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Yorodumi- PDB-6r4o: Structure of a truncated adenylyl cyclase bound to MANT-GTP, fors... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6r4o | ||||||
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Title | Structure of a truncated adenylyl cyclase bound to MANT-GTP, forskolin and an activated stimulatory Galphas protein | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Adenylyl cyclase / G protein / MANT-GTP / forskolin | ||||||
Function / homology | Function and homology information Adenylate cyclase activating pathway / Adenylate cyclase inhibitory pathway / sensory perception of chemical stimulus / PKA activation / adenylate cyclase / mu-type opioid receptor binding / Hedgehog 'off' state / corticotropin-releasing hormone receptor 1 binding / cAMP biosynthetic process / adenylate cyclase activity ...Adenylate cyclase activating pathway / Adenylate cyclase inhibitory pathway / sensory perception of chemical stimulus / PKA activation / adenylate cyclase / mu-type opioid receptor binding / Hedgehog 'off' state / corticotropin-releasing hormone receptor 1 binding / cAMP biosynthetic process / adenylate cyclase activity / G alpha (z) signalling events / beta-2 adrenergic receptor binding / D1 dopamine receptor binding / adenylate cyclase-activating adrenergic receptor signaling pathway / insulin-like growth factor receptor binding / adenylate cyclase activator activity / ionotropic glutamate receptor binding / 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 / in utero embryonic development / intracellular signal transduction / GTPase activity / GTP binding / ATP binding / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.2 Å | ||||||
Authors | Qi, C. / Sorrentino, S. / Medalia, O. / Korkhov, V.M. | ||||||
Funding support | Switzerland, 1items
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Citation | Journal: Science / Year: 2019 Title: The structure of a membrane adenylyl cyclase bound to an activated stimulatory G protein. Authors: Chao Qi / Simona Sorrentino / Ohad Medalia / Volodymyr M Korkhov / Abstract: Membrane-integral adenylyl cyclases (ACs) are key enzymes in mammalian heterotrimeric GTP-binding protein (G protein)-dependent signal transduction, which is important in many cellular processes. ...Membrane-integral adenylyl cyclases (ACs) are key enzymes in mammalian heterotrimeric GTP-binding protein (G protein)-dependent signal transduction, which is important in many cellular processes. Signals received by the G protein-coupled receptors are conveyed to ACs through G proteins to modulate the levels of cellular cyclic adenosine monophosphate (cAMP). Here, we describe the cryo-electron microscopy structure of the bovine membrane AC9 bound to an activated G protein αs subunit at 3.4-angstrom resolution. The structure reveals the organization of the membrane domain and helical domain that spans between the membrane and catalytic domains of AC9. The carboxyl-terminal extension of the catalytic domain occludes both the catalytic and the allosteric sites of AC9, inducing a conformation distinct from the substrate- and activator-bound state, suggesting a regulatory role in cAMP production. #1: Journal: To Be Published Title: The structure of a membrane adenylyl cyclase bound to an activated stimulatory G protein Authors: Qi, C. / Sorrentino, S. / Medalia, O. / Korkhov, V.M. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6r4o.cif.gz | 246.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r4o.ent.gz | 183.9 KB | Display | PDB format |
PDBx/mmJSON format | 6r4o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6r4o_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6r4o_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 6r4o_validation.xml.gz | 45.6 KB | Display | |
Data in CIF | 6r4o_validation.cif.gz | 66.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r4/6r4o ftp://data.pdbj.org/pub/pdb/validation_reports/r4/6r4o | HTTPS FTP |
-Related structure data
Related structure data | 4721MC 4719C 4722C 4723C 4724C 4725C 4726C 6r3qC 6r4pC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 170951.953 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: Bovine AC9, residues 1-1250, tagged with 3C-YFP-twinStrep tag Source: (gene. exp.) Bos taurus (cattle) / Gene: ADCY9, BOS_22626 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: E1BM79 |
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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 / Cell line (production host): High Five / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P04896 |
-Non-polymers , 5 types, 6 molecules
#3: Chemical | ChemComp-ONM / | ||||
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#4: Chemical | ChemComp-FOK / | ||||
#5: Chemical | #6: Chemical | ChemComp-GSP / | #7: Chemical | ChemComp-MG / | |
-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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Source (recombinant) |
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Buffer solution | pH: 8 | ||||||||||||||||||||||||
Specimen | 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: 278 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: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 60 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of grids imaged: 2 / Num. of real images: 10758 Details: Two datasets were merged using two different microscopes, using pixel size of 0.831 A/pix (4453 micrographs; 60 e-/A2) and 0.8544 A/pix (6305 micrographs; 45 e-/A2). Final dataset was scaled to 0.8544 A/pix. |
-Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 1107881 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 142147 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | B value: 110.92 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient |