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- EMDB-9382: A high-resolution cryo-electron microscopy structure of a calcito... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-9382 | |||||||||||||||
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Title | A high-resolution cryo-electron microscopy structure of a calcitonin receptor-heterotrimeric Gs protein complex | |||||||||||||||
![]() | Calcitonin receptor-heterotrimeric Gs protein complex, Sharpened map (B -80) | |||||||||||||||
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![]() | GPCR / transmembrane / receptor / calcitonin / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | ![]() calcitonin receptor binding / calcitonin binding / calcitonin family receptor activity / amylin receptor complex 1 / amylin receptor complex 2 / calcitonin family receptor signaling pathway / amylin receptor complex 3 / amylin receptor activity / calcitonin receptor activity / calcitonin gene-related peptide receptor signaling pathway ...calcitonin receptor binding / calcitonin binding / calcitonin family receptor activity / amylin receptor complex 1 / amylin receptor complex 2 / calcitonin family receptor signaling pathway / amylin receptor complex 3 / amylin receptor activity / calcitonin receptor activity / calcitonin gene-related peptide receptor signaling pathway / calcitonin gene-related peptide receptor activity / amylin receptor 3 signaling pathway / amylin receptor 2 signaling pathway / amylin receptor 1 signaling pathway / amylin receptor signaling pathway / Calcitonin-like ligand receptors / negative regulation of ossification / positive regulation of cAMP/PKA signal transduction / response to amyloid-beta / PKA activation in glucagon signalling / hair follicle placode formation / developmental growth / D1 dopamine receptor binding / intracellular transport / renal water homeostasis / Hedgehog 'off' state / response to glucocorticoid / adenylate cyclase-activating adrenergic receptor signaling pathway / activation of adenylate cyclase activity / cellular response to glucagon stimulus / regulation of mRNA stability / adenylate cyclase activator activity / regulation of insulin secretion / positive regulation of calcium-mediated signaling / ossification / osteoclast differentiation / acrosomal vesicle / trans-Golgi network membrane / negative regulation of inflammatory response to antigenic stimulus / bone development / hormone activity / cilium / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / platelet aggregation / Activation of the phototransduction cascade / adenylate cyclase-activating G protein-coupled receptor signaling pathway / cognition / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / 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 / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / Glucagon-type ligand receptors / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / cellular response to catecholamine stimulus / ADP signalling through P2Y purinoceptor 1 / 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 / GPER1 signaling / sensory perception of smell / cellular response to prostaglandin E stimulus / Inactivation, recovery and regulation of the phototransduction cascade / 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) / High laminar flow shear stress activates signaling by PIEZO1 and PECAM1:CDH5:KDR in endothelial cells / positive regulation of cold-induced thermogenesis / amyloid-beta binding / G protein activity / GTPase binding / Ca2+ pathway / retina development in camera-type eye / positive regulation of cytosolic calcium ion concentration / fibroblast proliferation / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / G alpha (s) signalling events / G alpha (q) signalling events / Ras protein signal transduction Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.34 Å | |||||||||||||||
![]() | dal Maso E / Glukhova A | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The Molecular Control of Calcitonin Receptor Signaling. Authors: Emma Dal Maso / Alisa Glukhova / Yue Zhu / Javier Garcia-Nafria / Christopher G Tate / Silvia Atanasio / Christopher A Reynolds / Erney Ramírez-Aportela / Jose-Maria Carazo / Caroline A ...Authors: Emma Dal Maso / Alisa Glukhova / Yue Zhu / Javier Garcia-Nafria / Christopher G Tate / Silvia Atanasio / Christopher A Reynolds / Erney Ramírez-Aportela / Jose-Maria Carazo / Caroline A Hick / Sebastian G B Furness / Debbie L Hay / Yi-Lynn Liang / Laurence J Miller / Arthur Christopoulos / Ming-Wei Wang / Denise Wootten / Patrick M Sexton / ![]() ![]() ![]() ![]() ![]() ![]() Abstract: The calcitonin receptor (CTR) is a class B G protein-coupled receptor (GPCR) that responds to the peptide hormone calcitonin (CT). CTs are clinically approved for the treatment of bone diseases. We ...The calcitonin receptor (CTR) is a class B G protein-coupled receptor (GPCR) that responds to the peptide hormone calcitonin (CT). CTs are clinically approved for the treatment of bone diseases. We previously reported a 4.1 Å structure of the activated CTR bound to salmon CT (sCT) and heterotrimeric Gs protein by cryo-electron microscopy (Liang, Y.-L., . Phase-plate cryo- EM structure of a class B GPCR-G protein complex. , , 118-123). In the current study, we have reprocessed the electron micrographs to yield a 3.3 Å map of the complex. This has allowed us to model extracellular loops (ECLs) 2 and 3, and the peptide N-terminus that previously could not be resolved. We have also performed alanine scanning mutagenesis of ECL1 and the upper segment of transmembrane helix 1 (TM1) and its extension into the receptor extracellular domain (TM1 stalk), with effects on peptide binding and function assessed by cAMP accumulation and ERK1/2 phosphorylation. These data were combined with previously published alanine scanning mutagenesis of ECL2 and ECL3 and the new structural information to provide a comprehensive 3D map of the molecular surface of the CTR that controls binding and signaling of distinct CT and related peptides. The work highlights distinctions in how different, related, class B receptors may be activated. The new mutational data on the TM1 stalk and ECL1 have also provided critical insights into the divergent control of cAMP versus pERK signaling and, collectively with previous mutagenesis data, offer evidence that the conformations linked to these different signaling pathways are, in many ways, mutually exclusive. This study furthers our understanding of the complex nature of signaling elicited by GPCRs and, in particular, that of the therapeutically important class B subfamily. | |||||||||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 2.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 28.3 KB 28.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 6.5 KB | Display | ![]() |
Images | ![]() | 106.7 KB | ||
Masks | ![]() | 22.2 MB | ![]() | |
Filedesc metadata | ![]() | 7.6 KB | ||
Others | ![]() ![]() ![]() ![]() | 20.9 MB 16.9 MB 17 MB 17 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 713 KB | Display | ![]() |
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Full document | ![]() | 712.6 KB | Display | |
Data in XML | ![]() | 12 KB | Display | |
Data in CIF | ![]() | 16.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6niyMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Calcitonin receptor-heterotrimeric Gs protein complex, Sharpened map (B -80) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
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Projections & Slices |
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Density Histograms |
-Additional map: Calcitonin receptor-heterotrimeric Gs protein complex, LocalDeblur sharpened map...
File | emd_9382_additional_1.map | ||||||||||||
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Annotation | Calcitonin receptor-heterotrimeric Gs protein complex, LocalDeblur sharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Calcitonin receptor-heterotrimeric Gs protein complex, unsharpened map...
File | emd_9382_additional_2.map | ||||||||||||
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Annotation | Calcitonin receptor-heterotrimeric Gs protein complex, unsharpened map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Calcitonin receptor-heterotrimeric Gs protein complex, final half map...
File | emd_9382_half_map_1.map | ||||||||||||
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Annotation | Calcitonin receptor-heterotrimeric Gs protein complex, final half map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Calcitonin receptor-heterotrimeric Gs protein complex, final half map...
File | emd_9382_half_map_2.map | ||||||||||||
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Annotation | Calcitonin receptor-heterotrimeric Gs protein complex, final half map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Complex of a full-length, active-state calcitonin receptor with p...
Entire | Name: Complex of a full-length, active-state calcitonin receptor with peptide ligand, heterotrimeric Gs protein and nanobody 35 |
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Components |
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-Supramolecule #1: Complex of a full-length, active-state calcitonin receptor with p...
Supramolecule | Name: Complex of a full-length, active-state calcitonin receptor with peptide ligand, heterotrimeric Gs protein and nanobody 35 type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 150 KDa |
-Macromolecule #1: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
Macromolecule | Name: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 45.72552 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKSTIVKQM RILHVNGFNG EGGEEDPQAA RSNSDGEKA TKVQDIKNNL KEAIETIVAA MSNLVPPVEL ANPENQFRVD YILSVMNVPD FDFPPEFYEH AKALWEDEGV R ACYERSNE ...String: MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKSTIVKQM RILHVNGFNG EGGEEDPQAA RSNSDGEKA TKVQDIKNNL KEAIETIVAA MSNLVPPVEL ANPENQFRVD YILSVMNVPD FDFPPEFYEH AKALWEDEGV R ACYERSNE YQLIDCAQYF LDKIDVIKQA DYVPSDQDLL RCRVLTSGIF ETKFQVDKVN FHMFDVGGQR DERRKWIQCF ND VTAIIFV VASSSYNMVI REDNQTNRLQ EALNLFKSIW NNRWLRTISV ILFLNKQDLL AEKVLAGKSK IEDYFPEFAR YTT PEDATP EPGEDPRVTR AKYFIRDEFL RISTASGDGR HYCYPHFTCA VDTENIRRVF NDCRDIIQRM HLRQYELL UniProtKB: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short |
-Macromolecule #2: Nanobody35
Macromolecule | Name: Nanobody35 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 15.140742 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: QVQLQESGGG LVQPGGSLRL SCAASGFTFS NYKMNWVRQA PGKGLEWVSD ISQSGASISY TGSVKGRFTI SRDNAKNTLY LQMNSLKPE DTAVYYCARC PAPFTRDCFD VTSTTYAYRG QGTQVTVSSH HHHHHEPEA |
-Macromolecule #3: Calcitonin receptor
Macromolecule | Name: Calcitonin receptor / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 55.387316 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MRFTFTSRCL ALFLLLNHPT PILPAFSNQT YPTIEPKPFL YVVGRKKMMD AQYKCYDRMQ QLPAYQGEGP YCNRTWDGWL CWDDTPAGV LSYQFCPDYF PDFDPSEKVT KYCDEKGVWF KHPENNRTWS NYTMCNAFTP EKLKNAYVLY YLAIVGHSLS I FTLVISLG ...String: MRFTFTSRCL ALFLLLNHPT PILPAFSNQT YPTIEPKPFL YVVGRKKMMD AQYKCYDRMQ QLPAYQGEGP YCNRTWDGWL CWDDTPAGV LSYQFCPDYF PDFDPSEKVT KYCDEKGVWF KHPENNRTWS NYTMCNAFTP EKLKNAYVLY YLAIVGHSLS I FTLVISLG IFVFFRSLGC QRVTLHKNMF LTYILNSMII IIHLVEVVPN GELVRRDPVS CKILHFFHQY MMACNYFWML CE GIYLHTL IVVAVFTEKQ RLRWYYLLGW GFPLVPTTIH AITRAVYFND NCWLSVETHL LYIIHGPVMA ALVVNFFFLL NIV RVLVTK MRETHEAESH MYLKAVKATM ILVPLLGIQF VVFPWRPSNK MLGKIYDYVM HSLIHFQGFF VATIYCFCNN EVQT TVKRQ WAQFKIQWNQ RWGRRPSNRS ARAAAAAAEA GDIPIYICHQ EPRNEPANNQ GEESAEIIPL NIIEQESSA UniProtKB: Calcitonin receptor |
-Macromolecule #4: 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: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 37.41693 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL ...String: MSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL WDIETGQQTT TFTGHTGDVM SLSLAPDTRL FVSGACDASA KLWDVREGMC RQTFTGHESD INAICFFPNG NA FATGSDD ATCRLFDLRA DQELMTYSHD NIICGITSVS FSKSGRLLLA GYDDFNCNVW DALKADRAGV LAGHDNRVSC LGV TDDGMA VATGSWDSFL KIWN UniProtKB: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 |
-Macromolecule #5: 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: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 7.861143 KDa |
Recombinant expression | Organism: ![]() |
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 #6: Calcitonin
Macromolecule | Name: Calcitonin / type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 3.438886 KDa |
Sequence | String: CSNLSTCVLG KLSQELHKLQ TYPRTNTGSG TP UniProtKB: Calcitonin |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL |
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Buffer | pH: 7.5 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Phase plate: OTHER |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated magnification: 47170 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |