[English] 日本語
Yorodumi
- EMDB-35382: Cryo-EM structure of GPR156A/B of G-protein free GPR156 (local refine) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-35382
TitleCryo-EM structure of GPR156A/B of G-protein free GPR156 (local refine)
Map data
Sample
  • Complex: GPR156A/B
    • Protein or peptide: Probable G-protein coupled receptor 156
  • Ligand: [(2R)-3-[(E)-hexadec-9-enoyl]oxy-2-octadecanoyloxy-propyl] 2-(trimethylazaniumyl)ethyl phosphate
KeywordsMembrane protein / G-protein coupled receptor / Signal transduction / Phospholipid
Function / homology
Function and homology information


G protein-coupled GABA receptor activity / G protein-coupled receptor heterodimeric complex / gamma-aminobutyric acid signaling pathway / plasma membrane
Similarity search - Function
GPR156, 7TM domain / GPCR family 3, GABA-B receptor / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR / G-protein coupled receptors family 3 profile.
Similarity search - Domain/homology
Probable G-protein coupled receptor 156
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.62 Å
AuthorsShin J / Park J / Cho Y
Funding support Korea, Republic Of, 1 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1A2C301335711 Korea, Republic Of
CitationJournal: Nat Struct Mol Biol / Year: 2024
Title: Constitutive activation mechanism of a class C GPCR.
Authors: Jinwoo Shin / Junhyeon Park / Jieun Jeong / Jordy Homing Lam / Xingyu Qiu / Di Wu / Kuglae Kim / Joo-Youn Lee / Carol V Robinson / Jaekyung Hyun / Vsevolod Katritch / Kwang Pyo Kim / Yunje Cho /
Abstract: Class C G-protein-coupled receptors (GPCRs) are activated through binding of agonists to the large extracellular domain (ECD) followed by rearrangement of the transmembrane domains (TMDs). GPR156, a ...Class C G-protein-coupled receptors (GPCRs) are activated through binding of agonists to the large extracellular domain (ECD) followed by rearrangement of the transmembrane domains (TMDs). GPR156, a class C orphan GPCR, is unique because it lacks an ECD and exhibits constitutive activity. Impaired GPR156-G signaling contributes to loss of hearing. Here we present the cryo-electron microscopy structures of human GPR156 in the G-free and G-coupled states. We found that an endogenous phospholipid molecule is located within each TMD of the GPR156 dimer. Asymmetric binding of Gα to the phospholipid-bound GPR156 dimer restructures the first and second intracellular loops and the carboxy-terminal part of the elongated transmembrane 7 (TM7) without altering dimer conformation. Our findings reveal that GPR156 is a transducer for phospholipid signaling. Constant binding of abundant phospholipid molecules and the G-protein-induced reshaping of the cytoplasmic face provide a basis for the constitutive activation of GPR156.
History
DepositionFeb 15, 2023-
Header (metadata) releaseFeb 14, 2024-
Map releaseFeb 14, 2024-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Supplemental images

emd_35382.png

Downloads & links

-
Map

FileDownload / File: emd_35382.map.gz / Format: CCP4 / Size: 262.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.81 Å
Density
Contour LevelBy AUTHOR: 0.041
Minimum - Maximum-0.0018175549 - 1.5257516
Average (Standard dev.)0.00027348404 (±0.011161214)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions410410410
Spacing410410410
CellA=B=C: 332.1 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: #2

Fileemd_35382_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #1

Fileemd_35382_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : GPR156A/B

EntireName: GPR156A/B
Components
  • Complex: GPR156A/B
    • Protein or peptide: Probable G-protein coupled receptor 156
  • Ligand: [(2R)-3-[(E)-hexadec-9-enoyl]oxy-2-octadecanoyloxy-propyl] 2-(trimethylazaniumyl)ethyl phosphate

-
Supramolecule #1: GPR156A/B

SupramoleculeName: GPR156A/B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 131.2 kDa/nm

-
Macromolecule #1: Probable G-protein coupled receptor 156

MacromoleculeName: Probable G-protein coupled receptor 156 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 65.628484 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MEPEINCSEL CDSFPGQELD RRPLHDLCKT TITSSHHSSK TISSLSPVLL GIVWTFLSCG LLLILFFLAF TIHCRKNRIV KMSSPNLNI VTLLGSCLTY SSAYLFGIQD VLVGSSMETL IQTRLSMLCI GTSLVFGPIL GKSWRLYKVF TQRVPDKRVI I KDLQLLGL ...String:
MEPEINCSEL CDSFPGQELD RRPLHDLCKT TITSSHHSSK TISSLSPVLL GIVWTFLSCG LLLILFFLAF TIHCRKNRIV KMSSPNLNI VTLLGSCLTY SSAYLFGIQD VLVGSSMETL IQTRLSMLCI GTSLVFGPIL GKSWRLYKVF TQRVPDKRVI I KDLQLLGL VAALLMADVI LLMTWVLTDP IQCLQILSVS MTVTGKDVSC TSTSTHFCAS RYSDVWIALI WGCKGLLLLY GA YLAGLTG HVSSPPVNQS LTIMVGVNLL VLAAGLLFVV TRYLHSWPNL VFGLTSGGIF VCTTTINCFI FIPQLKQWKA FEE ENQTIR RMAKYFSTPN KSFHTQYGEE ENCHPRGEKS SMERLLTEKN AVIESLQEQV NNAKEKIVRL MSAECTYDLP EGAA PPASS PNKDVQAVAS VHTLAAAQGP SGHLSDFQND PGMAARDSQC TSGPSSYAQS LEGPGKDSSF SPGKEEKISD SKDFS DHLD SGCSQKPWTE QSLGPERGDQ VPMNPSQSLL PERGGSDPQR QRHLENSEEP PERRSRVSSV IREKLQEVLQ DLGSGS GSG RGRGGSENLY FQGGSGSGGD YKDDDDKDYK DDDDK

UniProtKB: Probable G-protein coupled receptor 156

-
Macromolecule #2: [(2R)-3-[(E)-hexadec-9-enoyl]oxy-2-octadecanoyloxy-propyl] 2-(tri...

MacromoleculeName: [(2R)-3-[(E)-hexadec-9-enoyl]oxy-2-octadecanoyloxy-propyl] 2-(trimethylazaniumyl)ethyl phosphate
type: ligand / ID: 2 / Number of copies: 2 / Formula: A1LYA
Molecular weightTheoretical: 760.076 Da

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: OTHER
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 64.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

8ieb

Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.62 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 493410

+
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