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- EMDB-33555: Cryo-EM structure of apo-state MrgD-Gi complex (local) -

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Basic information

Entry
Database: EMDB / ID: EMD-33555
TitleCryo-EM structure of apo-state MrgD-Gi complex (local)
Map datapost-process map
Sample
  • Complex: Soluble cytochrome b562,Mas-related G-protein coupled receptor member D
    • Protein or peptide: Soluble cytochrome b562,Mas-related G-protein coupled receptor member D
  • Ligand: PALMITIC ACID
  • Ligand: water
KeywordsGPCR / Complex / SIGNALING PROTEIN
Function / homology
Function and homology information


angiotensin-mediated vasodilation involved in regulation of systemic arterial blood pressure / G protein-coupled peptide receptor activity / electron transport chain / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / periplasmic space / electron transfer activity / G protein-coupled receptor signaling pathway / iron ion binding / heme binding ...angiotensin-mediated vasodilation involved in regulation of systemic arterial blood pressure / G protein-coupled peptide receptor activity / electron transport chain / G protein-coupled receptor activity / adenylate cyclase-activating G protein-coupled receptor signaling pathway / periplasmic space / electron transfer activity / G protein-coupled receptor signaling pathway / iron ion binding / heme binding / extracellular space / plasma membrane
Similarity search - Function
Mas-related G protein-coupled receptor D / Mas-related G protein-coupled receptor family / Cytochrome b562 / Cytochrome b562 / Cytochrome c/b562 / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family)
Similarity search - Domain/homology
Soluble cytochrome b562 / Mas-related G-protein coupled receptor member D
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsSuzuki S / Iida M / Kawamoto A / Oshima A
Funding support Japan, 2 items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19H03165 Japan
Japan Agency for Medical Research and Development (AMED)JP21am0101074 Japan
CitationJournal: 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
DepositionJun 6, 2022-
Header (metadata) releaseJul 20, 2022-
Map releaseJul 20, 2022-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_33555.png

Downloads & links

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Map

FileDownload / File: emd_33555.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationpost-process map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 320 pix.
= 216. Å		0.68 Å/pix.
x 320 pix.
= 216. Å		0.68 Å/pix.
x 320 pix.
= 216. Å

Surface

Projections

Slices (1/3)

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.675 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6
Minimum - Maximum-3.1970413 - 5.142856
Average (Standard dev.)-0.0008621311 (±0.07015523)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 216.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_33555_msk_1.map
Projections & Slices
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Half map: half map1

Fileemd_33555_half_map_1.map
Annotationhalf map1
Projections & Slices
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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map2

Fileemd_33555_half_map_2.map
Annotationhalf map2
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Histogram (log scale)

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Sample components

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Entire : Soluble cytochrome b562,Mas-related G-protein coupled receptor me...

EntireName: Soluble cytochrome b562,Mas-related G-protein coupled receptor member D
Components
  • Complex: Soluble cytochrome b562,Mas-related G-protein coupled receptor member D
    • Protein or peptide: Soluble cytochrome b562,Mas-related G-protein coupled receptor member D
  • Ligand: PALMITIC ACID
  • Ligand: water

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Supramolecule #1: Soluble cytochrome b562,Mas-related G-protein coupled receptor me...

SupramoleculeName: Soluble cytochrome b562,Mas-related G-protein coupled receptor member D
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Soluble cytochrome b562,Mas-related G-protein coupled receptor me...

MacromoleculeName: Soluble cytochrome b562,Mas-related G-protein coupled receptor member D
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 50.141285 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
SequenceString: MKTIIALSYI FCLVFADYKD DDDKADLEDN WETLNDNLKV IEKADNAAQV KDALTKMRAA ALDAQKATPP KLEDKSPDSP EMKDFRHGF DILVGQIDDA LKLANEGKVK EAQAAAEQLK TTRNAYIQKY LNSSGTVESA LNYSRGSTVH TAYLVLSSLA M FTCLCGMA ...String:
MKTIIALSYI FCLVFADYKD DDDKADLEDN WETLNDNLKV IEKADNAAQV KDALTKMRAA ALDAQKATPP KLEDKSPDSP EMKDFRHGF DILVGQIDDA LKLANEGKVK EAQAAAEQLK TTRNAYIQKY LNSSGTVESA LNYSRGSTVH TAYLVLSSLA M FTCLCGMA GNSMVIWLLG FRMHRNPFCI YILNLAAADL LFLFSMASTL SLETQPLVNT TDKVHELMKR LMYFAYTVGL SL LTAISTQ RCLSVLFPIW FKCHRPRHLS AWVCGLLWTL CLLMNGLTSS FCSKFLKFNE DRCFRVDMVQ AALIMGVLTP VMT LSSLTL FVWVRRSSQQ WRRQPTRLFV VVLASVLVFL ICSLPLSIYW FVLYWLSLPP EMQVLCFSLS RLSSSVSSSA NPVI YFLVG SRRSHRLPTR SLGTVLQQAL REEPELEGGE TPTVGTNEMG A

UniProtKB: Soluble cytochrome b562, Mas-related G-protein coupled receptor member D

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Macromolecule #2: PALMITIC ACID

MacromoleculeName: PALMITIC ACID / type: ligand / ID: 2 / Number of copies: 7 / Formula: PLM
Molecular weightTheoretical: 256.424 Da
Chemical component information

ChemComp-PLM:
PALMITIC ACID

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 2 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration10 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot time 3 seconds blot force 5.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsSpherical aberration corrector: The Microscope implicated Cs corrector.
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.7000000000000001 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 349331
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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