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Yorodumi- PDB-8bv5: Focus refinement of soluble domain of Adenylyl cyclase 8 bound to... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bv5 | |||||||||
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Title | Focus refinement of soluble domain of Adenylyl cyclase 8 bound to stimulatory G protein, Forskolin, ATPalphaS, and Ca2+/Calmodulin in lipid nanodisc conditions | |||||||||
Components |
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Keywords | MEMBRANE PROTEIN / Adenylyl Cyclase / cAMP signaling / G proteins / Calmodulin | |||||||||
Function / homology | Function and homology information cellular response to morphine / Adenylate cyclase activating pathway / Adenylate cyclase inhibitory pathway / positive regulation of long-term synaptic depression / glucose mediated signaling pathway / calcium- and calmodulin-responsive adenylate cyclase activity / regulation of cellular response to stress / PKA activation / neuroinflammatory response / sensory perception of chemical stimulus ...cellular response to morphine / Adenylate cyclase activating pathway / Adenylate cyclase inhibitory pathway / positive regulation of long-term synaptic depression / glucose mediated signaling pathway / calcium- and calmodulin-responsive adenylate cyclase activity / regulation of cellular response to stress / PKA activation / neuroinflammatory response / sensory perception of chemical stimulus / adenylate cyclase / positive regulation of synaptic plasticity / Hedgehog 'off' state / cAMP biosynthetic process / adenylate cyclase activity / G alpha (z) signalling events / neuronal cell body membrane / cellular response to glucagon stimulus / presynaptic active zone / positive regulation of insulin secretion involved in cellular response to glucose stimulus / excitatory synapse / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / D1 dopamine receptor binding / long-term memory / beta-2 adrenergic receptor binding / adenylate cyclase-activating adrenergic receptor signaling pathway / regulation of cytosolic calcium ion concentration / adenylate cyclase activator activity / hippocampal mossy fiber to CA3 synapse / positive regulation of long-term synaptic potentiation / locomotory behavior / ionotropic glutamate receptor binding / insulin-like growth factor receptor binding / Schaffer collateral - CA1 synapse / G-protein beta/gamma-subunit complex binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / adenylate cyclase-activating dopamine receptor signaling pathway / heterotrimeric G-protein complex / presynaptic membrane / basolateral plasma membrane / postsynaptic density / intracellular signal transduction / apical plasma membrane / axon / GTPase activity / glutamatergic synapse / dendrite / GTP binding / ATP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.54 Å | |||||||||
Authors | Khanppnavar, B. / Korkhov, V.M. | |||||||||
Funding support | Switzerland, 2items
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Citation | Journal: EMBO Rep / Year: 2024 Title: Regulatory sites of CaM-sensitive adenylyl cyclase AC8 revealed by cryo-EM and structural proteomics. Authors: Basavraj Khanppnavar / Dina Schuster / Pia Lavriha / Federico Uliana / Merve Özel / Ved Mehta / Alexander Leitner / Paola Picotti / Volodymyr M Korkhov / Abstract: Membrane adenylyl cyclase AC8 is regulated by G proteins and calmodulin (CaM), mediating the crosstalk between the cAMP pathway and Ca signalling. Despite the importance of AC8 in physiology, the ...Membrane adenylyl cyclase AC8 is regulated by G proteins and calmodulin (CaM), mediating the crosstalk between the cAMP pathway and Ca signalling. Despite the importance of AC8 in physiology, the structural basis of its regulation by G proteins and CaM is not well defined. Here, we report the 3.5 Å resolution cryo-EM structure of the bovine AC8 bound to the stimulatory Gαs protein in the presence of Ca/CaM. The structure reveals the architecture of the ordered AC8 domains bound to Gαs and the small molecule activator forskolin. The extracellular surface of AC8 features a negatively charged pocket, a potential site for unknown interactors. Despite the well-resolved forskolin density, the captured state of AC8 does not favour tight nucleotide binding. The structural proteomics approaches, limited proteolysis and crosslinking mass spectrometry (LiP-MS and XL-MS), allowed us to identify the contact sites between AC8 and its regulators, CaM, Gαs, and Gβγ, as well as to infer the conformational changes induced by these interactions. Our results provide a framework for understanding the role of flexible regions in the mechanism of AC regulation. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bv5.cif.gz | 175.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bv5.ent.gz | 122.2 KB | Display | PDB format |
PDBx/mmJSON format | 8bv5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bv5_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8bv5_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8bv5_validation.xml.gz | 46.5 KB | Display | |
Data in CIF | 8bv5_validation.cif.gz | 66.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/8bv5 ftp://data.pdbj.org/pub/pdb/validation_reports/bv/8bv5 | HTTPS FTP |
-Related structure data
Related structure data | 16255MC 8buzC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 140192.328 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: ADCY8 / Production host: Homo sapiens (human) / References: UniProt: E1BQ12, adenylate cyclase |
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#2: Protein | Mass: 47003.801 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Gene: GNAS, GNAS1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P04896 |
#3: Chemical | ChemComp-FOK / |
#4: Chemical | ChemComp-GSP / |
#5: Chemical | ChemComp-MG / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Buffer solution | pH: 8 | ||||||||||||||||||||||||||||||
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277.15 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 55 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.54 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 150262 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE |