[English] 日本語
Yorodumi
- EMDB-57526: Cryo-EM map of the occluded-state full-length human Adenylyl cycl... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-57526
TitleCryo-EM map of the occluded-state full-length human Adenylyl cyclase 9 in complex with stimulatory G protein, ATPalphaS, and forskolin
Map data
Sample
  • Complex: Cryo-EM map of the occluded-state 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 / cAMP synthesis / MEMBRANE PROTEIN
Biological speciesHomo sapiens (human) / Bos taurus (domestic cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.32 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

-
Structure visualization

Supplemental images

emd_57526.png

Downloads & links

-
Map

FileDownload / File: emd_57526.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.65 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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0998
Minimum - Maximum-0.73293763 - 0.93687344
Average (Standard dev.)-0.000032830998 (±0.016480217)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Half map: #1

Fileemd_57526_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: #2

Fileemd_57526_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Cryo-EM map of the occluded-state full-length human Adenylyl cycl...

EntireName: Cryo-EM map of the occluded-state full-length human Adenylyl cyclase 9 in complex with stimulatory G protein, ATPalphaS, and forskolin
Components
  • Complex: Cryo-EM map of the occluded-state 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

-
Supramolecule #1: Cryo-EM map of the occluded-state full-length human Adenylyl cycl...

SupramoleculeName: Cryo-EM map of the occluded-state 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)

-
Supramolecule #2: Human Adenylyl Cyclase 9

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

-
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)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

-
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

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.32 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 190827
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more