+Open data
-Basic information
Entry | Database: PDB / ID: 7y14 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of MrgD-Gi complex with beta-alanine (local) | |||||||||
Components | Soluble cytochrome b562,Mas-related G-protein coupled receptor member D | |||||||||
Keywords | SIGNALING PROTEIN / GPCR / Complex | |||||||||
Function / homology | Function and homology information G protein-coupled receptor activity / electron transport chain / periplasmic space / electron transfer activity / iron ion binding / G protein-coupled receptor signaling pathway / heme binding / extracellular space / plasma membrane Similarity search - Function | |||||||||
Biological species | Escherichia coli (E. coli) Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Suzuki, S. / Iida, M. / Kawamoto, A. / Oshima, A. | |||||||||
Funding support | Japan, 2items
| |||||||||
Citation | Journal: Commun Biol / Year: 2022 Title: Structural insight into the activation mechanism of MrgD with heterotrimeric Gi-protein revealed by cryo-EM. Authors: Shota Suzuki / Momoko Iida / Yoko Hiroaki / Kotaro Tanaka / Akihiro Kawamoto / Takayuki Kato / Atsunori Oshima / Abstract: MrgD, a member of the Mas-related G protein-coupled receptor (MRGPR) family, has high basal activity for Gi activation. It recognizes endogenous ligands, such as β-alanine, and is involved in pain ...MrgD, a member of the Mas-related G protein-coupled receptor (MRGPR) family, has high basal activity for Gi activation. It recognizes endogenous ligands, such as β-alanine, and is involved in pain and itch signaling. The lack of a high-resolution structure for MrgD hinders our understanding of whether its activation is ligand-dependent or constitutive. Here, we report two cryo-EM structures of the MrgD-Gi complex in the β-alanine-bound and apo states at 3.1 Å and 2.8 Å resolution, respectively. These structures show that β-alanine is bound to a shallow pocket at the extracellular domains. The extracellular half of the sixth transmembrane helix undergoes a significant movement and is tightly packed into the third transmembrane helix through hydrophobic residues, creating the active form. Our structures demonstrate a structural basis for the characteristic ligand recognition of MrgD. These findings provide a framework to guide drug designs targeting the MrgD receptor. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 7y14.cif.gz | 60.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb7y14.ent.gz | 43.2 KB | Display | PDB format |
PDBx/mmJSON format | 7y14.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7y14_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 7y14_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7y14_validation.xml.gz | 26.2 KB | Display | |
Data in CIF | 7y14_validation.cif.gz | 35.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y1/7y14 ftp://data.pdbj.org/pub/pdb/validation_reports/y1/7y14 | HTTPS FTP |
-Related structure data
Related structure data | 33556MC 7y12C 7y13C 7y15C M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
EM raw data | EMPIAR-11073 (Title: Cryo-EM structure of MrgD-Gi complex with beta-alanine Data size: 4.1 TB Data #1: K3 movies for MrgD-Gi complex with beta-alanine [micrographs - multiframe]) |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 50141.285 Da / Num. of mol.: 1 Fragment: Chimera protein of Cytochrome b-562 (UNP residues 23-127) and MrgD (UNP residues 5-321) Mutation: M29W ,H124I Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human) Gene: cybC, MRGPRD, MRGD / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P0ABE7, UniProt: Q8TDS7 | ||
---|---|---|---|
#2: Chemical | ChemComp-BAL / | ||
#3: Chemical | ChemComp-PLM / Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: beta-alanine bound MrgD-Gi complex with the scFv16 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: blot time 3 seconds blot force 5 |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1900 nm / Nominal defocus min: 700 nm / Cs: 0.01 mm |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
EM imaging optics | Spherical aberration corrector: The Microscope implicated Cs corrector. |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
EM software |
| ||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97282 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|