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Yorodumi- EMDB-31360: Cryo-EM structure of human GPR158 in complex with RGS7-Gbeta5 in ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-31360 | ||||||||||||
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Title | Cryo-EM structure of human GPR158 in complex with RGS7-Gbeta5 in a 2:1:1 ratio | ||||||||||||
Map data | Overall refined map | ||||||||||||
Sample |
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Function / homology | Function and homology information G protein-coupled glycine receptor activity / GTPase activator complex / light adaption / dark adaptation / G-protein gamma-subunit binding / negative regulation of voltage-gated calcium channel activity / positive regulation of potassium ion transmembrane transport / regulation of G protein-coupled receptor signaling pathway / positive regulation of neurotransmitter secretion / G protein-coupled dopamine receptor signaling pathway ...G protein-coupled glycine receptor activity / GTPase activator complex / light adaption / dark adaptation / G-protein gamma-subunit binding / negative regulation of voltage-gated calcium channel activity / positive regulation of potassium ion transmembrane transport / regulation of G protein-coupled receptor signaling pathway / positive regulation of neurotransmitter secretion / G protein-coupled dopamine receptor signaling pathway / negative regulation of G protein-coupled receptor signaling pathway / regulation of synapse organization / G-protein alpha-subunit binding / enzyme activator activity / response to amphetamine / GTPase activator activity / positive regulation of GTPase activity / protein localization to plasma membrane / cell projection / brain development / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / transmembrane signaling receptor activity / G beta:gamma signalling through CDC42 / cognition / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / nuclear envelope / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / G alpha (12/13) signalling events / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / presynapse / Ca2+ pathway / presynaptic membrane / protein-folding chaperone binding / G alpha (i) signalling events / G alpha (s) signalling events / G alpha (q) signalling events / postsynaptic membrane / response to ethanol / Extra-nuclear estrogen signaling / intracellular signal transduction / neuron projection / G protein-coupled receptor signaling pathway / GTPase activity / signal transduction / protein-containing complex / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.3 Å | ||||||||||||
Authors | Kim Y / Jeong E / Jeong J / Cho Y | ||||||||||||
Funding support | 3 items
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Citation | Journal: Nat Commun / Year: 2021 Title: Structure of the class C orphan GPCR GPR158 in complex with RGS7-Gβ5. Authors: Eunyoung Jeong / Yoojoong Kim / Jihong Jeong / Yunje Cho / Abstract: GPR158, a class C orphan GPCR, functions in cognition, stress-induced mood control, and synaptic development. Among class C GPCRs, GPR158 is unique as it lacks a Venus flytrap-fold ligand-binding ...GPR158, a class C orphan GPCR, functions in cognition, stress-induced mood control, and synaptic development. Among class C GPCRs, GPR158 is unique as it lacks a Venus flytrap-fold ligand-binding domain and terminates Gαi/o protein signaling through the RGS7-Gβ5 heterodimer. Here, we report the cryo-EM structures of GPR158 alone and in complex with one or two RGS7-Gβ5 heterodimers. GPR158 dimerizes through Per-Arnt-Sim-fold extracellular and transmembrane (TM) domains connected by an epidermal growth factor-like linker. The TM domain (TMD) reflects both inactive and active states of other class C GPCRs: a compact intracellular TMD, conformations of the two intracellular loops (ICLs) and the TMD interface formed by TM4/5. The ICL2, ICL3, TM3, and first helix of the cytoplasmic coiled-coil provide a platform for the DHEX domain of one RGS7 and the second helix recruits another RGS7. The unique features of the RGS7-binding site underlie the selectivity of GPR158 for RGS7. | ||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_31360.map.gz | 154.4 MB | EMDB map data format | |
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Header (meta data) | emd-31360-v30.xml emd-31360.xml | 16.7 KB 16.7 KB | Display Display | EMDB header |
Images | emd_31360.png | 73.1 KB | ||
Others | emd_31360_additional_1.map.gz | 154.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-31360 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-31360 | HTTPS FTP |
-Validation report
Summary document | emd_31360_validation.pdf.gz | 405.5 KB | Display | EMDB validaton report |
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Full document | emd_31360_full_validation.pdf.gz | 405.1 KB | Display | |
Data in XML | emd_31360_validation.xml.gz | 6.9 KB | Display | |
Data in CIF | emd_31360_validation.cif.gz | 7.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31360 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-31360 | HTTPS FTP |
-Related structure data
Related structure data | 7ewpMC 7ewlC 7ewrC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_31360.map.gz / Format: CCP4 / Size: 163.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Overall refined map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06995 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Locally refined map
File | emd_31360_additional_1.map | ||||||||||||
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Annotation | Locally refined map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : GPR158-RGS7-Gb5 in a 2:1:1 ratio
Entire | Name: GPR158-RGS7-Gb5 in a 2:1:1 ratio |
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Components |
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-Supramolecule #1: GPR158-RGS7-Gb5 in a 2:1:1 ratio
Supramolecule | Name: GPR158-RGS7-Gb5 in a 2:1:1 ratio / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Homo sapiens (human) |
-Macromolecule #1: Probable G-protein coupled receptor 158
Macromolecule | Name: Probable G-protein coupled receptor 158 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 127.547109 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MGAMAYPLLL CLLLAQLGLG AVGASRDPQG RPDSPRERTP KGKPHAQQPG RASASDSSAP WSRSTDGTIL AQKLAEEVPM DVASYLYTG DSHQLKRANC SGRYELAGLP GKWPALASAH PSLHRALDTL THATNFLNVM LQSNKSREQN LQDDLDWYQA L VWSLLEGE ...String: MGAMAYPLLL CLLLAQLGLG AVGASRDPQG RPDSPRERTP KGKPHAQQPG RASASDSSAP WSRSTDGTIL AQKLAEEVPM DVASYLYTG DSHQLKRANC SGRYELAGLP GKWPALASAH PSLHRALDTL THATNFLNVM LQSNKSREQN LQDDLDWYQA L VWSLLEGE PSISRAAITF