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- EMDB-57527: Cryo-EM map of the ATPalphaS-bound full-length human Adenylyl cyc... -

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Basic information

Entry
Database: EMDB / ID: EMD-57527
TitleCryo-EM map of the ATPalphaS-bound full-length human Adenylyl cyclase 9 in complex with stimulatory G protein, ATPalphaS, and forskolin
Map data
Sample
  • Complex: Cryo-EM map of the ATPalphaS-bound full-length human adenylyl cyclase 9 in complex with stimulatory G protein, ATPalphaS, and forskolin
    • Complex: Human Adenylyl Cyclase 9
    • Complex: Guanine nucleotide-binding protein G(s) subunit alpha
KeywordsMembrane bound adenylyl cyclase / Adenylyl cyclase 9 / G protein signaling / ATPalphaS / forskolin / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human) / Bos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.68 Å
AuthorsKantarci I / Korkhov VM
Funding support Switzerland, 1 items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
CitationJournal: Protein Sci / Year: 2026
Title: Adenylyl cyclase 9 as a molecular scaffold to dissect the mechanisms of membrane adenylyl cyclases.
Authors: Ilayda Kantarci / Haoriwa Haoriwa / Volodymyr M Korkhov /
Abstract: Adenylyl cyclases (ACs) convert ATP into the second messenger cAMP, thus directly influencing cellular signaling in response to a wide variety of stimuli. Despite their physiological importance, ...Adenylyl cyclases (ACs) convert ATP into the second messenger cAMP, thus directly influencing cellular signaling in response to a wide variety of stimuli. Despite their physiological importance, structural studies of isoform-specific AC regulation are compounded by difficulties in AC expression and purification. Here, we designed a chimeric construct AC95, combining human AC9 as a molecular scaffold and incorporating the catalytic-allosteric core of human AC5. Cryo-EM analysis of AC95 at 3.5 Å resolution revealed a state of AC95 bound to both ATPαS and forskolin, demonstrating that the chimera partially reproduces allosteric regulation by forskolin while retaining the structural features of the AC9 scaffold. Although AC95 chimera retained the ability to bind to and be activated by forskolin, it lost the ability to be autoinhibited by the C2b domain of AC9. Moreover, AC95 is insensitive to inhibition by AC5 inhibitors SQ22,536 and NKY80, due to either targeting a site distinct from the catalytic-allosteric core of AC5, altered conformational dynamics or long-range allosteric effects imposed by chimeric scaffold, or a requirement for additional AC5 features absent in AC95. Our results establish an approach for investigating isoform-specific regulation of mammalian ACs by small molecules, offering a potential path for structure-based drug discovery targeting distinct AC isoforms.
History
DepositionApr 19, 2026-
Header (metadata) releaseSep 30, 2026-
Map releaseSep 30, 2026-
UpdateSep 30, 2026-
Current statusSep 30, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_57527.png

Downloads & links

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Map

FileDownload / File: emd_57527.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.65 Å/pix.
x 500 pix.
= 325. Å		0.65 Å/pix.
x 500 pix.
= 325. Å		0.65 Å/pix.
x 500 pix.
= 325. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0799
Minimum - Maximum-0.50434685 - 0.7521909
Average (Standard dev.)0.000052023337 (±0.01068063)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 325.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_57527_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_57527_half_map_2.map
Projections & Slices
AxesZYX

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Histogram

Histogram (log scale)

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Sample components

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Entire : Cryo-EM map of the ATPalphaS-bound full-length human adenylyl cyc...

EntireName: Cryo-EM map of the ATPalphaS-bound full-length human adenylyl cyclase 9 in complex with stimulatory G protein, ATPalphaS, and forskolin
Components
  • Complex: Cryo-EM map of the ATPalphaS-bound full-length human adenylyl cyclase 9 in complex with stimulatory G protein, ATPalphaS, and forskolin
    • Complex: Human Adenylyl Cyclase 9
    • Complex: Guanine nucleotide-binding protein G(s) subunit alpha

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Supramolecule #1: Cryo-EM map of the ATPalphaS-bound full-length human adenylyl cyc...

SupramoleculeName: Cryo-EM map of the ATPalphaS-bound full-length human adenylyl cyclase 9 in complex with stimulatory G protein, ATPalphaS, and forskolin
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: Human Adenylyl Cyclase 9

SupramoleculeName: Human Adenylyl Cyclase 9 / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: Guanine nucleotide-binding protein G(s) subunit alpha

SupramoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Bos taurus (domestic cattle)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.68 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 134651
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

Initial model
PDB IDChain

6r3q

source_name: PDB, initial_model_type: experimental model

1-v6

source_name: AlphaFold, initial_model_type: in silico model
RefinementProtocol: RIGID BODY FIT

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