+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0993 | ||||||||||||||||||
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Title | Cryo-EM map of PAC1 receptor bound to PACAP38 and Gs protein | ||||||||||||||||||
Map data | Sharpened map of PAC1 receptor bound to PACAP38 and Gs protein | ||||||||||||||||||
Sample |
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Function / homology | Function and homology information negative regulation of response to reactive oxygen species / development of primary female sexual characteristics / vasoactive intestinal polypeptide receptor activity / NGF-independant TRKA activation / neuropeptide binding / G protein-coupled peptide receptor activity / positive regulation of small GTPase mediated signal transduction / positive regulation of inositol phosphate biosynthetic process / positive regulation of calcium ion transport into cytosol / PKA activation in glucagon signalling ...negative regulation of response to reactive oxygen species / development of primary female sexual characteristics / vasoactive intestinal polypeptide receptor activity / NGF-independant TRKA activation / neuropeptide binding / G protein-coupled peptide receptor activity / positive regulation of small GTPase mediated signal transduction / positive regulation of inositol phosphate biosynthetic process / positive regulation of calcium ion transport into cytosol / PKA activation in glucagon signalling / peptide hormone binding / cAMP-mediated signaling / hair follicle placode formation / adenylate cyclase binding / intracellular transport / D1 dopamine receptor binding / developmental growth / bicellular tight junction / multicellular organismal response to stress / Hedgehog 'off' state / positive regulation of cAMP-mediated signaling / adenylate cyclase-activating adrenergic receptor signaling pathway / activation of adenylate cyclase activity / adenylate cyclase activator activity / trans-Golgi network membrane / caveola / G-protein beta/gamma-subunit complex binding / Olfactory Signaling Pathway / Activation of the phototransduction cascade / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / bone development / G-protein activation / G protein-coupled acetylcholine receptor signaling pathway / Activation of G protein gated Potassium channels / Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits / Prostacyclin signalling through prostacyclin receptor / Glucagon signaling in metabolic regulation / G beta:gamma signalling through CDC42 / adenylate cyclase-activating G protein-coupled receptor signaling pathway / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Sensory perception of sweet, bitter, and umami (glutamate) taste / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / platelet aggregation / small GTPase binding / Glucagon-type ligand receptors / cognition / Vasopressin regulates renal water homeostasis via Aquaporins / positive regulation of GTPase activity / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / ADP signalling through P2Y purinoceptor 1 / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / sensory perception of taste / GPER1 signaling / G-protein beta-subunit binding / heterotrimeric G-protein complex / Inactivation, recovery and regulation of the phototransduction cascade / extracellular vesicle / G alpha (12/13) signalling events / signaling receptor complex adaptor activity / sensory perception of smell / Thrombin signalling through proteinase activated receptors (PARs) / response to estradiol / retina development in camera-type eye / signaling receptor activity / GTPase binding / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cold-induced thermogenesis / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / spermatogenesis / response to ethanol / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / cell differentiation / cell surface receptor signaling pathway / receptor complex / endosome / response to xenobiotic stimulus / G protein-coupled receptor signaling pathway / lysosomal membrane / intracellular membrane-bounded organelle / GTPase activity / synapse / protein-containing complex binding Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.65 Å | ||||||||||||||||||
Authors | Liang YL / Belousoff MJ / Zhao P / Danev R / Sexton PM / Wootten D | ||||||||||||||||||
Funding support | Australia, Japan, 5 items
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Citation | Journal: Mol Cell / Year: 2020 Title: Toward a Structural Understanding of Class B GPCR Peptide Binding and Activation. Authors: Yi-Lynn Liang / Matthew J Belousoff / Peishen Zhao / Cassandra Koole / Madeleine M Fletcher / Tin T Truong / Villy Julita / George Christopoulos / H Eric Xu / Yan Zhang / Maryam Khoshouei / ...Authors: Yi-Lynn Liang / Matthew J Belousoff / Peishen Zhao / Cassandra Koole / Madeleine M Fletcher / Tin T Truong / Villy Julita / George Christopoulos / H Eric Xu / Yan Zhang / Maryam Khoshouei / Arthur Christopoulos / Radostin Danev / Patrick M Sexton / Denise Wootten / Abstract: Class B G protein-coupled receptors (GPCRs) are important therapeutic targets for major diseases. Here, we present structures of peptide and Gs-bound pituitary adenylate cyclase-activating peptide, ...Class B G protein-coupled receptors (GPCRs) are important therapeutic targets for major diseases. Here, we present structures of peptide and Gs-bound pituitary adenylate cyclase-activating peptide, PAC1 receptor, and corticotropin-releasing factor (CRF), (CRF1) receptor. Together with recently solved structures, these provide coverage of the major class B GPCR subfamilies. Diverse orientations of the extracellular domain to the receptor core in different receptors are at least partially dependent on evolutionary conservation in the structure and nature of peptide interactions. Differences in peptide interactions to the receptor core also influence the interlinked TM2-TM1-TM6/ECL3/TM7 domain, and this is likely important in their diverse signaling. However, common conformational reorganization of ECL2, linked to reorganization of ICL2, modulates G protein contacts. Comparison between receptors reveals ICL2 as a key domain forming dynamic G protein interactions in a receptor- and ligand-specific manner. This work advances our understanding of class B GPCR activation and Gs coupling. | ||||||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0993.map.gz | 19.5 MB | EMDB map data format | |
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Header (meta data) | emd-0993-v30.xml emd-0993.xml | 20.4 KB 20.4 KB | Display Display | EMDB header |
Images | emd_0993.png | 121.4 KB | ||
Masks | emd_0993_msk_1.map | 20.8 MB | Mask map | |
Others | emd_0993_additional.map.gz emd_0993_additional_1.map.gz emd_0993_half_map_1.map.gz emd_0993_half_map_2.map.gz | 15.8 MB 15.8 MB 15.8 MB 15.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0993 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0993 | HTTPS FTP |
-Related structure data
Related structure data | 6p9xC 6p9yC C: citing same article (ref.) |
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Similar structure data | |
EM raw data | EMPIAR-10359 (Title: Cryo-EM of PAC1 receptor bound to PACAP38 and Gs protein Data size: 4.8 TB Data #1: Unaligned multi-frame gain-normalized movies in LZW compressed TIFF format [micrographs - multiframe]) |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0993.map.gz / Format: CCP4 / Size: 20.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Sharpened map of PAC1 receptor bound to PACAP38 and Gs protein | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.207 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_0993_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Unprocessed map of PAC1 receptor bound to PACAP38 and Gs protein
File | emd_0993_additional.map | ||||||||||||
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Annotation | Unprocessed map of PAC1 receptor bound to PACAP38 and Gs protein | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Unprocessed map of PAC1 receptor bound to PACAP38 and Gs protein
File | emd_0993_additional_1.map | ||||||||||||
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Annotation | Unprocessed map of PAC1 receptor bound to PACAP38 and Gs protein | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unprocessed half-map of PAC1 receptor bound to PACAP38 and Gs protein
File | emd_0993_half_map_1.map | ||||||||||||
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Annotation | Unprocessed half-map of PAC1 receptor bound to PACAP38 and Gs protein | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Unprocessed half-map of PAC1 receptor bound to PACAP38 and Gs protein
File | emd_0993_half_map_2.map | ||||||||||||
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Annotation | Unprocessed half-map of PAC1 receptor bound to PACAP38 and Gs protein | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : PAC1 receptor bound to PACAP38 and Gs protein
Entire | Name: PAC1 receptor bound to PACAP38 and Gs protein |
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Components |
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-Supramolecule #1: PAC1 receptor bound to PACAP38 and Gs protein
Supramolecule | Name: PAC1 receptor bound to PACAP38 and Gs protein / type: complex / ID: 1 / Parent: 0 |
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Source (natural) | Organism: Homo sapiens (human) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Molecular weight | Theoretical: 150 kDa/nm |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 4.35 mg/mL |
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Buffer | pH: 7.4 |
Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER/RHODIUM / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: blot time 10 s. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | C2 aperture diameter: 50.0 µm / Calibrated defocus max: 1.6 µm / Calibrated defocus min: 0.4 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.4 µm / Nominal magnification: 105000 |
Specialist optics | Phase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF Quantum LS / Energy filter - Slit width: 25 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 7650 / Average exposure time: 3.715 sec. / Average electron dose: 64.0 e/Å2 Details: Volta phase plate images: 4032; Conventional defocus images: 3618 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 5500000 |
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CTF correction | Software - Name: Gctf |
Startup model | Type of model: OTHER Details: 20A low-pass filtered GPCR map from previous experiment. |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION / Software - details: 3 |
Final 3D classification | Number classes: 3 / Software - Name: RELION / Software - details: 3 |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION / Software - details: 3 |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.65 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Software - details: 3 / Number images used: 390000 |