STDSLSAPAP QVFLQATREE SRILLQDLSS SAPHLANATL ETEWFHGLRR KWRPHLHRRG PN QGPRGLG HSWRRKDGLG GDKSHFKWSP PYLECENGSY KPGWLVTLSS AIYGLQPNLV PEFRGVMKVD INLQKVDIDQ CSS DGWFSG THKCHLNNSE CMPIKGLGFV LGAYECICKA GFYHPGVLPV NNFRRRGPDQ HISGSTKDVS EEAYVCLPCR EGCP FCADD SPCFVQEDKY LRLAIISFQA LCMLLDFVSM LVVYHFRKAK SIRASGLILL ETILFGSLLL YFPVVILYFE PSTFR CILL RWARLLGFAT VYGTVTLKLH RVLKVFLSRT AQRIPYMTGG RVMRMLAVIL LVVFWFLIGW TSSVCQNLEK QISLIG QGK TSDHLIFNMC LIDRWDYMTA VAEFLFLLWG VYLCYAVRTV PSAFHEPRYM AVAVHNELII SAIFHTIRFV LASRLQS DW MLMLYFAHTH LTVTVTIGLL LIPKFSHSSN NPRDDIATEA YEDELDMGRS GSYLNSSINS AWSEHSLDPE DIRDELKK L YAQLEIYKRK KMITNNPHLQ KKRCSKKGLG RSIMRRITEI PETVSRQCSK EDKEGADHGT AKGTALIRKN PPESSGNTG KSKEETLKNR VFSLKKSHST YDHVRDQTEE SSSLPTESQE EETTENSTLE SLSGKKLTQK LKERGRLEVL FQGPGGSMSK GEELFTGVV PILVELDGDV NGHKFSVRGE GEGDATNGKL TLKFICTTGK LPVPWPTLVT TLTYGVQCFS RYPDHMKRHD F FKSAMPEG YVQERTISFK DDGTYKTRAE VKFEGDTLVN RIELKGIDFK EDGNILGHKL EYNFNSHNVY ITADKQKNGI KA NFKIRHN VEDGSVQLAD HYQQNTPIGD GPVLLPDNHY LSTQSVLSKD PNEKRDHMVL LEFVTAAGIT HGGSWSHPQF EKG GGSGGG SGGSAWSHPQ FE |
-Macromolecule #2: Regulator of G-protein signaling 7
Macromolecule | Name: Regulator of G-protein signaling 7 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 61.570086 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MAQGNNYGQT SNGVADESPN MLVYRKMEDV IARMQDEKNG IPIRTVKSFL SKIPSVFSGS DIVQWLIKNL TIEDPVEALH LGTLMAAHG YFFPISDHVL TLKDDGTFYR FQTPYFWPSN CWEPENTDYA VYLCKRTMQN KARLELADYE AESLARLQRA F ARKWEFIF ...String: MAQGNNYGQT SNGVADESPN MLVYRKMEDV IARMQDEKNG IPIRTVKSFL SKIPSVFSGS DIVQWLIKNL TIEDPVEALH LGTLMAAHG YFFPISDHVL TLKDDGTFYR FQTPYFWPSN CWEPENTDYA VYLCKRTMQN KARLELADYE AESLARLQRA F ARKWEFIF MQAEAQAKVD KKRDKIERKI LDSQERAFWD VHRPVPGCVN TTEVDIKKSS RMRNPHKTRK SVYGLQNDIR SH SPTHTPT PETKPPTEDE LQQQIKYWQI QLDRHRLKMS KVADSLLSYT EQYLEYDPFL LPPDPSNPWL SDDTTFWELE ASK EPSQQR VKRWGFGMDE ALKDPVGREQ FLKFLESEFS SENLRFWLAV EDLKKRPIKE VPSRVQEIWQ EFLAPGAPSA INLD SKSYD KTTQNVKEPG RYTFEDAQEH IYKLMKSDSY PRFIRSSAYQ ELLQAKKKSG NSMDRRTSFE KFAQNVGRNI PIFPC HKNC TPTLRASTNL LRGRGGSENL YFQGGSGSGG DYKDDDDKDY KDDDDK |
-Macromolecule #3: Guanine nucleotide-binding protein subunit beta-5
Macromolecule | Name: Guanine nucleotide-binding protein subunit beta-5 / 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: 43.619297 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: MCDQTFLVNV FGSCDKCFKQ RALRPVFKKS QQLSYCSTCA EIMATEGLHE NETLASLKSE AESLKGKLEE ERAKLHDVEL HQVAERVEA LGQFVMKTRR TLKGHGNKVL CMDWCKDKRR IVSSSQDGKV IVWDSFTTNK EHAVTMPCTW VMACAYAPSG C AIACGGLD ...String: MCDQTFLVNV FGSCDKCFKQ RALRPVFKKS QQLSYCSTCA EIMATEGLHE NETLASLKSE AESLKGKLEE ERAKLHDVEL HQVAERVEA LGQFVMKTRR TLKGHGNKVL CMDWCKDKRR IVSSSQDGKV IVWDSFTTNK EHAVTMPCTW VMACAYAPSG C AIACGGLD NKCSVYPLTF DKNENMAAKK KSVAMHTNYL SACSFTNSDM QILTASGDGT CALWDVESGQ LLQSFHGHGA DV LCLDLAP SETGNTFVSG GCDKKAMVWD MRSGQCVQAF ETHESDINSV RYYPSGDAFA SGSDDATCRL YDLRADREVA IYS KESIIF GASSVDFSLS GRLLFAGYND YTINVWDVLK GSRVSILFGH ENRVSTLRVS PDGTAFCSGS WDHTLRVWA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4.5 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: C-flat-1.2/1.3 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: DIFFRACTION |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 362999 |
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Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |