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- EMDB-4722: Structure of a soluble domain of adenylyl cyclase bound to an act... -

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Basic information

Entry
Database: EMDB / ID: EMD-4722
TitleStructure of a soluble domain of adenylyl cyclase bound to an activatedstimulatory G protein
Map dataSoluble domain of AC9 bound to GalphaS
Sample
  • Complex: Complex of adenylyl cyclase AC9 with G protein subunit Galphas
    • Complex: Adenylate cyclase 9
      • Protein or peptide: Adenylate cyclase 9
    • Complex: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
      • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
  • Ligand: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
  • Ligand: MAGNESIUM ION
KeywordsMembrane protein / adenylyl cyclase / G protein / occluded state
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 / beta-2 adrenergic receptor binding / G alpha (z) signalling events / D1 dopamine receptor binding / adenylate cyclase-activating adrenergic receptor signaling pathway / insulin-like growth factor receptor binding / adenylate cyclase activator activity / 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 / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / in utero embryonic development / intracellular signal transduction / GTPase activity / GTP binding / ATP binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanylate cyclase domain profile. / Nucleotide cyclase / G-protein alpha subunit, group S / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion ...Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylate and Guanylate cyclase catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Guanylate cyclase domain profile. / Nucleotide cyclase / G-protein alpha subunit, group S / Guanine nucleotide binding protein (G-protein), alpha subunit / G protein alpha subunit, helical insertion / G-protein alpha subunit / G-alpha domain profile. / 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: 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.
History
DepositionMar 22, 2019-
Header (metadata) releaseMay 8, 2019-
Map releaseMay 8, 2019-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

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

emd_4722.png

Downloads & links

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Map

FileDownload / File: emd_4722.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSoluble domain of AC9 bound to GalphaS
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

Histogram

Histogram (log scale)
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

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Supplemental data

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Sample components

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Entire : Complex of adenylyl cyclase AC9 with G protein subunit Galphas

EntireName: Complex of adenylyl cyclase AC9 with G protein subunit Galphas
Components
  • Complex: Complex of adenylyl cyclase AC9 with G protein subunit Galphas
    • Complex: Adenylate cyclase 9
      • Protein or peptide: Adenylate cyclase 9
    • Complex: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
      • Protein or peptide: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
  • Ligand: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Complex of adenylyl cyclase AC9 with G protein subunit Galphas

SupramoleculeName: Complex of adenylyl cyclase AC9 with G protein subunit Galphas
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Adenylate cyclase 9

SupramoleculeName: Adenylate cyclase 9 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Bos taurus (cattle)

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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)

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Macromolecule #1: Adenylate cyclase 9

MacromoleculeName: Adenylate cyclase 9 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 182.404422 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: MASPPHQQLL QHHSTEVSCD SSGDSNSVRV RINPKQPSSN SHPKHCKYSI SSSCSSSGDS GGVPRRMGAG GRLRRRKKLP QLFERASSR WWDPKFDSVN LEEACMERCF PQTQRRFRYA LFYIGFACLL WSIYFGVHMK SKLIVMVAPA LCFLVVCVGF F LFTFTKLY ...String:
MASPPHQQLL QHHSTEVSCD SSGDSNSVRV RINPKQPSSN SHPKHCKYSI SSSCSSSGDS GGVPRRMGAG GRLRRRKKLP QLFERASSR WWDPKFDSVN LEEACMERCF PQTQRRFRYA LFYIGFACLL WSIYFGVHMK SKLIVMVAPA LCFLVVCVGF F LFTFTKLY ARHYVWTSLV LTLLVFALTL AAQFQVLTPL SGRVDNFNHT RAARPTDTCL SQVGSFSMCI EVLFLLYTVM HL PLYLSLI LGVAYSVLFE TFGYHFQDEA CFASPGAEAL HWELLSRALL HLCIHAIGIH LFIMSQVRSR STFLKVGQSI MHG KDLEVE KALKERMIHS VMPRIIADDL MKQGDEESEN SVKRHATSSP KNRKKKSSIQ KAPIAFRPFK MQQIEEVSIL FADI VGFTK MSANKSAHAL VGLLNDLFGR FDRLCEETKC EKISTLGDCY YCVAGCPEPR ADHAYCCIEM GLGMIRAIEQ FCQEK KEMV NMRVGVHTGT VLCGILGMRR FKFDVWSNDV NLANLMEQLG VAGKVHISEA TAKYLDDRYE MEDGKVTERL GQSVVA DQL KGLKTYLIAG QRAKESHCSC SEALLSGFEV LDGSRVSSGP RGQGTASPGS VSDLAQTVKT FDNLKTCPSC GITFTPK PE AGAEGGAVQN GCQEEPKNSA KASGGPSSKT QNGLLSPPPE EKLTNSQTSL CEILQEKGRW AGVSLDQSAL LPLRFKNI R EKTDAHFVDV IKEDSLMKDY FFKPPINQFS LNFLDPELER AYRTSYQEEV VKSSPVRTFA SATFSSLLDV LLSTTVFLI LSITCFLRYG AASTPPPPAA LAVFGAALLL EILSLVVSVR MVFFLEDVMT CTKRLLEWIA GWLPRHFIGA ILVSLPALAV YSHVTSEFE TNIHSTMFTG SAVLTAVVQY CNFCQLSSWM RSSLATVVGA GPLLLLLYVS LCPDSSTVIS HLDAVQNFSS T RKLCNASL PHDGRSPASL IGQEVILVFF LLLLLVWFLN REFEVSYRLH YHGDVEADLH RTKIQSMRDQ ADWLLRNIIP YH VAEQLKV SQTYSKNHDS GGVIFASIVN FSEFYEENYE GGKECYRVLN ELIGDFDELL SKPDYSSIEK IKTIGATYMA ASG LNATQC RDGSHPQEHL QILFEFAKEM MRVVDDFNNN MLWFNFKLRV GFNHGPLTAG VIGTTKLLYD IWGDTVNIAS RMDT TGVEC RIQVSEESYR VLSKMGYEFD YRGTVNVKGK GQMKTYLYPK CTDSGLVPQH QLSISPDIRV QVDGSIGRSP TDEIA SLVP SVQNPDQVPP GSENNAQTRD AHPSAKRPWK EPVRAEERCR FGKAIEKSDC EEVGMEEANE LTKLNVSERA AAALEV LFQ GPGGVSKGEE LFTGVVPILV ELDGDVNGHK FSVSGEGEGD ATYGKLTLKF ICTTGKLPVP WPTLVTTFGY GLQCFAR YP DHMKQHDFFK SAMPEGYVQE RTIFFKDDGN YKTRAEVKFE GDTLVNRIEL KGIDFKEDGN ILGHKLEYNY NSHNVYIM A DKQKNGIKVN FKIRHNIEDG SVQLADHYQQ NTPIGDGPVL LPDNHYLSYQ SALSKDPNEK RDHMVLLEFV TAAGITLGM DELYKAASAW SHPQFEKGGG SGGGSGGSAW SHPQFEK

UniProtKB: adenylate cyclase

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

MacromoleculeName: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
Molecular weightTheoretical: 46.932727 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKSTIVKQM RILHVNGFNG GEGGEEDPNA KSNSDGEKA TKVQDIKNNL KEAIETIVAA MSNLVPPVEL ANPENQFRVD YILSVMNVPD FDFPPEFYEH AKALWEDEGV R ACYERSNE ...String:
MGCLGNSKTE DQRNEEKAQR EANKKIEKQL QKDKQVYRAT HRLLLLGAGE SGKSTIVKQM RILHVNGFNG GEGGEEDPNA KSNSDGEKA TKVQDIKNNL KEAIETIVAA MSNLVPPVEL ANPENQFRVD YILSVMNVPD FDFPPEFYEH AKALWEDEGV R ACYERSNE YQLIDCAQYF LDKIDVIKQD DYVPSDQDLL RCRVLTSGIF ETKFQVDKVN FHMFDVGGQR DERRKWIQCF ND VTAIIFV VASSSYNMVI REDNQTNRLQ EALNLFKSIW NNRWLRTISV ILFLNKQDLL AEKVLAGKSK IEDYFPEFAR YTT PEDATP EPGEDPRVTR AKYFIRDEFL RISTASGDGR HYCYPHFTCA VDTENIRRVF NDCRDIIQRM HLRQYELLGG HHHH HHHH

UniProtKB: Guanine nucleotide-binding protein G(s) subunit alpha isoforms short

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Macromolecule #3: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE

MacromoleculeName: 5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: GSP
Molecular weightTheoretical: 539.246 Da
Chemical component information

ChemComp-GSP:
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

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

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm 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 beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.75 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 656817
Startup modelType of model: OTHER / Details: Initial model generated using cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1.0)
Details: Masked refinement in relion continued after the last iteration, using a mask excluding the micelle and the membrane portion of the complex.
Number images used: 170456
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1.0)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 2.1.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 86.68 / Target criteria: Cross-correlation coefficient
Output model

PDB-6r4p:
Structure of a soluble domain of adenylyl cyclase bound to an activated stimulatory G protein

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