+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33556 | |||||||||
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Title | Cryo-EM structure of MrgD-Gi complex with beta-alanine (local) | |||||||||
Map data | post-process map | |||||||||
Sample |
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Keywords | GPCR / Complex / SIGNALING PROTEIN | |||||||||
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 | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Suzuki S / Iida M / Kawamoto A / Oshima A | |||||||||
Funding support | Japan, 2 items
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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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33556.map.gz | 117.8 MB | EMDB map data format | |
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Header (meta data) | emd-33556-v30.xml emd-33556.xml | 16.3 KB 16.3 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_33556_fsc.xml | 14.9 KB | Display | FSC data file |
Images | emd_33556.png | 67 KB | ||
Masks | emd_33556_msk_1.map | 125 MB | Mask map | |
Filedesc metadata | emd-33556.cif.gz | 6.1 KB | ||
Others | emd_33556_half_map_1.map.gz emd_33556_half_map_2.map.gz | 115.9 MB 115.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33556 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33556 | HTTPS FTP |
-Validation report
Summary document | emd_33556_validation.pdf.gz | 1004.9 KB | Display | EMDB validaton report |
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Full document | emd_33556_full_validation.pdf.gz | 1004.4 KB | Display | |
Data in XML | emd_33556_validation.xml.gz | 16.2 KB | Display | |
Data in CIF | emd_33556_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33556 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33556 | HTTPS FTP |
-Related structure data
Related structure data | 7y14MC 7y12C 7y13C 7y15C M: atomic model generated by this map C: citing same article (ref.) |
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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
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_33556.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | post-process map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.675 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_33556_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: half map 1
File | emd_33556_half_map_1.map | ||||||||||||
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Annotation | half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: half map 2
File | emd_33556_half_map_2.map | ||||||||||||
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Annotation | half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : beta-alanine bound MrgD-Gi complex with the scFv16
Entire | Name: beta-alanine bound MrgD-Gi complex with the scFv16 |
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Components |
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-Supramolecule #1: beta-alanine bound MrgD-Gi complex with the scFv16
Supramolecule | Name: beta-alanine bound MrgD-Gi complex with the scFv16 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Soluble cytochrome b562,Mas-related G-protein coupled receptor me...
Macromolecule | Name: Soluble cytochrome b562,Mas-related G-protein coupled receptor member D type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 50.141285 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: 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 |
-Macromolecule #2: BETA-ALANINE
Macromolecule | Name: BETA-ALANINE / type: ligand / ID: 2 / Number of copies: 1 / Formula: BAL |
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Molecular weight | Theoretical: 89.093 Da |
Chemical component information | ChemComp-BAL: |
-Macromolecule #3: PALMITIC ACID
Macromolecule | Name: PALMITIC ACID / type: ligand / ID: 3 / Number of copies: 4 / Formula: PLM |
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Molecular weight | Theoretical: 256.424 Da |
Chemical component information | ChemComp-PLM: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 10 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: 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. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot time 3 seconds blot force 5. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Spherical aberration corrector: The Microscope implicated Cs corrector. |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 0.01 mm / Nominal defocus max: 1.9000000000000001 µm / Nominal defocus min: 0.7000000000000001 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |