[English] 日本語
Yorodumi
- EMDB-4722: Structure of a soluble domain of adenylyl cyclase bound to an act... -

+
Open data


ID or keywords:

Loading...

-
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


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, helical insertion / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanine nucleotide binding protein (G-protein), alpha subunit / G-protein alpha subunit, group S / Nucleotide cyclase / P-loop containing nucleoside triphosphate hydrolase / Adenylyl cyclase class-4/guanylyl cyclase, conserved site
Adenylate cyclase 9 / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKorkhov VM / Qi C
Funding support Switzerland, 1 items
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 ReportPDB-ID: 6r4p

SummaryFull reportAbout validation report
History
DepositionMar 22, 2019-
Header (metadata) releaseMay 8, 2019-
Map releaseMay 8, 2019-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBe / Status: Released

-
Structure visualization

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

Downloads & links

-
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

-
Supplemental data

-
Sample components

+
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

+
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

+
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

+
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

+
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)

+
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)

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

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

+
Component #7: ligand, MAGNESIUM ION

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

-
Experimental details

-
Sample preparation

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

-
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)

-
Image acquisition

Image acquisitionNumber of digital images: 5817

-
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)

-
Atomic model buiding

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

+
About Yorodumi

-
News

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices

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. (see PDBe EMDB page)
  • 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 at PDBe / 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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.:Changes in new EM Navigator and Yorodumi

Read more

-
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.

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