+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-33098 | |||||||||
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Title | Structure of somatostatin receptor 2 bound with SST14. | |||||||||
Map data | Cryo-EM density map of SST14 bound SSTR2-DNGi complex. | |||||||||
Sample |
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Function / homology | Function and homology information somatostatin signaling pathway / MECP2 regulates transcription of neuronal ligands / somatostatin receptor activity / hormone-mediated apoptotic signaling pathway / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / peristalsis / Activation of the phototransduction cascade / neuropeptide binding ...somatostatin signaling pathway / MECP2 regulates transcription of neuronal ligands / somatostatin receptor activity / hormone-mediated apoptotic signaling pathway / Olfactory Signaling Pathway / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / peristalsis / Activation of the phototransduction cascade / neuropeptide binding / response to acidic pH / hyperosmotic response / 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 / response to steroid hormone / 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 / G alpha (q) signalling events / digestion / G alpha (i) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / response to starvation / neuronal dense core vesicle / regulation of postsynaptic membrane neurotransmitter receptor levels / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / neuropeptide signaling pathway / GABA-ergic synapse / Adenylate cyclase inhibitory pathway / positive regulation of protein localization to cell cortex / response to amino acid / regulation of cAMP-mediated signaling / D2 dopamine receptor binding / G protein-coupled serotonin receptor binding / response to nutrient / regulation of mitotic spindle organization / forebrain development / cellular response to forskolin / cellular response to estradiol stimulus / : / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / regulation of cell migration / Peptide ligand-binding receptors / cerebellum development / Regulation of insulin secretion / G protein-coupled receptor binding / PDZ domain binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / hormone activity / response to peptide hormone / ADP signalling through P2Y purinoceptor 12 / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / G alpha (z) signalling events / cellular response to catecholamine stimulus / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / cellular response to prostaglandin E stimulus / GPER1 signaling / GDP binding / G-protein beta-subunit binding / heterotrimeric G-protein complex / signaling receptor complex adaptor activity / cell-cell signaling / cell cortex / midbody / G alpha (i) signalling events / G alpha (s) signalling events / spermatogenesis / chemical synaptic transmission / Extra-nuclear estrogen signaling / cell surface receptor signaling pathway / neuron projection / response to xenobiotic stimulus / G protein-coupled receptor signaling pathway / cell division / negative regulation of cell population proliferation / lysosomal membrane / GTPase activity / centrosome / neuronal cell body Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / synthetic construct (others) / Bos taurus (cattle) / Rattus (rat) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.85 Å | |||||||||
Authors | Bo Q / Yang F / Li YG / Meng XY / Zhang HH / Zhou YX / Ling SL / Sun DM / Lv P / Liu L ...Bo Q / Yang F / Li YG / Meng XY / Zhang HH / Zhou YX / Ling SL / Sun DM / Lv P / Liu L / Shi P / Tian CL | |||||||||
Funding support | China, 1 items
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Citation | Journal: Cell Discov / Year: 2022 Title: Structural insights into the activation of somatostatin receptor 2 by cyclic SST analogues. Authors: Qing Bo / Fan Yang / Yingge Li / Xianyu Meng / Huanhuan Zhang / Yingxin Zhou / Shenglong Ling / Demeng Sun / Pei Lv / Lei Liu / Pan Shi / Changlin Tian / Abstract: The endogenous cyclic tetradecapeptide SST14 was reported to stimulate all five somatostatin receptors (SSTR1-5) for hormone release, neurotransmission, cell growth arrest and cancer suppression. Two ...The endogenous cyclic tetradecapeptide SST14 was reported to stimulate all five somatostatin receptors (SSTR1-5) for hormone release, neurotransmission, cell growth arrest and cancer suppression. Two SST14-derived short cyclic SST analogues (lanreotide or octreotide) with improved stability and longer lifetime were developed as drugs to preferentially activate SSTR2 and treat acromegalia and neuroendocrine tumors. Here, cryo-EM structures of the human SSTR2-Gi complex bound with SST14, octreotide or lanreotide were determined at resolutions of 2.85 Å, 2.97 Å, and 2.87 Å, respectively. Structural and functional analysis revealed that interactions between β-turn residues in SST analogues and transmembrane SSTR2 residues in the ligand-binding pocket are crucial for receptor binding and functional stimulation of the two SST14-derived cyclic octapeptides. Additionally, Q102, N276, and F294 could be responsible for the selectivity of lanreotide or octreotide for SSTR2 over SSTR1 or SSTR4. These results provide valuable insights into further rational development of SST analogue drugs targeting SSTR2. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_33098.map.gz | 28.6 MB | EMDB map data format | |
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Header (meta data) | emd-33098-v30.xml emd-33098.xml | 20.1 KB 20.1 KB | Display Display | EMDB header |
Images | emd_33098.png | 85.5 KB | ||
Others | emd_33098_half_map_1.map.gz emd_33098_half_map_2.map.gz | 28.3 MB 28.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-33098 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-33098 | HTTPS FTP |
-Validation report
Summary document | emd_33098_validation.pdf.gz | 645.8 KB | Display | EMDB validaton report |
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Full document | emd_33098_full_validation.pdf.gz | 645.4 KB | Display | |
Data in XML | emd_33098_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | emd_33098_validation.cif.gz | 12.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33098 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-33098 | HTTPS FTP |
-Related structure data
Related structure data | 7xatMC 7xauC 7xavC 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_33098.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Cryo-EM density map of SST14 bound SSTR2-DNGi complex. | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Cryo-EM half map A of SST14 bound SSTR2-DNGi complex.
File | emd_33098_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM half map A of SST14 bound SSTR2-DNGi complex. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM half map B of SST14 bound SSTR2-DNGi complex.
File | emd_33098_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM half map B of SST14 bound SSTR2-DNGi complex. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The endogenous ligand SST14-bound somatostatin receptor 2 and Gi ...
Entire | Name: The endogenous ligand SST14-bound somatostatin receptor 2 and Gi heterotrimer complex. |
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Components |
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-Supramolecule #1: The endogenous ligand SST14-bound somatostatin receptor 2 and Gi ...
Supramolecule | Name: The endogenous ligand SST14-bound somatostatin receptor 2 and Gi heterotrimer complex. type: complex / Chimera: Yes / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Somatostatin receptor type 2,LargeBit
Macromolecule | Name: Somatostatin receptor type 2,LargeBit / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 63.274395 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MKTIIALSYI FCLVFADYKD DDDKGSGSHH HHHHHHHHLE VLFQGPMDMA DEPLNGSHTW LSIPFDLNGS VVSTNTSNQT EPYYDLTSN AVLTFIYFVV CIIGLCGNTL VIYVILRYAK MKTITNIYIL NLAIADELFM LGLPFLAMQV ALVHWPFGKA I CRVVMTVD ...String: MKTIIALSYI FCLVFADYKD DDDKGSGSHH HHHHHHHHLE VLFQGPMDMA DEPLNGSHTW LSIPFDLNGS VVSTNTSNQT EPYYDLTSN AVLTFIYFVV CIIGLCGNTL VIYVILRYAK MKTITNIYIL NLAIADELFM LGLPFLAMQV ALVHWPFGKA I CRVVMTVD GINQFTSIFC LTVMSIDRYL AVVHPIKSAK WRRPRTAKMI TMAVWGVSLL VILPIMIYAG LRSNQWGRSS CT INWPGES GAWYTGFIIY TFILGFLVPL TIICLCYLFI IIKVKSSGIR VGSSKRKKSE KKVTRMVSIV VAVFIFCWLP FYI FNVSSV SMAISPTPAL KGMFDFVVVL TYANSCANPI LYAFLSDNFK KSFQNVLCLV KVSGTDDGER SDSKQDKSRL NETT ETQRT VFTLEDFVGD WEQTAAYNLD QVLEQGGVSS LLQNLAVSVT PIQRIVRSGE NALKIDIHVI IPYEGLSADQ MAQIE EVFK VVYPVDDHHF KVILPYGTLV IDGVTPNMLN YFGRPYEGIA VFDGKKITVT GTLWNGNKII DERLITPDGS MLFRVT INS |
-Macromolecule #2: Guanine nucleotide-binding protein G(i) subunit alpha-1
Macromolecule | Name: Guanine nucleotide-binding protein G(i) subunit alpha-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: 40.472082 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKNTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI ...String: MGCTLSAEDK AAVERSKMID RNLREDGEKA AREVKLLLLG AGESGKNTIV KQMKIIHEAG YSEEECKQYK AVVYSNTIQS IIAIIRAMG RLKIDFGDSA RADDARQLFV LAGAAEEGFM TAELAGVIKR LWKDSGVQAC FNRSREYQLN DSAAYYLNDL D RIAQPNYI PTQQDVLRTR VKTTGIVETH FTFKDLHFKM FDVGAQRSER KKWIHCFEGV TAIIFCVALS DYDLVLAEDE EM NRMHESM KLFDSICNNK WFTDTSIILF LNKKDLFEEK IKKSPLTICY PEYAGSNTYE EAAAYIQCQF EDLNKRKDTK EIY THFTCS TDTKNVQFVF DAVTDVIIKN NLKDCGLF |
-Macromolecule #3: 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: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Bos taurus (cattle) |
Molecular weight | Theoretical: 38.975578 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 LKIWNGSS |
-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: Bos taurus (cattle) |
Molecular weight | Theoretical: 7.861143 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MASNNTASIA QARKLVEQLK MEANIDRIKV SKAAADLMAY CEAHAKEDPL LTPVPASENP FREKKFFCAI L |
-Macromolecule #5: ScFv16
Macromolecule | Name: ScFv16 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Rattus (rat) |
Molecular weight | Theoretical: 32.768484 KDa |
Recombinant expression | Organism: Spodoptera frugiperda (fall armyworm) |
Sequence | String: MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFDVQ LVESGGGLVQ PGGSRKLSCS ASGFAFSSFG MHWVRQAPEK GLEWVAYIS SGSGTIYYAD TVKGRFTISR DDPKNTLFLQ MTSLRSEDTA MYYCVRSIYY YGSSPFDFWG QGTTLTVSSG G GGSGGGGS ...String: MLLVNQSHQG FNKEHTSKMV SAIVLYVLLA AAAHSAFDVQ LVESGGGLVQ PGGSRKLSCS ASGFAFSSFG MHWVRQAPEK GLEWVAYIS SGSGTIYYAD TVKGRFTISR DDPKNTLFLQ MTSLRSEDTA MYYCVRSIYY YGSSPFDFWG QGTTLTVSSG G GGSGGGGS GGGGSSDIVM TQATSSVPVT PGESVSISCR SSKSLLHSNG NTYLYWFLQR PGQSPQLLIY RMSNLASGVP DR FSGSGSG TAFTLTISRL EAEDVGVYYC MQHLEYPLTF GAGTKLELVD ENLYFQGASH HHHHHHH |
-Macromolecule #6: Somatostatin-14
Macromolecule | Name: Somatostatin-14 / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 1.641909 KDa |
Sequence | String: AGCKNFFWKT FTSC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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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 (6k x 4k) / Average electron dose: 55.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: DIFFRACTION / Nominal defocus max: 2.2 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE / Details: AlphaFold |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 457712 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |