+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29285 | |||||||||||||||
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Title | Human PTH1R in complex with Abaloparatide and Gs | |||||||||||||||
Map data | Consensus map sharpened; rescaled to 0.85 angstrom/px | |||||||||||||||
Sample |
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Keywords | GPCR / agonist / hormone / MEMBRANE PROTEIN | |||||||||||||||
Function / homology | Function and homology information parathyroid hormone receptor activity / G protein-coupled peptide receptor activity / Class B/2 (Secretin family receptors) / osteoblast development / positive regulation of inositol phosphate biosynthetic process / bone mineralization / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / chondrocyte differentiation / bone resorption ...parathyroid hormone receptor activity / G protein-coupled peptide receptor activity / Class B/2 (Secretin family receptors) / osteoblast development / positive regulation of inositol phosphate biosynthetic process / bone mineralization / peptide hormone binding / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / chondrocyte differentiation / bone resorption / cell maturation / skeletal system development / adenylate cyclase-activating G protein-coupled receptor signaling pathway / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / Olfactory Signaling Pathway / Activation of the phototransduction cascade / Prostacyclin signalling through prostacyclin receptor / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / Glucagon signaling in metabolic regulation / 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 / G beta:gamma signalling through CDC42 / Vasopressin regulates renal water homeostasis via Aquaporins / G beta:gamma signalling through BTK / ADP signalling through P2Y purinoceptor 12 / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Glucagon-type ligand receptors / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / G alpha (z) signalling events / Adrenaline,noradrenaline inhibits insulin secretion / intracellular calcium ion homeostasis / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / cellular response to catecholamine stimulus / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / GPER1 signaling / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / Inactivation, recovery and regulation of the phototransduction cascade / G-protein beta-subunit binding / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / basolateral plasma membrane / G alpha (q) signalling events / in utero embryonic development / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / receptor complex / cell surface receptor signaling pathway / G protein-coupled receptor signaling pathway / apical plasma membrane / negative regulation of cell population proliferation / lysosomal membrane / GTPase activity / positive regulation of cell population proliferation / synapse / protein-containing complex binding / signal transduction / protein homodimerization activity / extracellular exosome / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) / Lama glama (llama) / synthetic construct (others) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.09 Å | |||||||||||||||
Authors | Cary BP / Belousoff MJ / Piper SJ / Wootten D / Sexton PM | |||||||||||||||
Funding support | Australia, 4 items
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Citation | Journal: Structure / Year: 2023 Title: Molecular insights into peptide agonist engagement with the PTH receptor. Authors: Brian P Cary / Elliot J Gerrard / Matthew J Belousoff / Madeleine M Fletcher / Yan Jiang / Isabella C Russell / Sarah J Piper / Denise Wootten / Patrick M Sexton / Abstract: The parathyroid hormone (PTH) 1 receptor (PTH1R) is a G protein-coupled receptor (GPCR) that regulates skeletal development and calcium homeostasis. Here, we describe cryo-EM structures of the PTH1R ...The parathyroid hormone (PTH) 1 receptor (PTH1R) is a G protein-coupled receptor (GPCR) that regulates skeletal development and calcium homeostasis. Here, we describe cryo-EM structures of the PTH1R in complex with fragments of the two hormones, PTH and PTH-related protein, the drug abaloparatide, as well as the engineered tool compounds, long-acting PTH (LA-PTH) and the truncated peptide, M-PTH(1-14). We found that the critical N terminus of each agonist engages the transmembrane bundle in a topologically similar fashion, reflecting similarities in measures of Gαs activation. The full-length peptides induce subtly different extracellular domain (ECD) orientations relative to the transmembrane domain. In the structure bound to M-PTH, the ECD is unresolved, demonstrating that the ECD is highly dynamic when unconstrained by a peptide. High resolutions enabled identification of water molecules near peptide and G protein binding sites. Our results illuminate the action of orthosteric agonists of the PTH1R. | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29285.map.gz | 85.3 MB | EMDB map data format | |
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Header (meta data) | emd-29285-v30.xml emd-29285.xml | 31.7 KB 31.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29285_fsc.xml | 9.5 KB | Display | FSC data file |
Images | emd_29285.png | 53.5 KB | ||
Masks | emd_29285_msk_1.map | 91.1 MB | Mask map | |
Others | emd_29285_additional_1.map.gz emd_29285_additional_2.map.gz emd_29285_additional_3.map.gz emd_29285_half_map_1.map.gz emd_29285_half_map_2.map.gz | 45.7 MB 44.2 MB 45.7 MB 84.6 MB 84.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29285 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29285 | HTTPS FTP |
-Validation report
Summary document | emd_29285_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_29285_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_29285_validation.xml.gz | 17.9 KB | Display | |
Data in CIF | emd_29285_validation.cif.gz | 22.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29285 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-29285 | HTTPS FTP |
-Related structure data
Related structure data | 8flsMC 8flqC 8flrC 8fltC 8fluC C: citing same article (ref.) M: atomic model generated by this map |
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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_29285.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Consensus map sharpened; rescaled to 0.85 angstrom/px | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_29285_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Consensus map unsharpened; rescaled to 0.85 angstrom/px
File | emd_29285_additional_1.map | ||||||||||||
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Annotation | Consensus map unsharpened; rescaled to 0.85 angstrom/px | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Local refinement on receptor; rescaled to 0.85 angstrom/px
File | emd_29285_additional_2.map | ||||||||||||
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Annotation | Local refinement on receptor; rescaled to 0.85 angstrom/px | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: unsharpened consensus map; original pixel size
File | emd_29285_additional_3.map | ||||||||||||
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Annotation | unsharpened consensus map; original pixel size | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map
File | emd_29285_half_map_1.map | ||||||||||||
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Annotation | Half-map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map
File | emd_29285_half_map_2.map | ||||||||||||
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Annotation | Half-map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Abaloparatide bound to the PTH1R in complex with G protein
Entire | Name: Abaloparatide bound to the PTH1R in complex with G protein |
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Components |
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-Supramolecule #1: Abaloparatide bound to the PTH1R in complex with G protein
Supramolecule | Name: Abaloparatide bound to the PTH1R in complex with G protein type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Homo sapiens (human) |
-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: Homo sapiens (human) |
Molecular weight | Theoretical: 45.683434 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKNTIVKQM RILHVNGFNG EGGEEDPQAA RSNSDGEKA TKVQDIKNNL KEAIETIVAA MSNLVPPVEL ANPENQFRVD YILSVMNVPD FDFPPEFYEH AKALWEDEGV R ACYERSNE ...String: MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKNTIVKQM RILHVNGFNG EGGEEDPQAA RSNSDGEKA TKVQDIKNNL KEAIETIVAA MSNLVPPVEL ANPENQFRVD YILSVMNVPD FDFPPEFYEH AKALWEDEGV R ACYERSNE YQLIDCAQYF LDKIDVIKQA DYVPSDQDLL RCRVLTSGIF ETKFQVDKVN FHMFDVGAQR DERRKWIQCF ND VTAIIFV VASSSYNMVI REDNQTNRLQ AALKLFDSIW NNKWLRDTSV ILFLNKQDLL AEKVLAGKSK IEDYFPEFAR YTT PEDATP EPGEDPRVTR AKYFIRDEFL RISTASGDGR HYCYPHFTCA VDTENIRRVF NDCRDIIQRM HLRQYELL |
-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: Homo sapiens (human) |
Molecular weight | Theoretical: 37.413863 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: QSELDQLRQE AEQLKNQIRD ARKACADATL SQITNNIDPV GRIQMRTRRT LRGHLAKIYA MHWGTDSRLL VSASQDGKLI IWDSYTTNK VHAIPLRSSW VMTCAYAPSG NYVACGGLDN ICSIYNLKTR EGNVRVSREL AGHTGYLSCC RFLDDNQIVT S SGDTTCAL ...String: QSELDQLRQE 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 |
-Macromolecule #3: 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: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 6.375332 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: NTASIAQARK LVEQLKMEAN IDRIKVSKAA ADLMAYCEAH AKEDPLLTPV PASENPFR |
-Macromolecule #4: Nanobody35
Macromolecule | Name: Nanobody35 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Lama glama (llama) |
Molecular weight | Theoretical: 13.885439 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: QVQLQESGGG LVQPGGSLRL SCAASGFTFS NYKMNWVRQA PGKGLEWVSD ISQSGASISY TGSVKGRFTI SRDNAKNTLY LQMNSLKPE DTAVYYCARC PAPFTRDCFD VTSTTYAYRG QGTQVTVSS |
-Macromolecule #5: Abaloparatide
Macromolecule | Name: Abaloparatide / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 3.971654 KDa |
Sequence | String: AVSEHQLLHD KGKSIQDLRR RELLEKLL(AIB)K LHTA |
-Macromolecule #6: Parathyroid hormone/parathyroid hormone-related peptide receptor
Macromolecule | Name: Parathyroid hormone/parathyroid hormone-related peptide receptor 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: 69.513758 KDa |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: MKTIIALSYI FCLVFADYKD DDDLEVLFQG PADDVMTKEE QIFLLHRAQA QCEKRLKEVL QRPASIMESD KGWTSASTSG KPRKDKASG KLYPESEEDK EAPTGSRYRG RPCLPEWDHI LCWPLGAPGE VVAVPCPDYI YDFNHKGHAY RRCDRNGSWE L VPGHNRTW ...String: MKTIIALSYI FCLVFADYKD DDDLEVLFQG PADDVMTKEE QIFLLHRAQA QCEKRLKEVL QRPASIMESD KGWTSASTSG KPRKDKASG KLYPESEEDK EAPTGSRYRG RPCLPEWDHI LCWPLGAPGE VVAVPCPDYI YDFNHKGHAY RRCDRNGSWE L VPGHNRTW ANYSECVKFL TNETREREVF DRLGMIYTVG YSVSLASLTV AVLILAYFRR LHCTRNYIHM HLFLSFMLRA VS IFVKDAV LYSGATLDEA ERLTEEELRA IAQAPPPPAT AAAGYAGCRV AVTFFLYFLA TNYYWILVEG LYLHSLIFMA FFS EKKYLW GFTVFGWGLP AVFVAVWVSV RATLANTGCW DLSSGNKKWI IQVPILASIV LNFILFINIV RVLATKLRET NAGR CDTRQ QYRKLLKSTL VLMPLFGVHY IVFMATPYTE VSGTLWQVQM HYEMLFNSFQ GFFVAIIYCF CNGEVQAEIK KSWSR WTLA LDFKRKARSG SSSYSYGPMV SHTSVTNVGP RVGLGLPLSP RLLPTATTNG HPQLPGHAKP GTPALETLET TPPAMA APK DDGFLNGSCS GLDEEASGPE RPPALLQEEW ETVMPAGLEV LFQGPHHHHH HHH |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 3.9 mg/mL | |||||||||||||||||||||
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Buffer | pH: 7.4 Component:
Details: Buffer also contained 2 micromolar abaloparatide peptide. | |||||||||||||||||||||
Grid | Model: UltrAuFoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec. / Pretreatment - Atmosphere: AIR / Details: 20 mA current, negative polarity | |||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | TFS GLACIOS |
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Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Number grids imaged: 1 / Number real images: 2317 / Average exposure time: 8.29 sec. / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.3 µm / Nominal defocus min: 0.6 µm |
Sample stage | Cooling holder cryogen: NITROGEN |