+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-27874 | ||||||||||||||||||
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Title | Cryo-EM structure of the VPAC1R-VIP-Gs complex | ||||||||||||||||||
Map data | Main consensus map of VPAC1R-VIP-Gs complex, postprocessed, -20 b-factor sharpened | ||||||||||||||||||
Sample |
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Keywords | membrane protein / drug discovery / G protein coupled receptor / signalling | ||||||||||||||||||
Function / homology | Function and homology information epinephrine secretion / prolactin secretion / body fluid secretion / vasoactive intestinal polypeptide receptor activity / neuropeptide hormone activity / G protein-coupled peptide receptor activity / mRNA stabilization / peptide hormone receptor binding / peptide hormone binding / PKA activation in glucagon signalling ...epinephrine secretion / prolactin secretion / body fluid secretion / vasoactive intestinal polypeptide receptor activity / neuropeptide hormone activity / G protein-coupled peptide receptor activity / mRNA stabilization / peptide hormone receptor binding / peptide hormone binding / PKA activation in glucagon signalling / G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger / hair follicle placode formation / developmental growth / D1 dopamine receptor binding / intracellular transport / Hedgehog 'off' state / adenylate cyclase-activating adrenergic receptor signaling pathway / activation of adenylate cyclase activity / adenylate cyclase activator activity / trans-Golgi network membrane / G-protein beta/gamma-subunit complex binding / bone development / Olfactory Signaling Pathway / Activation of the phototransduction cascade / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / G beta:gamma signalling through PLC beta / Presynaptic function of Kainate receptors / Thromboxane signalling through TP receptor / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G protein-coupled acetylcholine receptor signaling pathway / G-protein activation / hormone activity / 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 / cognition / platelet aggregation / ADP signalling through P2Y purinoceptor 12 / G beta:gamma signalling through BTK / Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Sensory perception of sweet, bitter, and umami (glutamate) taste / photoreceptor disc membrane / Adrenaline,noradrenaline inhibits insulin secretion / Glucagon-type ligand receptors / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / cellular response to catecholamine stimulus / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / sensory perception of taste / ADP signalling through P2Y purinoceptor 1 / positive regulation of protein catabolic process / adenylate cyclase-activating dopamine receptor signaling pathway / G beta:gamma signalling through PI3Kgamma / cellular response to prostaglandin E stimulus / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GPER1 signaling / regulation of protein localization / G-protein beta-subunit binding / Inactivation, recovery and regulation of the phototransduction cascade / heterotrimeric G-protein complex / G alpha (12/13) signalling events / extracellular vesicle / sensory perception of smell / signaling receptor complex adaptor activity / Thrombin signalling through proteinase activated receptors (PARs) / GTPase binding / retina development in camera-type eye / Ca2+ pathway / positive regulation of cold-induced thermogenesis / phospholipase C-activating G protein-coupled receptor signaling pathway / G alpha (i) signalling events / fibroblast proliferation / G alpha (s) signalling events / G alpha (q) signalling events / Ras protein signal transduction / cell population proliferation / Extra-nuclear estrogen signaling / cell surface receptor signaling pathway / receptor complex / neuron projection / G protein-coupled receptor signaling pathway / lysosomal membrane / GTPase activity / synapse / positive regulation of cell population proliferation / protein-containing complex binding / GTP binding / signal transduction / extracellular exosome / extracellular region / membrane / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Homo sapiens (human) / Lama glama (llama) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.7 Å | ||||||||||||||||||
Authors | Piper SJ / Danev R / Sexton P / Wootten D | ||||||||||||||||||
Funding support | Australia, United Kingdom, Japan, 5 items
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Citation | Journal: Nat Commun / Year: 2022 Title: Understanding VPAC receptor family peptide binding and selectivity. Authors: Sarah J Piper / Giuseppe Deganutti / Jessica Lu / Peishen Zhao / Yi-Lynn Liang / Yao Lu / Madeleine M Fletcher / Mohammed Akhter Hossain / Arthur Christopoulos / Christopher A Reynolds / ...Authors: Sarah J Piper / Giuseppe Deganutti / Jessica Lu / Peishen Zhao / Yi-Lynn Liang / Yao Lu / Madeleine M Fletcher / Mohammed Akhter Hossain / Arthur Christopoulos / Christopher A Reynolds / Radostin Danev / Patrick M Sexton / Denise Wootten / Abstract: The vasoactive intestinal peptide (VIP) and pituitary adenylate cyclase-activating polypeptide (PACAP) receptors are key regulators of neurological processes. Despite recent structural data, a ...The vasoactive intestinal peptide (VIP) and pituitary adenylate cyclase-activating polypeptide (PACAP) receptors are key regulators of neurological processes. Despite recent structural data, a comprehensive understanding of peptide binding and selectivity among different subfamily receptors is lacking. Here, we determine structures of active, Gs-coupled, VIP-VPAC1R, PACAP27-VPAC1R, and PACAP27-PAC1R complexes. Cryo-EM structural analyses and molecular dynamics simulations (MDSs) reveal fewer stable interactions between VPAC1R and VIP than for PACAP27, more extensive dynamics of VIP interaction with extracellular loop 3, and receptor-dependent differences in interactions of conserved N-terminal peptide residues with the receptor core. MD of VIP modelled into PAC1R predicts more transient VIP-PAC1R interactions in the receptor core, compared to VIP-VPAC1R, which may underlie the selectivity of VIP for VPAC1R over PAC1R. Collectively, our work improves molecular understanding of peptide engagement with the PAC1R and VPAC1R that may benefit the development of novel selective agonists. | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_27874.map.gz | 6.4 MB | EMDB map data format | |
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Header (meta data) | emd-27874-v30.xml emd-27874.xml | 32 KB 32 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_27874_fsc.xml | 10.2 KB | Display | FSC data file |
Images | emd_27874.png | 79.4 KB | ||
Masks | emd_27874_msk_1.map | 91.1 MB | Mask map | |
Filedesc metadata | emd-27874.cif.gz | 7.3 KB | ||
Others | emd_27874_additional_1.map.gz emd_27874_additional_2.map.gz emd_27874_additional_3.map.gz emd_27874_additional_4.map.gz emd_27874_half_map_1.map.gz emd_27874_half_map_2.map.gz | 71.4 MB 2.9 MB 7.7 MB 44.2 MB 71.7 MB 71.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-27874 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-27874 | HTTPS FTP |
-Related structure data
Related structure data | 8e3zMC 8e3xC 8e3yC 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_27874.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Main consensus map of VPAC1R-VIP-Gs complex, postprocessed, -20 b-factor sharpened | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.83 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_27874_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: Consensus map of VPAC1R-VIP-Gs complex, refinement map
File | emd_27874_additional_1.map | ||||||||||||
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Annotation | Consensus map of VPAC1R-VIP-Gs complex, refinement map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Receptor-focused map of VPAC1R-VIP-Gs complex, postprocessed, -25 b-factor...
File | emd_27874_additional_2.map | ||||||||||||
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Annotation | Receptor-focused map of VPAC1R-VIP-Gs complex, postprocessed, -25 b-factor sharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Consensus map of VPAC1R-VIP-Gs complex, postprocessed, auto b-factor...
File | emd_27874_additional_3.map | ||||||||||||
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Annotation | Consensus map of VPAC1R-VIP-Gs complex, postprocessed, auto b-factor sharpened | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: CryoSPARC Non-uniform refinement, Consensus map of VPAC1R-VIP-Gs complex...
File | emd_27874_additional_4.map | ||||||||||||
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Annotation | CryoSPARC Non-uniform refinement, Consensus map of VPAC1R-VIP-Gs complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 of consensus map of VPAC1R-VIP-Gs complex
File | emd_27874_half_map_1.map | ||||||||||||
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Annotation | Half map 1 of consensus map of VPAC1R-VIP-Gs complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half map 1 of consensus map of VPAC1R-VIP-Gs complex
File | emd_27874_half_map_2.map | ||||||||||||
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Annotation | Half map 1 of consensus map of VPAC1R-VIP-Gs complex | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Gs coupled Vasoactive intestinal polypeptide receptor 1 (VPAC1) c...
+Supramolecule #1: Gs coupled Vasoactive intestinal polypeptide receptor 1 (VPAC1) c...
+Supramolecule #2: Guanine nucleotide-binding protein G(s) subunit alpha isoforms sh...
+Supramolecule #3: Nanobody35
+Supramolecule #4: Vasoactive Intestinal Peptide-VIP
+Macromolecule #1: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
+Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
+Macromolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
+Macromolecule #4: Nanobody 35
+Macromolecule #5: Vasoactive intestinal peptide
+Macromolecule #6: Vasoactive intestinal polypeptide receptor 1
+Macromolecule #7: water
-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 |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Detector mode: COUNTING / Average electron dose: 47.0 e/Å2 Details: Movies were collected in two sets with 64.9 e-/A2 dose (1134 movies) and 47 e-/A2 dose (4329 movies) and combined in the data processing. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 µm / Nominal defocus min: 0.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |