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Yorodumi- EMDB-38529: Cryo-EM structure of GPR30-Gq complex structure in the presence of E2 -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38529 | |||||||||
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Title | Cryo-EM structure of GPR30-Gq complex structure in the presence of E2 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | GPCR / estrogen / GPR30 / Gq / MEMBRANE PROTEIN / MEMBRANE PROTEIN-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information negative regulation of leukocyte activation / nuclear fragmentation involved in apoptotic nuclear change / positive regulation of cardiac vascular smooth muscle cell differentiation / negative regulation of cell cycle process / positive regulation of inositol trisphosphate biosynthetic process / keratin filament / positive regulation of uterine smooth muscle contraction / negative regulation of lipid biosynthetic process / apoptotic chromosome condensation / steroid hormone binding ...negative regulation of leukocyte activation / nuclear fragmentation involved in apoptotic nuclear change / positive regulation of cardiac vascular smooth muscle cell differentiation / negative regulation of cell cycle process / positive regulation of inositol trisphosphate biosynthetic process / keratin filament / positive regulation of uterine smooth muscle contraction / negative regulation of lipid biosynthetic process / apoptotic chromosome condensation / steroid hormone binding / positive regulation of G protein-coupled receptor signaling pathway / cellular response to mineralocorticoid stimulus / positive regulation of endothelial cell apoptotic process / positive regulation of extrinsic apoptotic signaling pathway / dendritic spine membrane / positive regulation of neurotransmitter secretion / cellular response to peptide hormone stimulus / positive regulation of neurogenesis / positive regulation of epidermal growth factor receptor signaling pathway / G protein-coupled estrogen receptor activity / negative regulation of fat cell differentiation / dendritic spine head / nuclear estrogen receptor activity / presynaptic active zone / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of release of cytochrome c from mitochondria / positive regulation of cysteine-type endopeptidase activity involved in apoptotic process / steroid hormone receptor signaling pathway / neuronal action potential / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / nuclear receptor-mediated steroid hormone signaling pathway / axon terminus / regulation of cytosolic calcium ion concentration / steroid binding / hippocampal mossy fiber to CA3 synapse / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / dendritic shaft / cellular response to estradiol stimulus / G protein-coupled receptor activity / mitochondrial membrane / cellular response to glucose stimulus / positive regulation of protein localization to plasma membrane / Olfactory Signaling Pathway / cytoplasmic vesicle membrane / Activation of the phototransduction cascade / trans-Golgi network / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of insulin secretion / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / recycling endosome / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / negative regulation of ERK1 and ERK2 cascade / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / negative regulation of inflammatory response / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / vasodilation / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / nuclear envelope / presynaptic membrane / phospholipase C-activating G protein-coupled receptor signaling pathway / Ca2+ pathway / cellular response to tumor necrosis factor / nervous system development / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / fibroblast proliferation Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Liu H / Xu P / Xu HE | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Res / Year: 2024 Title: Structural and functional evidence that GPR30 is not a direct estrogen receptor. Authors: Heng Liu / Shimeng Guo / Antao Dai / Peiyu Xu / Xin Li / Sijie Huang / Xinheng He / Kai Wu / Xinyue Zhang / Dehua Yang / Xin Xie / H Eric Xu / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38529.map.gz | 28.5 MB | EMDB map data format | |
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Header (meta data) | emd-38529-v30.xml emd-38529.xml | 19.8 KB 19.8 KB | Display Display | EMDB header |
Images | emd_38529.png | 34.5 KB | ||
Masks | emd_38529_msk_1.map | 30.5 MB | Mask map | |
Filedesc metadata | emd-38529.cif.gz | 6.4 KB | ||
Others | emd_38529_half_map_1.map.gz emd_38529_half_map_2.map.gz | 23.4 MB 23.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38529 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38529 | HTTPS FTP |
-Validation report
Summary document | emd_38529_validation.pdf.gz | 921.1 KB | Display | EMDB validaton report |
