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Yorodumi- EMDB-4725: Structure of a membrane adenylyl cyclase bound to an activated st... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4725 | |||||||||
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Title | Structure of a membrane adenylyl cyclase bound to an activated stimulatory G protein (AC9-Gas-TM) | |||||||||
Map data | Complex of AC9 bound to GalphaS (AC9-Gas-TM) | |||||||||
Sample |
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Function / homology | Function and homology information Adenylate cyclase activating pathway / Adenylate cyclase inhibitory pathway / sensory perception of chemical stimulus / PKA activation / adenylate cyclase / Hedgehog 'off' state / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / D1 dopamine receptor binding / cAMP biosynthetic process ...Adenylate cyclase activating pathway / Adenylate cyclase inhibitory pathway / sensory perception of chemical stimulus / PKA activation / adenylate cyclase / Hedgehog 'off' state / mu-type opioid receptor binding / corticotropin-releasing hormone receptor 1 binding / D1 dopamine receptor binding / cAMP biosynthetic process / adenylate cyclase activity / beta-2 adrenergic receptor binding / G alpha (z) signalling events / adenylate cyclase-activating adrenergic receptor signaling pathway / adenylate cyclase activator activity / insulin-like growth factor receptor binding / ionotropic glutamate receptor binding / G-protein beta/gamma-subunit complex binding / adenylate cyclase-activating G protein-coupled receptor signaling pathway / adenylate cyclase-activating dopamine receptor signaling pathway / heterotrimeric G-protein complex / in utero embryonic development / intracellular signal transduction / GTPase activity / GTP binding / ATP binding / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Bos taurus (cattle) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Korkhov VM / Qi C | |||||||||
Funding support | Switzerland, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4725.map.gz | 8 MB | EMDB map data format | |
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Header (meta data) | emd-4725-v30.xml emd-4725.xml | 16.1 KB 16.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_4725_fsc.xml | 10.7 KB | Display | FSC data file |
Images | emd_4725.png | 43.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4725 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4725 | HTTPS FTP |
-Validation report
Summary document | emd_4725_validation.pdf.gz | 235.8 KB | Display | EMDB validaton report |
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Full document | emd_4725_full_validation.pdf.gz | 234.9 KB | Display | |
Data in XML | emd_4725_validation.xml.gz | 11.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4725 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4725 | HTTPS FTP |
-Related structure data
Related structure data | 4719C 4721C 4722C 4723C 4724C 4726C 6r3qC 6r4oC 6r4pC C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4725.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Complex of AC9 bound to GalphaS (AC9-Gas-TM) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.814 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Complex of adenylyl cyclase AC9 with G protein subunit Galphas
Entire | Name: Complex of adenylyl cyclase AC9 with G protein subunit Galphas |
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Components |
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-Supramolecule #1: Complex of adenylyl cyclase AC9 with G protein subunit Galphas
Supramolecule | Name: Complex of adenylyl cyclase AC9 with G protein subunit Galphas type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: Adenylate cyclase 9
Supramolecule | Name: Adenylate cyclase 9 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Bos taurus (cattle) |
Recombinant expression | Organism: Homo sapiens (human) / Recombinant cell: HEK293F / Recombinant plasmid: pEZT-BM |
-Supramolecule #3: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
Supramolecule | Name: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Bos taurus (cattle) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) / Recombinant cell: High Five / Recombinant plasmid: pFastbac |
-Macromolecule #1: Adenylyl cyclase 9
Macromolecule | Name: Adenylyl cyclase 9 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: adenylate cyclase |
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Source (natural) | Organism: Bos taurus (cattle) |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: 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 |
-Macromolecule #2: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
Macromolecule | Name: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Bos taurus (cattle) |
Recombinant expression | Organism: Trichoplusia ni (cabbage looper) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Number real images: 5817 / Average exposure time: 8.0 sec. / Average electron dose: 47.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
+Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: AB INITIO MODEL / Overall B value: 111.82 / Target criteria: Cross-correlation coefficient |
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