[English] 日本語
Yorodumi
- EMDB-31351: apo GPR158 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-31351
Titleapo GPR158
Map data
Sample
  • Complex: GPR158
    • Protein or peptide: Probable G-protein coupled receptor 158
KeywordsClass C orphan GPCR / depression / neuronal signaling / PAS-folded GPCR / noncanonical signaling GPCR / signaling protein
Function / homology
Function and homology information


G protein-coupled glycine receptor activity / regulation of G protein-coupled receptor signaling pathway / positive regulation of neurotransmitter secretion / regulation of synapse organization / protein localization to plasma membrane / cell projection / enzyme activator activity / postsynaptic density membrane / brain development / cognition ...G protein-coupled glycine receptor activity / regulation of G protein-coupled receptor signaling pathway / positive regulation of neurotransmitter secretion / regulation of synapse organization / protein localization to plasma membrane / cell projection / enzyme activator activity / postsynaptic density membrane / brain development / cognition / transmembrane signaling receptor activity / presynaptic membrane / postsynaptic membrane / G protein-coupled receptor signaling pathway / nucleus / plasma membrane
Similarity search - Function
G-protein coupled receptor 158/179 / : / GPR158/179 extracellular domain / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR
Similarity search - Domain/homology
Metabotropic glycine receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.52 Å
AuthorsJeong E / Kim Y
Funding support Korea, Republic Of, 3 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)2021R1A2C301335711 Korea, Republic Of
National Research Foundation (NRF, Korea)2017M3A9F6029736 Korea, Republic Of
National Research Foundation (NRF, Korea)2021R1A6A1A10042944 Korea, Republic Of
CitationJournal: Nat Commun / Year: 2021
Title: Structure of the class C orphan GPCR GPR158 in complex with RGS7-Gβ5.
Authors: Eunyoung Jeong / Yoojoong Kim / Jihong Jeong / Yunje Cho /
Abstract: GPR158, a class C orphan GPCR, functions in cognition, stress-induced mood control, and synaptic development. Among class C GPCRs, GPR158 is unique as it lacks a Venus flytrap-fold ligand-binding ...GPR158, a class C orphan GPCR, functions in cognition, stress-induced mood control, and synaptic development. Among class C GPCRs, GPR158 is unique as it lacks a Venus flytrap-fold ligand-binding domain and terminates Gαi/o protein signaling through the RGS7-Gβ5 heterodimer. Here, we report the cryo-EM structures of GPR158 alone and in complex with one or two RGS7-Gβ5 heterodimers. GPR158 dimerizes through Per-Arnt-Sim-fold extracellular and transmembrane (TM) domains connected by an epidermal growth factor-like linker. The TM domain (TMD) reflects both inactive and active states of other class C GPCRs: a compact intracellular TMD, conformations of the two intracellular loops (ICLs) and the TMD interface formed by TM4/5. The ICL2, ICL3, TM3, and first helix of the cytoplasmic coiled-coil provide a platform for the DHEX domain of one RGS7 and the second helix recruits another RGS7. The unique features of the RGS7-binding site underlie the selectivity of GPR158 for RGS7.
History
DepositionMay 25, 2021-
Header (metadata) releaseDec 1, 2021-
Map releaseDec 1, 2021-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: PDBj / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7ewl
  • Surface level: 0.012
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31351.png

Downloads & links

-
Map

FileDownload / File: emd_31351.map.gz / Format: CCP4 / Size: 113.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 310 pix.
= 257.3 Å		0.83 Å/pix.
x 310 pix.
= 257.3 Å		0.83 Å/pix.
x 310 pix.
= 257.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.012
Minimum - Maximum-0.07422876 - 0.11969404
Average (Standard dev.)0.000119012264 (±0.0019084729)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions310310310
Spacing310310310
CellA=B=C: 257.3 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z310310310
origin x/y/z0.0000.0000.000
length x/y/z257.300257.300257.300
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS310310310
D min/max/mean-0.0740.1200.000

-
Supplemental data

-
Sample components

-
Entire : GPR158

EntireName: GPR158
Components
  • Complex: GPR158
    • Protein or peptide: Probable G-protein coupled receptor 158

-
Supramolecule #1: GPR158

SupramoleculeName: GPR158 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 200 kDa/nm

-
Macromolecule #1: Probable G-protein coupled receptor 158

MacromoleculeName: Probable G-protein coupled receptor 158 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 77.462703 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: ASRDPQGRPD SPRERTPKGK PHAQQPGRAS ASDSSAPWSR STDGTILAQK LAEEVPMDVA SYLYTGDSHQ LKRANCSGRY ELAGLPGKW PALASAHPSL HRALDTLTHA TNFLNVMLQS NKSREQNLQD DLDWYQALVW SLLEGEPSIS RAAITFSTDS L SAPAPQVF ...String:
ASRDPQGRPD SPRERTPKGK PHAQQPGRAS ASDSSAPWSR STDGTILAQK LAEEVPMDVA SYLYTGDSHQ LKRANCSGRY ELAGLPGKW PALASAHPSL HRALDTLTHA TNFLNVMLQS NKSREQNLQD DLDWYQALVW SLLEGEPSIS RAAITFSTDS L SAPAPQVF LQATREESRI LLQDLSSSAP HLANATLETE WFHGLRRKWR PHLHRRGPNQ GPRGLGHSWR RKDGLGGDKS HF KWSPPYL ECENGSYKPG WLVTLSSAIY GLQPNLVPEF RGVMKVDINL QKVDIDQCSS DGWFSGTHKC HLNNSECMPI KGL GFVLGA YECICKAGFY HPGVLPVNNF RRRGPDQHIS GSTKDVSEEA YVCLPCREGC PFCADDSPCF VQEDKYLRLA IISF QALCM LLDFVSMLVV YHFRKAKSIR ASGLILLETI LFGSLLLYFP VVILYFEPST FRCILLRWAR LLGFATVYGT VTLKL HRVL KVFLSRTAQR IPYMTGGRVM RMLAVILLVV FWFLIGWTSS VCQNLEKQIS LIGQGKTSDH LIFNMCLIDR WDYMTA VAE FLFLLWGVYL CYAVRTVPSA FHEPRYMAVA VHNELIISAI FHTIRFVLAS RLQSDWMLML YFAHTHLTVT VTIGLLL IP KFSHSSNNPR DDIATEAYED ELDMGRSGSY LNSSINSAWS EHSLD

UniProtKB: Metabotropic glycine receptor

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration12.7 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

-
Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DIFFRACTION
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Resolution.type: BY AUTHOR / Resolution: 3.52 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 425819
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

+
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