+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-34983 | |||||||||
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Title | Orphan GPR20 in complex with Fab046 | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information positive regulation of Rho protein signal transduction / G protein-coupled receptor activity / electron transport chain / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (s) signalling events / receptor complex / periplasmic space / electron transfer activity / iron ion binding / heme binding ...positive regulation of Rho protein signal transduction / G protein-coupled receptor activity / electron transport chain / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (s) signalling events / receptor complex / periplasmic space / electron transfer activity / iron ion binding / heme binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Rattus (rat) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.08 Å | |||||||||
Authors | Lin X / Jiang S / Xu F | |||||||||
Funding support | 1 items
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Citation | Journal: Cell Discov / Year: 2023 Title: The activation mechanism and antibody binding mode for orphan GPR20. Authors: Xi Lin / Shan Jiang / Yiran Wu / Xiaohu Wei / Gye-Won Han / Lijie Wu / Junlin Liu / Bo Chen / Zhibin Zhang / Suwen Zhao / Vadim Cherezov / Fei Xu / Abstract: GPR20 is a class-A orphan G protein-coupled receptor (GPCR) and a potential therapeutic target for gastrointestinal stromal tumors (GIST) owing to its differentially high expression. An antibody-drug ...GPR20 is a class-A orphan G protein-coupled receptor (GPCR) and a potential therapeutic target for gastrointestinal stromal tumors (GIST) owing to its differentially high expression. An antibody-drug conjugate (ADC) containing a GPR20-binding antibody (Ab046) was recently developed in clinical trials for GIST treatment. GPR20 constitutively activates Gi proteins in the absence of any known ligand, but it remains obscure how this high basal activity is achieved. Here we report three cryo-EM structures of human GPR20 complexes including Gi-coupled GPR20 in the absence or presence of the Fab fragment of Ab046 and Gi-free GPR20. Remarkably, the structures demonstrate a uniquely folded N-terminal helix capping onto the transmembrane domain and our mutagenesis study suggests a key role of this cap region in stimulating the basal activity of GPR20. We also uncover the molecular interactions between GPR20 and Ab046, which may enable the design of tool antibodies with enhanced affinity or new functionality for GPR20. Furthermore, we report the orthosteric pocket occupied by an unassigned density which might be essential for exploring opportunities for deorphanization. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_34983.map.gz | 45.4 MB | EMDB map data format | |
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Header (meta data) | emd-34983-v30.xml emd-34983.xml | 15.7 KB 15.7 KB | Display Display | EMDB header |
Images | emd_34983.png | 64.7 KB | ||
Masks | emd_34983_msk_1.map | 91.1 MB | Mask map | |
Others | emd_34983_half_map_1.map.gz emd_34983_half_map_2.map.gz | 84.7 MB 84.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-34983 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-34983 | HTTPS FTP |
-Validation report
Summary document | emd_34983_validation.pdf.gz | 769.9 KB | Display | EMDB validaton report |
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Full document | emd_34983_full_validation.pdf.gz | 769.5 KB | Display | |
Data in XML | emd_34983_validation.xml.gz | 13.2 KB | Display | |
Data in CIF | emd_34983_validation.cif.gz | 15.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34983 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-34983 | HTTPS FTP |
-Related structure data
Related structure data | 8hs2MC 8hs3C 8hscC 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 |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_34983.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.832 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_34983_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_34983_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_34983_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The complex of GPR20 with Fab046
Entire | Name: The complex of GPR20 with Fab046 |
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Components |
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-Supramolecule #1: The complex of GPR20 with Fab046
Supramolecule | Name: The complex of GPR20 with Fab046 / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: heavy chain of Fab046
Macromolecule | Name: heavy chain of Fab046 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus (rat) |
Molecular weight | Theoretical: 26.493723 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MEWNWVFLFL LSVTAEVHSQ VQLQQSGAEL AKPGSSVKIS CKASGYTFTS YYISWIKQTT GQGLKYIGFI NPGSGHTNYN EKFKGKATL TVDKSSSTAF MQLSSLTPDD SAIYYCARGA GGFLRIITKF DYWGQGVMVT VSSAQTTAPS VYPLAPGCGD T TSSTVTLG ...String: MEWNWVFLFL LSVTAEVHSQ VQLQQSGAEL AKPGSSVKIS CKASGYTFTS YYISWIKQTT GQGLKYIGFI NPGSGHTNYN EKFKGKATL TVDKSSSTAF MQLSSLTPDD SAIYYCARGA GGFLRIITKF DYWGQGVMVT VSSAQTTAPS VYPLAPGCGD T TSSTVTLG CLVKGYFPEP VTVTWNSGAL SSDVHTFPAV LQSGLYTLTS SVTSSTWPSQ TVTCNVAHPA SSTKVDKKVG GS GHHHHHH |
-Macromolecule #2: Light chain of Fab046
Macromolecule | Name: Light chain of Fab046 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus (rat) |
Molecular weight | Theoretical: 25.637654 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: METDRLLLWV LLLWVPGSTG DTVLTQSPAL AVSLGQRVTI SCRASKSVST YIHWYQQRSG QQPKLLIYSA SNLESGVPSR FSGSGSGTD FTLTIDPVEP DDIANYYCQQ INELPYTFGA GTKLELKRAD AAPTVSIFPP STERLATGGA SVVCLMNNFY P RDISVKWK ...String: METDRLLLWV LLLWVPGSTG DTVLTQSPAL AVSLGQRVTI SCRASKSVST YIHWYQQRSG QQPKLLIYSA SNLESGVPSR FSGSGSGTD FTLTIDPVEP DDIANYYCQQ INELPYTFGA GTKLELKRAD AAPTVSIFPP STERLATGGA SVVCLMNNFY P RDISVKWK IDGTERRDGV LDSVTDQDSK DSTYSMSSTL SLTKADYESH NLYTCEVVHK TSSSPVVKSF NRNEC |
-Macromolecule #3: Soluble cytochrome b562,G-protein coupled receptor 20
Macromolecule | Name: Soluble cytochrome b562,G-protein coupled receptor 20 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 50.631012 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MKTIIALSYI FCLVFADYKD DDDAGRAADL EDNWETLNDN LKVIEKADNA AQVKDALTKM RAAALDAQKA TPPKLEDKSP DSPEMKDFR HGFDILVGQI DDALKLANEG KVKEAQAAAE QLKTTRNAYI QKYLMPSVSP AGPSAGAVPN ATAVTTVRTN A SGLEVPLF ...String: MKTIIALSYI FCLVFADYKD DDDAGRAADL EDNWETLNDN LKVIEKADNA AQVKDALTKM RAAALDAQKA TPPKLEDKSP DSPEMKDFR HGFDILVGQI DDALKLANEG KVKEAQAAAE QLKTTRNAYI QKYLMPSVSP AGPSAGAVPN ATAVTTVRTN A SGLEVPLF HLFARLDEEL HGTFPGLWLA LMAVHGAIFL AGLVLNGLAL YVFCCRTRAK TPSVIYTINL VVTDLLVGLS LP TRFAVYY GARGCLRCAF PHVLGYFLNM HCSIWFLTCI CVDRYLAIVR PEGSRRCRQP ACARAVCAFV WLAAGAVTLS VLG VTGSRP CCRVFALTVL EFLLPLLVIS VFTGRIMCAL SRPGLLHQGR QRRVRAMQLL LTVLIIFLVC FTPFHARQVA VALW PDMPH HTSLVVYHVA VTLSSLNSCM NPIVYCFVTS GFQATVRGLF GQHGHHHHHH HHHH |
-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: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: OTHER |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.7000000000000001 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 418288 |
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Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |