[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 the activation of a metabotropic GABA receptor.
Journal, issue, pagesNature, Vol. 584, Issue 7820, Page 298-303, Year 2020
Publish dateJun 17, 2020
AuthorsHamidreza Shaye / Andrii Ishchenko / Jordy Homing Lam / Gye Won Han / Li Xue / Philippe Rondard / Jean-Philippe Pin / Vsevolod Katritch / Cornelius Gati / Vadim Cherezov /
PubMed AbstractMetabotropic γ-aminobutyric acid receptors (GABA) are involved in the modulation of synaptic responses in the central nervous system and have been implicated in neuropsychological conditions that ...Metabotropic γ-aminobutyric acid receptors (GABA) are involved in the modulation of synaptic responses in the central nervous system and have been implicated in neuropsychological conditions that range from addiction to psychosis. GABA belongs to class C of the G-protein-coupled receptors, and its functional entity comprises an obligate heterodimer that is composed of the GB1 and GB2 subunits. Each subunit possesses an extracellular Venus flytrap domain, which is connected to a canonical seven-transmembrane domain. Here we present four cryo-electron microscopy structures of the human full-length GB1-GB2 heterodimer: one structure of its inactive apo state, two intermediate agonist-bound forms and an active form in which the heterodimer is bound to an agonist and a positive allosteric modulator. The structures reveal substantial differences, which shed light on the complex motions that underlie the unique activation mechanism of GABA. Our results show that agonist binding leads to the closure of the Venus flytrap domain of GB1, triggering a series of transitions, first rearranging and bringing the two transmembrane domains into close contact along transmembrane helix 6 and ultimately inducing conformational rearrangements in the GB2 transmembrane domain via a lever-like mechanism to initiate downstream signalling. This active state is stabilized by a positive allosteric modulator binding at the transmembrane dimerization interface.
External linksNature / PubMed:32555460 / PubMed Central
MethodsEM (single particle)
Resolution3.63 - 6.3 Å
Structure data

20822

6uo8

EMDB-20822: Human metabotropic GABA(B) receptor bound to agonist SKF97541 and positive allosteric modulator GS39783.
PDB-6uo8: Human metabotropic GABA(B) receptor bound to agonist SKF97541 and positive allosteric modulator GS39783
Method: EM (single particle) / Resolution: 3.63 Å

20823

6uo9

EMDB-20823, PDB-6uo9:
Human metabotropic GABA(B) receptor bound to agonist SKF97541 in its intermediate state 2
Method: EM (single particle) / Resolution: 4.8 Å

20824

6uoa

EMDB-20824: Human metabotropic GABA(B) receptor in its intermediate state 1.
PDB-6uoa: Human metabotropic GABA(B) receptor in its intermediate state 1
Method: EM (single particle) / Resolution: 6.3 Å

21219

6vjm

EMDB-21219: Human metabotropic GABA(B) receptor in its apo state.
PDB-6vjm: Human metabotropic GABA(B) receptor in its apo state
Method: EM (single particle) / Resolution: 3.97 Å

Chemicals

ChemComp-QD7:
(R)-(3-aminopropyl)methylphosphinic acid / agonist*YM

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

ChemComp-QDA:
N~4~,N~6~-dicyclopentyl-2-(methylsulfanyl)-5-nitropyrimidine-4,6-diamine

Source
  • homo sapiens (human)
KeywordsMEMBRANE PROTEIN / G protein-coupled receptor / GABA / GABAB / PAM / Neurotransmitter

+
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