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Yorodumi- EMDB-22872: Cryo-EM structure of the human arginine vasopressin AVP-vasopress... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-22872 | |||||||||
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Title | Cryo-EM structure of the human arginine vasopressin AVP-vasopressin receptor V2R-Gs signaling complex | |||||||||
Map data | V2R unsharpen map | |||||||||
Sample |
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Function / homology | Function and homology information V1B vasopressin receptor binding / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / Defective AVP does not bind AVPR1A,B and causes neurohypophyseal diabetes insipidus (NDI) / maternal aggressive behavior / Vasopressin-like receptors / neurohypophyseal hormone activity / V1A vasopressin receptor binding / Transport of organic anions / penile erection / regulation of renal sodium excretion ...V1B vasopressin receptor binding / Defective AVP does not bind AVPR2 and causes neurohypophyseal diabetes insipidus (NDI) / Defective AVP does not bind AVPR1A,B and causes neurohypophyseal diabetes insipidus (NDI) / maternal aggressive behavior / Vasopressin-like receptors / neurohypophyseal hormone activity / V1A vasopressin receptor binding / Transport of organic anions / penile erection / regulation of renal sodium excretion / negative regulation of transmission of nerve impulse / negative regulation of female receptivity / protein kinase C signaling / hyperosmotic salinity response / positive regulation of systemic arterial blood pressure / water transport / positive regulation of prostaglandin biosynthetic process / grooming behavior / membrane organization / negative regulation of adenylate cyclase activity / neuropeptide hormone activity / maternal behavior / positive regulation of glutamate secretion / vasoconstriction / renal water homeostasis / GTP metabolic process / G protein-coupled dopamine receptor signaling pathway / negative regulation of release of cytochrome c from mitochondria / response to testosterone / cysteine-type endopeptidase inhibitor activity involved in apoptotic process / social behavior / positive regulation of macroautophagy / Adenylate cyclase inhibitory pathway / negative regulation of inflammatory response to antigenic stimulus / positive regulation of vasoconstriction / ERK1 and ERK2 cascade / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / positive regulation of cellular pH reduction / G-protein beta/gamma-subunit complex binding / : / BMAL1:CLOCK,NPAS2 activates circadian gene expression / secretory granule / generation of precursor metabolites and energy / G protein-coupled receptor binding / locomotory behavior / response to nicotine / clathrin-coated endocytic vesicle membrane / 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 / 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 / Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding / GDP binding / 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 / extracellular vesicle / Cargo recognition for clathrin-mediated endocytosis / signaling receptor complex adaptor activity / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / Thrombin signalling through proteinase activated receptors (PARs) / cell-cell signaling / positive regulation of peptidyl-serine phosphorylation / GTPase binding / Clathrin-mediated endocytosis / retina development in camera-type eye / Ca2+ pathway / phospholipase C-activating G protein-coupled receptor signaling pathway / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / midbody / fibroblast proliferation Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Lama glama (llama) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Wang L / Xu J / Gao S / Sun D / Liu H / Liu Z / Du Y / Zhang C | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Cell Res / Year: 2021 Title: Cryo-EM structure of the AVP-vasopressin receptor 2-G signaling complex. Authors: Lei Wang / Jun Xu / Sheng Cao / Dapeng Sun / Heng Liu / Qiuyuan Lu / Zheng Liu / Yang Du / Cheng Zhang / | |||||||||
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_22872.map.gz | 32.2 MB | EMDB map data format | |
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Header (meta data) | emd-22872-v30.xml emd-22872.xml | 18.5 KB 18.5 KB | Display Display | EMDB header |
Images | emd_22872.png | 127.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-22872 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-22872 | HTTPS FTP |
-Validation report
Summary document | emd_22872_validation.pdf.gz | 398.7 KB | Display | EMDB validaton report |
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Full document | emd_22872_full_validation.pdf.gz | 398.2 KB | Display | |
Data in XML | emd_22872_validation.xml.gz | 6.3 KB | Display | |
Data in CIF | emd_22872_validation.cif.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22872 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-22872 | HTTPS FTP |
-Related structure data
Related structure data | 7kh0MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_22872.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | V2R unsharpen map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Vasopressin V2 receptor complex with Gs and AVP
+Supramolecule #1: Vasopressin V2 receptor complex with Gs and AVP
+Supramolecule #2: Vasopressin V2 receptor, Arg-vasopressin
+Supramolecule #3: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1,...
+Supramolecule #4: Nanobody 35
+Macromolecule #1: Vasopressin V2 receptor
+Macromolecule #2: Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1
+Macromolecule #3: Guanine nucleotide-binding protein G(i) subunit alpha-3, Isoform ...
+Macromolecule #4: Arg-vasopressin
+Macromolecule #5: Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2
+Macromolecule #6: Single Fab chain (scFv16)
+Macromolecule #7: Nanobody 35
-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: OTHER |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 398038 |
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Initial angle assignment | Type: OTHER |
Final angle assignment | Type: OTHER |