[English] 日本語
Yorodumi
- EMDB-4723: Soluble domain of membrane adenylyl cyclase bound to an activated... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-4723
TitleSoluble domain of membrane adenylyl cyclase bound to an activated stimulatory G protein, in the presence of MANT-GTP (SOL-M)
Map dataSoluble domain of AC9-GalphaS, in the presence of MANT-GTP (map SOL-M)
Sample
  • Complex: Soluble domain of adenylyl cyclase AC9 bound to GalphaS, in the presence of MANT-GTP (SOL-M)
    • Complex: Adenylate cyclase 9Adenylyl cyclase
      • Other: Adenylyl cyclase AC9
    • Complex: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
      • Other: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
Function / homology
Function and homology information


Adenylate cyclase activating pathway / Adenylate cyclase inhibitory pathway / sensory perception of chemical stimulus / PKA activation / adenylate cyclase / mu-type opioid receptor binding / Hedgehog 'off' state / corticotropin-releasing hormone receptor 1 binding / cAMP biosynthetic process / adenylate cyclase activity ...Adenylate cyclase activating pathway / Adenylate cyclase inhibitory pathway / sensory perception of chemical stimulus / PKA activation / adenylate cyclase / mu-type opioid receptor binding / Hedgehog 'off' state / corticotropin-releasing hormone receptor 1 binding / cAMP biosynthetic process / adenylate cyclase activity / G alpha (z) signalling events / beta-2 adrenergic receptor binding / D1 dopamine receptor binding / positive regulation of cAMP-mediated signaling / adenylate cyclase-activating adrenergic receptor signaling pathway / ionotropic glutamate receptor binding / insulin-like growth factor receptor binding / adenylate cyclase activator activity / G-protein beta/gamma-subunit complex binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of GTPase activity / adenylate cyclase-activating dopamine receptor signaling pathway / heterotrimeric G-protein complex / in utero embryonic development / intracellular signal transduction / GTPase activity / GTP binding / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / G-protein alpha subunit, group S / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit ...Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / G-protein alpha subunit, group S / G-alpha domain profile. / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G protein alpha subunit / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
adenylate cyclase / Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
Similarity search - Component
Biological speciesBos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsQi C / Sorrentino S / Medalia O / Korkhov VM
Funding support Switzerland, 2 items
OrganizationGrant numberCountry
Swiss National Science Foundation150665 Switzerland
Swiss National Science Foundation31003A_179418 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.
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: 0.042
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.042
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_4723.png

Downloads & links

-
Map

FileDownload / File: emd_4723.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSoluble domain of AC9-GalphaS, in the presence of MANT-GTP (map SOL-M)
Voxel sizeX=Y=Z: 1.089 Å
Density
Contour LevelBy AUTHOR: 0.042 / Movie #1: 0.042
Minimum - Maximum-0.08217961 - 0.15531243
Average (Standard dev.)0.00012704714 (±0.0026195599)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 326.69998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0891.0891.089
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z326.700326.700326.700
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0820.1550.000

-
Supplemental data

-
Sample components

-
Entire : Soluble domain of adenylyl cyclase AC9 bound to GalphaS, in the p...

EntireName: Soluble domain of adenylyl cyclase AC9 bound to GalphaS, in the presence of MANT-GTP (SOL-M)
Components
  • Complex: Soluble domain of adenylyl cyclase AC9 bound to GalphaS, in the presence of MANT-GTP (SOL-M)
    • Complex: Adenylate cyclase 9Adenylyl cyclase
      • Other: Adenylyl cyclase AC9
    • Complex: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
      • Other: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

-
Supramolecule #1: Soluble domain of adenylyl cyclase AC9 bound to GalphaS, in the p...

SupramoleculeName: Soluble domain of adenylyl cyclase AC9 bound to GalphaS, in the presence of MANT-GTP (SOL-M)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

-
Supramolecule #2: Adenylate cyclase 9

SupramoleculeName: Adenylate cyclase 9 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Bos taurus (cattle)
Recombinant expressionOrganism: Homo sapiens (human) / Recombinant cell: HEK293F / Recombinant plasmid: pEZT-BM

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

SupramoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Bos taurus (cattle)
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper) / Recombinant cell: High FIve / Recombinant plasmid: pFastbac

-
Macromolecule #1: Adenylyl cyclase AC9

MacromoleculeName: Adenylyl cyclase AC9 / type: other / ID: 1 / Classification: other
Source (natural)Organism: Bos taurus (cattle)
SequenceString: MASPPHQQLL QHHSTEVSCD SSGDSNSVRV RINPKQPSSN SHPKHCKYSI SSSCSSSGDS GGVPRRMGAG GRLRRRKKLP QLFERASSRW WDPKFDSVNL EEACMERCFP QTQRRFRYAL FYIGFACLLW SIYFGVHMKS KLIVMVAPAL CFLVVCVGFF LFTFTKLYAR ...String:
MASPPHQQLL QHHSTEVSCD SSGDSNSVRV RINPKQPSSN SHPKHCKYSI SSSCSSSGDS GGVPRRMGAG GRLRRRKKLP QLFERASSRW WDPKFDSVNL EEACMERCFP QTQRRFRYAL FYIGFACLLW SIYFGVHMKS KLIVMVAPAL CFLVVCVGFF LFTFTKLYAR HYVWTSLVLT LLVFALTLAA QFQVLTPLSG RVDNFNHTRA ARPTDTCLSQ VGSFSMCIEV LFLLYTVMHL PLYLSLILGV AYSVLFETFG YHFQDEACFA SPGAEALHWE LLSRALLHLC IHAIGIHLFI MSQVRSRSTF LKVGQSIMHG KDLEVEKALK ERMIHSVMPR IIADDLMKQG DEESENSVKR HATSSPKNRK KKSSIQKAPI AFRPFKMQQI EEVSILFADI VGFTKMSANK SAHALVGLLN DLFGRFDRLC EETKCEKIST LGDCYYCVAG CPEPRADHAY CCIEMGLGMI RAIEQFCQEK KEMVNMRVGV HTGTVLCGIL GMRRFKFDVW SNDVNLANLM EQLGVAGKVH ISEATAKYLD DRYEMEDGKV TERLGQSVVA DQLKGLKTYL IAGQRAKESH CSCSEALLSG FEVLDGSRVS SGPRGQGTAS PGSVSDLAQT VKTFDNLKTC PSCGITFTPK PEAGAEGGAV QNGCQEEPKN SAKASGGPSS KTQNGLLSPP PEEKLTNSQT SLCEILQEKG RWAGVSLDQS ALLPLRFKNI REKTDAHFVD VIKEDSLMKD YFFKPPINQF SLNFLDPELE RAYRTSYQEE VVKSSPVRTF ASATFSSLLD VLLSTTVFLI LSITCFLRYG AASTPPPPAA LAVFGAALLL EILSLVVSVR MVFFLEDVMT CTKRLLEWIA GWLPRHFIGA ILVSLPALAV YSHVTSEFET NIHSTMFTGS AVLTAVVQYC NFCQLSSWMR SSLATVVGAG PLLLLLYVSL CPDSSTVISH LDAVQNFSST RKLCNASLPH DGRSPASLIG QEVILVFFLL LLLVWFLNRE FEVSYRLHYH GDVEADLHRT KIQSMRDQAD WLLRNIIPYH VAEQLKVSQT YSKNHDSGGV IFASIVNFSE FYEENYEGGK ECYRVLNELI GDFDELLSKP DYSSIEKIKT IGATYMAASG LNATQCRDGS HPQEHLQILF EFAKEMMRVV DDFNNNMLWF NFKLRVGFNH GPLTAGVIGT TKLLYDIWGD TVNIASRMDT TGVECRIQVS EESYRVLSKM GYEFDYRGTV NVKGKGQMKT YLYPKCTDSG LVPQHQLSIS PDIRVQVDGS IGRSPTDEIA SLVPSVQNPD QVPPGSENNA QTRDAHPSAK RPWKEPVRAE ERCRFGKAIE KSDCEEVGME EANELTKLNV SERAAAALEV LFQGPGGVSK GEELFTGVVP ILVELDGDVN GHKFSVSGEG EGDATYGKLT LKFICTTGKL PVPWPTLVTT FGYGLQCFAR YPDHMKQHDF FKSAMPEGYV QERTIFFKDD GNYKTRAEVK FEGDTLVNRI ELKGIDFKED GNILGHKLEY NYNSHNVYIM ADKQKNGIKV NFKIRHNIED GSVQLADHYQ QNTPIGDGPV LLPDNHYLSY QSALSKDPNE KRDHMVLLEF VTAAGITLGM DELYKAASAW SHPQFEKGGG SGGGSGGSAW SHPQFEK
Recombinant expressionOrganism: Homo sapiens (human)

-
Macromolecule #2: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

MacromoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
type: other / ID: 2 / Classification: other
Source (natural)Organism: Bos taurus (cattle)
SequenceString: MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKSTIVKQM RILHVNGFNG GEGGEEDPNA KSNSDGEKAT KVQDIKNNLK EAIETIVAAM SNLVPPVELA NPENQFRVDY ILSVMNVPDF DFPPEFYEHA KALWEDEGVR ACYERSNEYQ ...String:
MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKSTIVKQM RILHVNGFNG GEGGEEDPNA KSNSDGEKAT KVQDIKNNLK EAIETIVAAM SNLVPPVELA NPENQFRVDY ILSVMNVPDF DFPPEFYEHA KALWEDEGVR ACYERSNEYQ LIDCAQYFLD KIDVIKQDDY VPSDQDLLRC RVLTSGIFET KFQVDKVNFH MFDVGGQRDE RRKWIQCFND VTAIIFVVAS SSYNMVIRED NQTNRLQEAL NLFKSIWNNR WLRTISVILF LNKQDLLAEK VLAGKSKIED YFPEFARYTT PEDATPEPGE DPRVTRAKYF IRDEFLRIST ASGDGRHYCY PHFTCAVDTE NIRRVFNDCR DIIQRMHLRQ YELLGGHHHH HHHH
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 3 / Number real images: 3233 / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 906170
CTF correctionSoftware - Name: Gctf
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1.0)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 2.1.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1.0)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1.0) / Number images used: 53394
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 125.16 / Target criteria: Cross-correlation coefficient

+
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