+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38330 | |||||||||
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Title | ETB-eGt complex bound to endothelin-1 | |||||||||
Map data | ||||||||||
Sample |
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Keywords | 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 / endothelin B receptor binding / rhythmic excitation / 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 / endothelin B receptor binding / rhythmic excitation / peptide hormone secretion / neural crest cell fate commitment / sympathetic neuron axon guidance / body fluid secretion / glomerular endothelium development / vein smooth muscle contraction / noradrenergic neuron differentiation / response to prostaglandin F / positive regulation of renal sodium excretion / leukocyte activation / positive regulation of sarcomere organization / histamine secretion / rough endoplasmic reticulum lumen / positive regulation of chemokine-mediated signaling pathway / positive regulation of odontogenesis / maternal process involved in parturition / regulation of glucose transmembrane transport / pharyngeal arch artery morphogenesis / endothelin receptor signaling pathway involved in heart process / semaphorin-plexin signaling pathway involved in axon guidance / epithelial fluid transport / podocyte differentiation / cardiac neural crest cell migration involved in outflow tract morphogenesis / negative regulation of hormone secretion / response to leptin / endothelin receptor signaling pathway / response to ozone / Weibel-Palade body / renal sodium ion absorption / positive regulation of cell growth involved in cardiac muscle cell development / artery smooth muscle contraction / glomerular filtration / axonogenesis involved in innervation / positive regulation of cation channel activity / positive regulation of prostaglandin secretion / cellular response to follicle-stimulating hormone stimulus / cellular response to luteinizing hormone stimulus / regulation of pH / negative regulation of nitric-oxide synthase biosynthetic process / cellular response to mineralocorticoid stimulus / positive regulation of urine volume / negative regulation of blood coagulation / respiratory gaseous exchange by respiratory system / basal part of cell / positive regulation of smooth muscle contraction / positive regulation of hormone secretion / regulation of systemic arterial blood pressure by endothelin / vasoconstriction / protein kinase C-activating G protein-coupled receptor signaling pathway / embryonic heart tube development / superoxide anion generation / axon extension / dorsal/ventral pattern formation / negative regulation of protein metabolic process / positive regulation of neutrophil chemotaxis / middle ear morphogenesis / positive regulation of signaling receptor activity / 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 / cellular response to glucocorticoid stimulus / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (12/13) signalling events / G beta:gamma signalling through BTK / cartilage development / 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 / nitric oxide transport / cellular response to fatty acid / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / positive regulation of heart rate / cellular response to organic substance / branching involved in blood vessel morphogenesis / Vasopressin regulates renal water homeostasis via Aquaporins / response to testosterone / response to dexamethasone Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Bos taurus (cattle) / Rattus rattus (black rat) / Lama glama (llama) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Oshima HS / Sano FK / Akasaka H / Iwama A / Shihoya W / Nureki O | |||||||||
Funding support | Japan, 1 items
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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 |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38330.map.gz | 25.3 MB | EMDB map data format | |
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Header (meta data) | emd-38330-v30.xml emd-38330.xml | 18.2 KB 18.2 KB | Display Display | EMDB header |
Images | emd_38330.png | 91.5 KB | ||
Filedesc metadata | emd-38330.cif.gz | 6.6 KB | ||
Others | emd_38330_half_map_1.map.gz emd_38330_half_map_2.map.gz | 26.1 MB 26.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38330 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38330 | HTTPS FTP |
-Related structure data
Related structure data | 8xgrMC 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_38330.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 0.96833 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #1
File | emd_38330_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_38330_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Complex of Endothelin-1, ETB, eGt trimer and Nb35*
Entire | Name: Complex of Endothelin-1, ETB, eGt trimer and Nb35* |
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Components |
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-Supramolecule #1: Complex of Endothelin-1, ETB, eGt trimer and Nb35*
Supramolecule | Name: Complex of Endothelin-1, ETB, eGt trimer and Nb35* / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #4-#5, #2-#3 |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: 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,eGt-alpha type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Theoretical: 48.998785 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI LGSAGSAGSA MGCTLSAED KAAVERSKMI DRNLREDGEK AARTVKLLLL GAGESGKSTI VKQMKIIHQD GYSLEECLEF IAIIYGNTLQ S ILAIVRAM ...String: MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI LGSAGSAGSA MGCTLSAED KAAVERSKMI DRNLREDGEK AARTVKLLLL GAGESGKSTI VKQMKIIHQD GYSLEECLEF IAIIYGNTLQ S ILAIVRAM TTLNIQYGDS ARQDDARKLM HMADTIEEGT MPKEMSDIIQ RLWKDSGIQA CFDRASEYQL NDSAGYYLSD LE RLVTPGY VPTEQDVLRS RVKTTGIIET QFSFKDLNFR MFDVGGQRDE RRKWIHCFEG VTAIIFCVAL SDYDMVLVED NQT NRMQES MNLFKSICNN KWFTDTSIIL FLNKKDLFEE KIKKSPLTDY YPEYAGSNTY EEAGNYIKVQ FLELNMASDV KEIY SHMTC ATDTQNVKFV FDAVTDIIIK ENLKDCGLF UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 |
-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: Rattus rattus (black rat) |
Molecular weight | Theoretical: 40.470105 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: GSQLQSELDQ LRQEAEQLKN QIRDARKACA DATLSQITNN IDPVGRIQMR TRRTLRGHLA KIYAMHWGTD SRLLVSASQD GKLIIWDSY TTNKVHAIPL RSSWVMTCAY APSGNYVACG GLDNICSIYN LKTREGNVRV SRELAGHTGY LSCCRFLDDN Q IVTSSGDT ...String: GSQLQSELDQ LRQEAEQLKN QIRDARKACA DATLSQITNN IDPVGRIQMR TRRTLRGHLA KIYAMHWGTD SRLLVSASQD GKLIIWDSY TTNKVHAIPL RSSWVMTCAY APSGNYVACG GLDNICSIYN LKTREGNVRV SRELAGHTGY LSCCRFLDDN Q IVTSSGDT TCALWDIETG QQTTTFTGHT GDVMSLSLAP DTRLFVSGAC DASAKLWDVR EGMCRQTFTG HESDINAICF FP NGNAFAT GSDDATCRLF DLRADQELMT YSHDNIICGI TSVSFSKSGR LLLAGYDDFN CNVWDALKAD RAGVLAGHDN RVS CLGVTD DGMAVATGSW DSFLKIWNGA SGGGSGGNSG SSGGSSGVSG WRLFKKIS |
-Macromolecule #3: Camelid antibody VHH fragment
Macromolecule | Name: Camelid antibody VHH fragment / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Lama glama (llama) |
Molecular weight | Theoretical: 17.395631 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MKYLLPTAAA GLLLLAAQPA MAMQVQLQES GGGLVQPGGS LRLSCAASGF TFSNYKMNWV RQAPGKGLQW VSDISQSGAS ISYTGSVKG RFTISRDDAK NTLYLQMNSL KPADTAVYYC ARCPAPFTRD CFDVTSTAYA YRGQGTQVTV SSHHHHHHEP E A |
-Macromolecule #4: Endothelin receptor type B
Macromolecule | Name: Endothelin receptor type B / 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: 67.492219 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: EERGFPPDRA TPLLQTAEIM TPPTKTLWPK GDYKDDDDKL APAEVPKGDR TAGSPPRTIS PPPCQGPIEI KETFKYINTV VSCLVFVLG IIGNSTLLRI IYKNKCMRNG PNILIASLAL GDLLHIVIDI PINVYKLLAE DWPFGAEMCK LVPFIQKASV G ITVLSLCA ...String: EERGFPPDRA TPLLQTAEIM TPPTKTLWPK GDYKDDDDKL APAEVPKGDR TAGSPPRTIS PPPCQGPIEI KETFKYINTV VSCLVFVLG IIGNSTLLRI IYKNKCMRNG PNILIASLAL GDLLHIVIDI PINVYKLLAE DWPFGAEMCK LVPFIQKASV G ITVLSLCA LSIDRYRAVA SWSRIKGIGV PKWTAVEIVL IWVVSVVLAV PEAIGFDIIT MDYKGSYLRI CLLHPVQKTA FM QFYKTAK DWWLFSFYFC LPLAITAFFY TLMTCEMLRK KSGMQIALND HLKQRREVAK TVFCLVLVFA LCWLPLHLSR ILK LTLYNQ NDPNRCELLS FLLVLDYIGI NMASLNSCIN PIALYLVSKR FKNCFKSCLC CWCQSFEEKQ SLEEKQSCLK FKAN DHGYD NFRSSNKYSS SGSGGGGSGG SSSGGVFTLE DFVGDWEQTA AYNLDQVLEQ GGVSSLLQNL AVSVTPIQRI VRSGE NALK IDIHVIIPYE GLSADQMAQI EEVFKVVYPV DDHHFKVILP YGTLVIDGVT PNMLNYFGRP YEGIAVFDGK KITVTG TLW NGNKIIDERL ITPDGSMLFR VTINSGGSGG GGSGGSSSGG LEVLFQ |
-Macromolecule #5: Endothelin-1
Macromolecule | Name: Endothelin-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: 2.497951 KDa |
Sequence | String: CSCSSLMDKE CVYFCHLDII W UniProtKB: Endothelin-1 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.8 µm |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 52285 |