-[[4-(1,2,3,4-tetrazol-1-yl)phenoxy]methyl]-1,3-thiazole

Source
  • escherichia coli (E. coli)
  • homo sapiens (human)
  • lama glama (llama)
  • oplophorus gracilirostris (crustacean)
  • synthetic construct (others)
KeywordsMEMBRANE PROTEIN/SIGNALING PROTEIN / CryoEM / GPCR / Orphan / G protein complex / Active / Agonist / MEMBRANE PROTEIN / Diabetes / native Mass Spectrometry / MEMBRANE PROTEIN-SIGNALING PROTEIN complex

+
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