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- EMDB-4722: Structure of a soluble domain of adenylyl cyclase bound to an act... -

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Basic information

Entry
Database: EMDB / ID: EMD-4722
TitleStructure of a soluble domain of adenylyl cyclase bound to an activated stimulatory G protein
Map data
SampleComplex of adenylyl cyclase AC9 with G protein subunit Galphas
  • (Adenylate cyclase ...Adenylyl cyclase) x 2
  • (Guanine nucleotide-binding protein G(s) subunit alpha isoforms ...) x 2
  • (ligand) x 2
Function / homology
Function and homology information


G alpha (z) signalling events / Glucagon signaling in metabolic regulation / PKA activation / PKA activation in glucagon signalling / Adenylate cyclase activating pathway / Adenylate cyclase inhibitory pathway / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (s) signalling events / Hedgehog 'off' state / corticotropin-releasing hormone receptor 1 binding ...G alpha (z) signalling events / Glucagon signaling in metabolic regulation / PKA activation / PKA activation in glucagon signalling / Adenylate cyclase activating pathway / Adenylate cyclase inhibitory pathway / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (s) signalling events / Hedgehog 'off' state / corticotropin-releasing hormone receptor 1 binding / cyclic nucleotide biosynthetic process / mu-type opioid receptor binding / adenylate cyclase-activating adrenergic receptor signaling pathway / adenylate cyclase activity / adenylate cyclase-activating dopamine receptor signaling pathway / positive regulation of cAMP-mediated signaling / D1 dopamine receptor binding / G-protein beta/gamma-subunit complex binding / beta-2 adrenergic receptor binding / heterotrimeric G-protein complex / adenylate cyclase-modulating G protein-coupled receptor signaling pathway / adenylate cyclase activator activity / ionotropic glutamate receptor binding / G protein-coupled receptor binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / insulin-like growth factor receptor binding / positive regulation of GTPase activity / GTPase activity / GTP binding / nucleotide binding / integral component of plasma membrane / metal ion binding
G-protein alpha subunit, group S / G-protein alpha subunit / Adenylyl cyclase class-3/4/guanylyl cyclase / G protein alpha subunit, helical insertion / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / P-loop containing nucleoside triphosphate hydrolase / Nucleotide cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase signature. / Guanylate cyclase domain profile. ...G-protein alpha subunit, group S / G-protein alpha subunit / Adenylyl cyclase class-3/4/guanylyl cyclase / G protein alpha subunit, helical insertion / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / P-loop containing nucleoside triphosphate hydrolase / Nucleotide cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase signature. / Guanylate cyclase domain profile. / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit
Adenylyl CYclase family member (Acy-1)-like / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
SourceBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKorkhov VM / Qi C
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 ReportPDB-ID: 6r4p

SummaryFull reportAbout validation report
DateDeposition: Mar 22, 2019 / Header (metadata) release: May 8, 2019 / Map release: May 8, 2019 / Update: May 8, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6r4p
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_4722.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 300 pix.
= 244.2 Å
0.81 Å/pix.
x 300 pix.
= 244.2 Å
0.81 Å/pix.
x 300 pix.
= 244.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.814 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.059749633 - 0.1378849
Average (Standard dev.)0.00023670131 (±0.0031314131)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 244.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.8140.8140.814
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z244.200244.200244.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0600.1380.000

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Supplemental data

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Sample components

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Entire Complex of adenylyl cyclase AC9 with G protein subunit Galphas

EntireName: Complex of adenylyl cyclase AC9 with G protein subunit Galphas
Number of components: 7

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Component #1: protein, Complex of adenylyl cyclase AC9 with G protein subunit G...

ProteinName: Complex of adenylyl cyclase AC9 with G protein subunit Galphas
Recombinant expression: No

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Component #2: protein, Adenylate cyclase 9

ProteinName: Adenylate cyclase 9Adenylyl cyclase / Recombinant expression: No
SourceSpecies: Bos taurus (cattle)
Source (engineered)Expression System: Homo sapiens (human) / Vector: pEZT-BM / Cell of expression system: HEK293F

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Component #3: protein, Guanine nucleotide-binding protein G(s) subunit alpha is...

ProteinName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
Recombinant expression: No
SourceSpecies: Bos taurus (cattle)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper) / Vector: pFastbac / Cell of expression system: High Five

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Component #4: protein, Adenylate cyclase 9

ProteinName: Adenylate cyclase 9Adenylyl cyclase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 182.404422 kDa
SourceSpecies: Bos taurus (cattle)
Source (engineered)Expression System: Homo sapiens (human)

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Component #5: protein, Guanine nucleotide-binding protein G(s) subunit alpha is...

ProteinName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 46.932727 kDa
SourceSpecies: Bos taurus (cattle)
Source (engineered)Expression System: Trichoplusia ni (cabbage looper)

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Component #6: ligand, 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE

LigandName: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 0.539246 kDa

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Component #7: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 278 K / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 47 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD / Defocus: 750.0 - 2500.0 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 QUANTUM (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 5817

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 170456
3D reconstructionSoftware: RELION / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF
Details: Masked refinement in relion continued after the last iteration, using a mask excluding the micelle and the membrane portion of the complex.
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Target criteria: Correlation coefficient / Refinement space: REAL / Overall bvalue: 86.68
Output model

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