[English] 日本語
Yorodumi
- PDB-6r4p: Structure of a soluble domain of adenylyl cyclase bound to an act... -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: PDB / ID: 6r4p
TitleStructure of a soluble domain of 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 / Membrane protein / adenylyl cyclase / G protein / occluded state
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
Specimen sourceBos taurus (cattle)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsKorkhov, V.M. / Qi, C.
Funding supportSwitzerland , 1件
OrganizationGrant numberCountry
Swiss National Science Foundation150665Switzerland
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
DateDeposition: Mar 22, 2019 / Release: May 8, 2019Array

-
Structure visualization

Movie
  • Deposited structure unit
  • Imaged by Jmol
  • Download
  • Superimposition on EM map
  • EMDB-4722
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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 area3060 Å2
ΔGint-27 kcal/mol
Surface area37960 Å2
MethodPISA

-
Components

#1: Protein/peptide 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: pEZT-BM / Cell line (production host): HEK293F / Production host: Homo sapiens (human) / References: UniProt: E1BM79
#2: Protein/peptide 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


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

-
Experimental details

-
Experiment

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

-
Sample preparation

Component

Type: COMPLEX

IDNameEntity IDParent-IDSource
1Complex of adenylyl cyclase AC9 with G protein subunit Galphas1, 20MULTIPLE SOURCES
2Adenylate cyclase 9Adenylyl cyclase11RECOMBINANT
3Guanine nucleotide-binding protein G(s) subunit alpha isoforms short21RECOMBINANT
Source (natural)

Ncbi tax-ID: 9913 / Organism: Bos taurus (cattle)

IDEntity assembly-ID
22
33
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-IDCellPlasmid
22Homo sapiens (human)9606HEK293FpEZT-BM
33Trichoplusia ni (cabbage looper)7111High FivepFastbac
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

-
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

-
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
13PHENIX1.13model refinement
CTF correctionType: NONE
Particle selectionNum. of particles selected: 656817
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 170456
Details: Masked refinement in relion continued after the last iteration, using a mask excluding the micelle and the membrane portion of the complex.
Symmetry type: POINT
Atomic model buildingB value: 86.68 / Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Correlation coefficient

+
About Yorodumi

-
News

-
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

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / 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