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- PDB-6r3q: The structure of a membrane adenylyl cyclase bound to an activate... -

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Basic information

Entry
Database: PDB / ID: 6r3q
TitleThe structure of a membrane adenylyl cyclase bound to an activated stimulatory G protein
Components
  • Adenylate cyclase 9Adenylyl cyclase
  • Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
KeywordsMEMBRANE PROTEIN / adenylyl cyclase / G protein / occluded state
Function / homology
Function and homology information


corticotropin-releasing hormone receptor 1 binding / sensory perception of chemical stimulus / mu-type opioid receptor binding / cAMP biosynthetic process / adenylate cyclase activity / adenylate cyclase-activating adrenergic receptor signaling pathway / positive regulation of cAMP-mediated signaling / adenylate cyclase-activating dopamine receptor signaling pathway / D1 dopamine receptor binding / beta-2 adrenergic receptor binding ...corticotropin-releasing hormone receptor 1 binding / sensory perception of chemical stimulus / mu-type opioid receptor binding / cAMP biosynthetic process / adenylate cyclase activity / adenylate cyclase-activating adrenergic receptor signaling pathway / positive regulation of cAMP-mediated signaling / adenylate cyclase-activating dopamine receptor signaling pathway / D1 dopamine receptor binding / beta-2 adrenergic receptor binding / G-protein beta/gamma-subunit complex binding / heterotrimeric G-protein complex / adenylate cyclase activator activity / ionotropic glutamate receptor binding / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase-activating G protein-coupled receptor signaling pathway / G protein-coupled receptor binding / insulin-like growth factor receptor binding / positive regulation of GTPase activity / in utero embryonic development / GTPase activity / GTP binding / nucleotide binding / integral component of plasma membrane / metal ion binding
G-protein alpha subunit / Nucleotide cyclase / P-loop containing nucleoside triphosphate hydrolase / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / G protein alpha subunit, helical insertion / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit, group S / Adenylate and Guanylate cyclase catalytic domain / GI Alpha 1, domain 2-like ...G-protein alpha subunit / Nucleotide cyclase / P-loop containing nucleoside triphosphate hydrolase / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / G protein alpha subunit, helical insertion / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit, group S / Adenylate and Guanylate cyclase catalytic domain / GI Alpha 1, domain 2-like / GI Alpha 1, domain 2-like / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Adenylate cyclase 9
Biological speciesBos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsKorkhov, V.M. / Qi, C.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation150665 Switzerland
CitationJournal: 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 20, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Refinement description / Category: em_3d_fitting / em_image_scans / Item: _em_3d_fitting.target_criteria

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Assembly

Deposited unit
A: Adenylate cyclase 9
B: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
hetero molecules


Theoretical massNumber of molelcules
Total (without water)229,9014
Polymers229,3372
Non-polymers5642
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area3020 Å2
ΔGint-28 kcal/mol
Surface area57380 Å2
MethodPISA

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Components

#1: Protein Adenylate cyclase 9 / Adenylyl cyclase / Adenylyl CYclase family member (Acy-1)-like


Mass: 182404.422 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: ADCY9, BOS_22626 / Plasmid: pUH3 / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: E1BM79
#2: Protein Guanine nucleotide-binding protein G(s) subunit alpha isoforms short / Adenylate cyclase-stimulating G alpha protein


Mass: 46932.727 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
#3: Chemical ChemComp-GSP / 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE


Mass: 539.246 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3S
#4: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Complex of adenylyl cyclase AC9 with G protein subunit GalphasCOMPLEX1, 20MULTIPLE SOURCES
2Adenylate cyclase 9Adenylyl cyclaseCOMPLEX11RECOMBINANT
3Guanine nucleotide-binding protein G(s) subunit alpha isoforms shortCOMPLEX21RECOMBINANT
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
22Bos taurus (cattle)9913
33Bos taurus (cattle)9913
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCell
22Homo sapiens (human)9606HEK293F
33Trichoplusia ni (cabbage looper)7111
Buffer solutionpH: 8
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 278 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 750 nm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 8 sec. / Electron dose: 47 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Num. of real images: 5817

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Processing

EM software
IDNameVersionCategory
1RELION2.1.0particle selection
2SerialEMimage acquisition
4GctfCTF correction
7Coot0.8.9.1model fitting
9RELION2.1.0initial Euler assignment
10RELION2.1.0final Euler assignment
11RELION2.1.0classification
12RELION2.1.03D reconstruction
13PHENIX1.11.1model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 656817
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 170456 / Symmetry type: POINT
Atomic model buildingB value: 110.92 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient

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