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Full document | emd_38529_full_validation.pdf.gz | 920.7 KB | Display | |
Data in XML | emd_38529_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | emd_38529_validation.cif.gz | 12.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38529 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38529 | HTTPS FTP |
-Related structure data
Related structure data | 8xohMC 8xofC 8xogC 8xoiC 8xojC 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_38529.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.071 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_38529_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_38529_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_38529_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : GPR30-Gq complex
Entire | Name: GPR30-Gq complex |
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Components |
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-Supramolecule #1: GPR30-Gq complex
Supramolecule | Name: GPR30-Gq complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: GPR30-G1
Supramolecule | Name: GPR30-G1 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2, #4-#5 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: ScFv16
Supramolecule | Name: ScFv16 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: synthetic construct (others) |
-Macromolecule #1: Guanine nucleotide-binding protein G(q) subunit alpha-q
Macromolecule | Name: Guanine nucleotide-binding protein G(q) subunit alpha-q 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: 41.632219 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MGCTLSAEDK AAVERSKMIE KQLQKDKQVY RRTLRLLLLG ADNSGKSTIV KQMRIYHVNG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String: MGCTLSAEDK AAVERSKMIE KQLQKDKQVY RRTLRLLLLG ADNSGKSTIV KQMRIYHVNG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTSGIFETK FQVDKVNFHM FDVGAQRDER RKWIQCFNDV TAIIFVVDSS DTNRLQEALN DF DSIWNNR WLRTISVILF LNKQDLLAEK VLAGKSKIED YFPEFARYTT PEDATPEPGE DPRVTRAKYF IRKEFVDIST ASG DGRHIC YPHFTCAVDT ENARRIFNDC KDIILQMNLR EYNLV |
-Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
Macromolecule | Name: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 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: 38.744371 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MHHHHHHGSL LQSELDQLRQ EAEQLKNQIR DARKACADAT LSQITNNIDP VGRIQMRTRR TLRGHLAKIY AMHWGTDSRL LVSASQDGK LIIWDSYTTN KVHAIPLRSS WVMTCAYAPS GNYVACGGLD NICSIYNLKT REGNVRVSRE LAGHTGYLSC C RFLDDNQI ...String: MHHHHHHGSL LQSELDQLRQ EAEQLKNQIR DARKACADAT LSQITNNIDP VGRIQMRTRR TLRGHLAKIY AMHWGTDSRL LVSASQDGK LIIWDSYTTN KVHAIPLRSS WVMTCAYAPS GNYVACGGLD NICSIYNLKT REGNVRVSRE LAGHTGYLSC C RFLDDNQI VTSSGDTTCA LWDIETGQQT TTFTGHTGDV MSLSLAPDTR LFVSGACDAS AKLWDVREGM CRQTFTGHES DI NAICFFP NGNAFATGSD DATCRLFDLR ADQELMTYSH DNIICGITSV SFSKSGRLLL AGYDDFNCNV WDALKADRAG VLA GHDNRV SCLGVTDDGM AVATGSWDSF LKIWN UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
-Macromolecule #3: scFv16
Macromolecule | Name: scFv16 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 26.293299 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: VQLVESGGGL VQPGGSRKLS CSASGFAFSS FGMHWVRQAP EKGLEWVAYI SSGSGTIYYA DTVKGRFTIS RDDPKNTLFL QMTSLRSED TAMYYCVRSI YYYGSSPFDF WGQGTTLTVS AGGGGSGGGG SGGGGSSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS ...String: VQLVESGGGL VQPGGSRKLS CSASGFAFSS FGMHWVRQAP EKGLEWVAYI SSGSGTIYYA DTVKGRFTIS RDDPKNTLFL QMTSLRSED TAMYYCVRSI YYYGSSPFDF WGQGTTLTVS AGGGGSGGGG SGGGGSSDIV MTQATSSVPV TPGESVSISC R SSKSLLHS NGNTYLYWFL QRPGQSPQLL IYRMSNLASG VPDRFSGSGS GTAFTLTISR LEAEDVGVYY CMQHLEYPLT FG AGTKLEL |
-Macromolecule #4: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
Macromolecule | Name: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 7.861143 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
-Macromolecule #5: G-protein coupled estrogen receptor 1
Macromolecule | Name: G-protein coupled estrogen receptor 1 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 42.291457 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MDVTSQARGV GLEMYPGTAQ PAAPNTTSPE LNLSHPLLGT ALANGTGELS EHQQYVIGLF LSCLYTIFLF PIGFVGNILI LVVNISFRE KMTIPDLYFI NLAVADLILV ADSLIEVFNL HERYYDIAVL CTFMSLFLQV NMYSSVFFLT WMSFDRYIAL A RAMRCSLF ...String: MDVTSQARGV GLEMYPGTAQ PAAPNTTSPE LNLSHPLLGT ALANGTGELS EHQQYVIGLF LSCLYTIFLF PIGFVGNILI LVVNISFRE KMTIPDLYFI NLAVADLILV ADSLIEVFNL HERYYDIAVL CTFMSLFLQV NMYSSVFFLT WMSFDRYIAL A RAMRCSLF RTKHHARLSC GLIWMASVSA TLVPFTAVHL QHTDEACFCF ADVREVQWLE VTLGFIVPFA IIGLCYSLIV RV LVRAHRH RGLRPRRQKA LRMILAVVLV FFVCWLPENV FISVHLLQRT QPGAAPCKQS FRHAHPLTGH IVNLAAFSNS CLN PLIYSF LGETFRDKLR LYIEQKTNLP ALNRFCHAAL KAVIPDSTEQ SDVRFSSAV UniProtKB: G-protein coupled estrogen receptor 1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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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 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 177591 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |