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- EMDB-35377: Cryo-EM structure of GPR156 of GPR156-miniGo-scFv16 complex (loca... -

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Basic information

Entry
Database: EMDB / ID: EMD-35377
TitleCryo-EM structure of GPR156 of GPR156-miniGo-scFv16 complex (local refine)
Map dataGPCR
Sample
  • Complex: GPR156
    • 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 / SIGNALING PROTEIN
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 / G-protein coupled receptors family 3 profile. / GPCR family 3, C-terminal / 7 transmembrane sweet-taste receptor of 3 GCPR
Similarity search - Domain/homology
Probable G-protein coupled receptor 156
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.03 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-
UpdateMay 1, 2024-
Current statusMay 1, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35377.png

Downloads & links

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Map

FileDownload / File: emd_35377.map.gz / Format: CCP4 / Size: 262.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGPCR
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 410 pix.
= 332.1 Å		0.81 Å/pix.
x 410 pix.
= 332.1 Å		0.81 Å/pix.
x 410 pix.
= 332.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0383
Minimum - Maximum-0.0021870884 - 1.9357507
Average (Standard dev.)0.00028285026 (±0.012493479)
SymmetrySpace group: 1
Details

EMDB XML:

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

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Supplemental data

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Half map: #2

Fileemd_35377_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_35377_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GPR156

EntireName: GPR156
Components
  • Complex: GPR156
    • Protein or peptide: Probable G-protein coupled receptor 156
  • Ligand: [(2R)-3-[(E)-hexadec-9-enoyl]oxy-2-octadecanoyloxy-propyl] 2-(trimethylazaniumyl)ethyl phosphate

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Supramolecule #1: GPR156

SupramoleculeName: GPR156 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 131.2 kDa/nm

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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

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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

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 64.0 e/Å2
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
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL / In silico model: AlphaFold2
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.03 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 205728
Initial angle assignmentType: OTHER
Final angle assignmentType: OTHER

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