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Yorodumi- EMDB-35524: Cryo-EM structure of the eicosapentaenoic acid bound GPR120-Gi1 c... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-35524 | |||||||||
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Title | Cryo-EM structure of the eicosapentaenoic acid bound GPR120-Gi1 complex(mask on receptor) | |||||||||
Map data | ||||||||||
Sample |
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Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.91 Å | |||||||||
Authors | Mao C / Xiao P / Tao X / Qin J / He Q / Zhang C / Yu X / Zhang Y / Sun J | |||||||||
Funding support | 1 items
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Citation | Journal: Science / Year: 2023 Title: Unsaturated bond recognition leads to biased signal in a fatty acid receptor. Authors: Chunyou Mao / Peng Xiao / Xiao-Na Tao / Jiao Qin / Qing-Tao He / Chao Zhang / Sheng-Chao Guo / Ya-Qin Du / Li-Nan Chen / Dan-Dan Shen / Zhi-Shuai Yang / Han-Qiong Zhang / Shen-Ming Huang / ...Authors: Chunyou Mao / Peng Xiao / Xiao-Na Tao / Jiao Qin / Qing-Tao He / Chao Zhang / Sheng-Chao Guo / Ya-Qin Du / Li-Nan Chen / Dan-Dan Shen / Zhi-Shuai Yang / Han-Qiong Zhang / Shen-Ming Huang / Yong-Hao He / Jie Cheng / Ya-Ni Zhong / Pan Shang / Jun Chen / Dao-Lai Zhang / Qian-Lang Wang / Mei-Xia Liu / Guo-Yu Li / Yongyuan Guo / H Eric Xu / Chuanxin Wang / Cheng Zhang / Shiqing Feng / Xiao Yu / Yan Zhang / Jin-Peng Sun / Abstract: Individual free fatty acids (FAs) play important roles in metabolic homeostasis, many through engagement with more than 40G protein-coupled receptors. Searching for receptors to sense beneficial ...Individual free fatty acids (FAs) play important roles in metabolic homeostasis, many through engagement with more than 40G protein-coupled receptors. Searching for receptors to sense beneficial omega-3 FAs of fish oil enabled the identification of GPR120, which is involved in a spectrum of metabolic diseases. Here, we report six cryo-electron microscopy structures of GPR120 in complex with FA hormones or TUG891 and G or G trimers. Aromatic residues inside the GPR120 ligand pocket were responsible for recognizing different double-bond positions of these FAs and connect ligand recognition to distinct effector coupling. We also investigated synthetic ligand selectivity and the structural basis of missense single-nucleotide polymorphisms. We reveal how GPR120 differentiates rigid double bonds and flexible single bonds. The knowledge gleaned here may facilitate rational drug design targeting to GPR120. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_35524.map.gz | 13.4 MB | EMDB map data format | |
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Header (meta data) | emd-35524-v30.xml emd-35524.xml | 13.5 KB 13.5 KB | Display Display | EMDB header |
Images | emd_35524.png | 54.6 KB | ||
Others | emd_35524_half_map_1.map.gz emd_35524_half_map_2.map.gz | 25 MB 25 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-35524 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-35524 | HTTPS FTP |
-Validation report
Summary document | emd_35524_validation.pdf.gz | 666.5 KB | Display | EMDB validaton report |
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Full document | emd_35524_full_validation.pdf.gz | 666.1 KB | Display | |
Data in XML | emd_35524_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | emd_35524_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35524 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-35524 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_35524.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.014 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_35524_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_35524_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Cryo-EM structure of the eicosapentaenoic acid bound GPR120-Gi1 c...
Entire | Name: Cryo-EM structure of the eicosapentaenoic acid bound GPR120-Gi1 complex(mask on receptor) |
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Components |
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-Supramolecule #1: Cryo-EM structure of the eicosapentaenoic acid bound GPR120-Gi1 c...
Supramolecule | Name: Cryo-EM structure of the eicosapentaenoic acid bound GPR120-Gi1 complex(mask on receptor) type: complex / ID: 1 / Chimera: Yes / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 52.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 880881 |
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Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |