+Open data
-Basic information
Entry | Database: PDB / ID: 8xgr | ||||||
---|---|---|---|---|---|---|---|
Title | ETB-eGt complex bound to endothelin-1 | ||||||
Components |
| ||||||
Keywords | PEPTIDE BINDING PROTEIN/IMMUNE SYSTEM / SIGNALING PROTEIN / PEPTIDE BINDING PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information positive regulation of prostaglandin-endoperoxide synthase activity / endothelin A receptor binding / protein kinase C deactivation / cellular response to human chorionic gonadotropin stimulus / meiotic cell cycle process involved in oocyte maturation / phospholipase D-activating G protein-coupled receptor signaling pathway / rhythmic excitation / endothelin B receptor binding / peptide hormone secretion / neural crest cell fate commitment ...positive regulation of prostaglandin-endoperoxide synthase activity / endothelin A receptor binding / protein kinase C deactivation / cellular response to human chorionic gonadotropin stimulus / meiotic cell cycle process involved in oocyte maturation / phospholipase D-activating G protein-coupled receptor signaling pathway / rhythmic excitation / endothelin B receptor binding / peptide hormone secretion / neural crest cell fate commitment / sympathetic neuron axon guidance / positive regulation of artery morphogenesis / glomerular endothelium development / vein smooth muscle contraction / body fluid secretion / noradrenergic neuron differentiation / response to prostaglandin F / positive regulation of sarcomere organization / leukocyte activation / positive regulation of renal sodium excretion / histamine secretion / positive regulation of chemokine-mediated signaling pathway / maternal process involved in parturition / rough endoplasmic reticulum lumen / pharyngeal arch artery morphogenesis / regulation of glucose transmembrane transport / positive regulation of odontogenesis / endothelin receptor signaling pathway involved in heart process / epithelial fluid transport / cardiac neural crest cell migration involved in outflow tract morphogenesis / negative regulation of hormone secretion / response to leptin / endothelin receptor signaling pathway / Weibel-Palade body / podocyte differentiation / response to ozone / renal sodium ion absorption / glomerular filtration / positive regulation of cell growth involved in cardiac muscle cell development / artery smooth muscle contraction / axonogenesis involved in innervation / positive regulation of cation channel activity / cellular response to follicle-stimulating hormone stimulus / positive regulation of prostaglandin secretion / cellular response to luteinizing hormone stimulus / negative regulation of nitric-oxide synthase biosynthetic process / cellular response to mineralocorticoid stimulus / basal part of cell / respiratory gaseous exchange by respiratory system / positive regulation of urine volume / positive regulation of smooth muscle contraction / response to salt / regulation of pH / semaphorin-plexin signaling pathway involved in axon guidance / positive regulation of hormone secretion / regulation of systemic arterial blood pressure by endothelin / vasoconstriction / : / embryonic heart tube development / negative regulation of blood coagulation / dorsal/ventral pattern formation / axon extension / superoxide anion generation / positive regulation of neutrophil chemotaxis / positive regulation of signaling receptor activity / cartilage development / middle ear morphogenesis / cellular response to glucocorticoid stimulus / Activation of G protein gated Potassium channels / G-protein activation / G beta:gamma signalling through PI3Kgamma / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / ADP signalling through P2Y purinoceptor 1 / Thromboxane signalling through TP receptor / Presynaptic function of Kainate receptors / G beta:gamma signalling through CDC42 / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Thrombin signalling through proteinase activated receptors (PARs) / Ca2+ pathway / G alpha (z) signalling events / Extra-nuclear estrogen signaling / G alpha (s) signalling events / prostaglandin biosynthetic process / G alpha (q) signalling events / negative regulation of protein metabolic process / nitric oxide transport / cellular response to fatty acid / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / branching involved in blood vessel morphogenesis / positive regulation of heart rate / Vasopressin regulates renal water homeostasis via Aquaporins / : Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) Rattus rattus (black rat) Lama glama (llama) Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.2 Å | ||||||
Authors | Oshima, H.S. / Sano, F.K. / Akasaka, H. / Iwama, A. / Shihoya, W. / Nureki, O. | ||||||
Funding support | Japan, 1items
| ||||||
Citation | Journal: Biochem Biophys Res Commun / Year: 2024 Title: Optimizing cryo-EM structural analysis of G-coupling receptors via engineered G and Nb35 application. Authors: Hidetaka S Oshima / Fumiya K Sano / Hiroaki Akasaka / Aika Iwama / Wataru Shihoya / Osamu Nureki / Abstract: Cryo-EM single particle analysis has recently facilitated the high-resolution structural determination of numerous GPCR-G complexes. Diverse methodologies have been devised with this trend, and in ...Cryo-EM single particle analysis has recently facilitated the high-resolution structural determination of numerous GPCR-G complexes. Diverse methodologies have been devised with this trend, and in the case of GPCR-G complexes, scFv16, an antibody that recognizes the intricate interface of the complex, has been mainly implemented to stabilize the complex. However, owing to their flexibility and heterogeneity, structural determinations of GPCR-G complexes remain both challenging and resource-intensive. By employing eGα, which exhibits binding affinity to modified nanobody Nb35, the cryo-EM structure of Rhodopsin-eGα complex was previously reported. Using this modified G protein, we determined the structure of the ET-eG complex bound to the modified Nb35. The determined structure of ET receptor was the same as the previously reported ET-G complex, and the resulting dataset demonstrated significantly improved anisotropy. This modified G protein will be utilized for the structural determination of other GPCR-G complexes. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8xgr.cif.gz | 224.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8xgr.ent.gz | 166.5 KB | Display | PDB format |
PDBx/mmJSON format | 8xgr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8xgr_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8xgr_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 8xgr_validation.xml.gz | 39.1 KB | Display | |
Data in CIF | 8xgr_validation.cif.gz | 56.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xg/8xgr ftp://data.pdbj.org/pub/pdb/validation_reports/xg/8xgr | HTTPS FTP |
-Related structure data
Related structure data | 38330MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 48998.785 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GNG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P63212 |
---|---|
#2: Protein | Mass: 40470.105 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus rattus (black rat) / Production host: Spodoptera frugiperda (fall armyworm) |
#3: Antibody | Mass: 17395.631 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lama glama (llama) / Production host: Spodoptera frugiperda (fall armyworm) |
#4: Protein | Mass: 67492.219 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: EDNRB, ETRB / Production host: Spodoptera frugiperda (fall armyworm) |
#5: Protein/peptide | Mass: 2497.951 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P05305 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Complex of Endothelin-1, ETB, eGt trimer and Nb35* / Type: COMPLEX / Entity ID: #4-#5, #2-#3 / Source: MULTIPLE SOURCES |
---|---|
Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Spodoptera frugiperda (fall armyworm) |
Buffer solution | pH: 8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
3D reconstruction | Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52285 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|