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- PDB-8xof: Cryo-EM structure of Lys05 bound GPR30-Gq complex structure -

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Entry
Database: PDB / ID: 8xof
TitleCryo-EM structure of Lys05 bound GPR30-Gq complex structure
Components
  • (Guanine nucleotide-binding protein ...) x 2
  • G protein subunit q
  • G-protein coupled estrogen receptor 1
  • Nanobody35
KeywordsMEMBRANE PROTEIN/IMMUNE SYSTEM / 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 / G protein-coupled estrogen receptor activity / positive regulation of cardiac vascular smooth muscle cell differentiation / negative regulation of cell cycle process / keratin filament / positive regulation of inositol trisphosphate biosynthetic process / apoptotic chromosome condensation / positive regulation of uterine smooth muscle contraction / negative regulation of lipid biosynthetic process ...negative regulation of leukocyte activation / nuclear fragmentation involved in apoptotic nuclear change / G protein-coupled estrogen receptor activity / positive regulation of cardiac vascular smooth muscle cell differentiation / negative regulation of cell cycle process / keratin filament / positive regulation of inositol trisphosphate biosynthetic process / apoptotic chromosome condensation / positive regulation of uterine smooth muscle contraction / negative regulation of lipid biosynthetic process / steroid hormone binding / cellular response to mineralocorticoid stimulus / positive regulation of G protein-coupled receptor signaling pathway / dendritic spine membrane / positive regulation of extrinsic apoptotic signaling pathway / presynaptic active zone / positive regulation of neurogenesis / cellular response to peptide hormone stimulus / positive regulation of epidermal growth factor receptor signaling pathway / nuclear estrogen receptor activity / dendritic spine head / steroid hormone receptor signaling pathway / positive regulation of neurotransmitter secretion / negative regulation of fat cell differentiation / positive regulation of release of cytochrome c from mitochondria / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of endothelial cell apoptotic process / nuclear receptor-mediated steroid hormone signaling pathway / regulation of cytosolic calcium ion concentration / neuronal action potential / steroid binding / axon terminus / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cytoplasmic vesicle membrane / Peptide ligand-binding receptors / hippocampal mossy fiber to CA3 synapse / positive regulation of release of sequestered calcium ion into cytosol / dendritic shaft / positive regulation of protein localization to plasma membrane / cellular response to glucose stimulus / cellular response to estradiol stimulus / trans-Golgi network / G protein-coupled receptor activity / positive regulation of insulin secretion / recycling endosome / mitochondrial membrane / negative regulation of ERK1 and ERK2 cascade / negative regulation of inflammatory response / vasodilation / Olfactory Signaling Pathway / Activation of the phototransduction cascade / positive regulation of protein phosphorylation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / G-protein activation / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through CDC42 / Glucagon signaling in metabolic regulation / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Sensory perception of sweet, bitter, and umami (glutamate) taste / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / cellular response to tumor necrosis factor / Vasopressin regulates renal water homeostasis via Aquaporins / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / ADORA2B mediated anti-inflammatory cytokines production / G beta:gamma signalling through PI3Kgamma / adenylate cyclase-activating dopamine receptor signaling pathway / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / nuclear envelope / GPER1 signaling / nervous system development / Inactivation, recovery and regulation of the phototransduction cascade / cellular response to prostaglandin E stimulus / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / sensory perception of taste / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / retina development in camera-type eye / positive regulation of cytosolic calcium ion concentration / presynaptic membrane / GTPase binding / Ca2+ pathway / fibroblast proliferation / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / G alpha (i) signalling events
Similarity search - Function
: / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit ...: / G-protein, gamma subunit / G-protein gamma subunit domain profile. / G-protein gamma-like domain / G-protein gamma-like domain superfamily / GGL domain / G protein gamma subunit-like motifs / GGL domain / G protein beta WD-40 repeat protein / Guanine nucleotide-binding protein, beta subunit / G-protein, beta subunit / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / G-protein beta WD-40 repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily
Similarity search - Domain/homology
: / Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / G-protein coupled estrogen receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
Lama glama (llama)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsLiu, H. / Xu, P. / Xu, H.E.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: 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
DepositionJan 1, 2024Deposition site: PDBJ / Processing site: PDBJ
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: G protein subunit q
B: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
G: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
N: Nanobody35
R: G-protein coupled estrogen receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)146,1106
Polymers145,6705
Non-polymers4401
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 2 types, 2 molecules AR

#1: Protein G protein subunit q


Mass: 41632.219 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Spodoptera frugiperda (fall armyworm)
#5: Protein G-protein coupled estrogen receptor 1 / Chemoattractant receptor-like 2 / Flow-induced endothelial G-protein coupled receptor 1 / FEG-1 / G ...Chemoattractant receptor-like 2 / Flow-induced endothelial G-protein coupled receptor 1 / FEG-1 / G protein-coupled estrogen receptor 1 / G-protein coupled receptor 30 / GPCR-Br / IL8-related receptor DRY12 / Lymphocyte-derived G-protein coupled receptor / LYGPR / Membrane estrogen receptor / mER


Mass: 42291.457 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GPER1, CEPR, CMKRL2, DRY12, GPER, GPR30 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q99527

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Guanine nucleotide-binding protein ... , 2 types, 2 molecules BG

#2: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 / Transducin beta chain 1


Mass: 38744.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNB1 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P62873
#3: Protein Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 / G gamma-I


Mass: 7861.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P59768

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Antibody / Non-polymers , 2 types, 2 molecules N

#4: Antibody Nanobody35


Mass: 15140.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#6: Chemical ChemComp-A1LVW / Lys01 / ~{N}-(7-chloranylquinolin-4-yl)-~{N}'-[2-[(7-chloranylquinolin-4-yl)amino]ethyl]-~{N}'-methyl-ethane-1,2-diamine


Mass: 440.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H23Cl2N5

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1GPR30-Gq complexCOMPLEX#1-#50RECOMBINANT
2GPR30-GqCOMPLEX#1-#3, #51RECOMBINANT
3Nanobody35COMPLEX#41RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Homo sapiens (human)9606
33Lama glama (llama)9844
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
22Spodoptera frugiperda (fall armyworm)7108
33Escherichia coli (E. coli)562
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: DARK FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 209371 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0028242
ELECTRON MICROSCOPYf_angle_d0.47811157
ELECTRON MICROSCOPYf_dihedral_angle_d4.8631114
ELECTRON MICROSCOPYf_chiral_restr0.041258
ELECTRON MICROSCOPYf_plane_restr0.0041420

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