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- EMDB-40573: Dimeric form of human adenylyl cyclase 5 -

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Basic information

Entry
Database: EMDB / ID: EMD-40573
TitleDimeric form of human adenylyl cyclase 5
Map data
Sample
  • Complex: Dimeric form of human adenylyl cyclase 5
    • Protein or peptide: Adenylate cyclase type 5
KeywordsAdenylyl cyclase / SIGNALING PROTEIN
Function / homology
Function and homology information


Adenylate cyclase activating pathway / adenylate cyclase-inhibiting dopamine receptor signaling pathway / G protein-coupled adenosine receptor signaling pathway / adenylate cyclase / regulation of insulin secretion involved in cellular response to glucose stimulus / cAMP biosynthetic process / adenylate cyclase activity / PKA activation / PKA activation in glucagon signalling / neuromuscular process controlling balance ...Adenylate cyclase activating pathway / adenylate cyclase-inhibiting dopamine receptor signaling pathway / G protein-coupled adenosine receptor signaling pathway / adenylate cyclase / regulation of insulin secretion involved in cellular response to glucose stimulus / cAMP biosynthetic process / adenylate cyclase activity / PKA activation / PKA activation in glucagon signalling / neuromuscular process controlling balance / adenylate cyclase binding / Adenylate cyclase inhibitory pathway / Hedgehog 'off' state / cellular response to forskolin / adenylate cyclase-inhibiting G protein-coupled receptor signaling pathway / FCGR3A-mediated IL10 synthesis / locomotory behavior / cilium / Glucagon signaling in metabolic regulation / adenylate cyclase-activating G protein-coupled receptor signaling pathway / Adrenaline,noradrenaline inhibits insulin secretion / Vasopressin regulates renal water homeostasis via Aquaporins / G alpha (z) signalling events / Glucagon-like Peptide-1 (GLP1) regulates insulin secretion / ADORA2B mediated anti-inflammatory cytokines production / adenylate cyclase-activating dopamine receptor signaling pathway / GPER1 signaling / positive regulation of cytosolic calcium ion concentration / G alpha (i) signalling events / G alpha (s) signalling events / scaffold protein binding / intracellular signal transduction / ATP binding / membrane / metal ion binding / plasma membrane
Similarity search - Function
Adenylate cyclase, conserved domain / Adenylate cyclase / Adenylate cyclase, N-terminal / Adenylate cyclase, conserved domain / Adenylyl cyclase N-terminal extracellular and transmembrane region / 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 ...Adenylate cyclase, conserved domain / Adenylate cyclase / Adenylate cyclase, N-terminal / Adenylate cyclase, conserved domain / Adenylyl cyclase N-terminal extracellular and transmembrane region / 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
Similarity search - Domain/homology
Adenylate cyclase type 5
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsYen YC / Tesmer JJG
Funding support United States, 5 items
OrganizationGrant numberCountry
American Heart Association903842 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA254402 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA221289 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA023168 United States
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)HL071818 United States
CitationJournal: To Be Published
Title: Isoform Specific Regulation of Adenylyl Cyclase 5 by Gbg
Authors: Yen YC / Li Y / Chen CC / Klose T / Watts VJ / Dessauer CW / Tesmer JJGT
History
DepositionApr 20, 2023-
Header (metadata) releaseApr 3, 2024-
Map releaseApr 3, 2024-
UpdateApr 3, 2024-
Current statusApr 3, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_40573.png

Downloads & links

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Map

FileDownload / File: emd_40573.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.2017711 - 0.39052048
Average (Standard dev.)0.0018082138 (±0.03418114)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_40573_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_40573_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Dimeric form of human adenylyl cyclase 5

EntireName: Dimeric form of human adenylyl cyclase 5
Components
  • Complex: Dimeric form of human adenylyl cyclase 5
    • Protein or peptide: Adenylate cyclase type 5

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Supramolecule #1: Dimeric form of human adenylyl cyclase 5

SupramoleculeName: Dimeric form of human adenylyl cyclase 5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 280 KDa

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Macromolecule #1: Adenylate cyclase type 5

MacromoleculeName: Adenylate cyclase type 5 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: adenylate cyclase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 139.066312 KDa
Recombinant expressionOrganism: Mammalia (mammals)
SequenceString: MSGSKSVSPP GYAAQKTAAP APRGGPEHRS AWGEADSRAN GYPHAPGGSA RGSTKKPGGA VTPQQQQRLA SRWRSDDDDD PPLSGDDPL AGGFGFSFRS KSAWQERGGD DCGRGSRRQR RGAASGGSTR APPAGGGGGS AAAAASAGGT EVRPRSVEVG L EERRGKGR ...String:
MSGSKSVSPP GYAAQKTAAP APRGGPEHRS AWGEADSRAN GYPHAPGGSA RGSTKKPGGA VTPQQQQRLA SRWRSDDDDD PPLSGDDPL AGGFGFSFRS KSAWQERGGD DCGRGSRRQR RGAASGGSTR APPAGGGGGS AAAAASAGGT EVRPRSVEVG L EERRGKGR AADELEAGAV EGGEGSGDGG SSADSGSGAG PGAVLSLGAC CLALLQIFRS KKFPSDKLER LYQRYFFRLN QS SLTMLMA VLVLVCLVML AFHAARPPLQ LPYLAVLAAA VGVILIMAVL CNRAAFHQDH MGLACYALIA VVLAVQVVGL LLP QPRSAS EGIWWTVFFI YTIYTLLPVR MRAAVLSGVL LSALHLAIAL RTNAQDQFLL KQLVSNVLIF SCTNIVGVCT HYPA EVSQR QAFQETRECI QARLHSQREN QQQERLLLSV LPRHVAMEMK ADINAKQEDM MFHKIYIQKH DNVSILFADI EGFTS LASQ CTAQELVMTL NELFARFDKL AAENHCLRIK ILGDCYYCVS GLPEARADHA HCCVEMGMDM IEAISLVREV TGVNVN MRV GIHSGRVHCG VLGLRKWQFD VWSNDVTLAN HMEAGGKAGR IHITKATLNY LNGDYEVEPG CGGERNAYLK EHSIETF LI LRCTQKRKEE KAMIAKMNRQ RTNSIGHNPP HWGAERPFYN HLGGNQVSKE MKRMGFEDPK DKNAQESANP EDEVDEFL G RAIDARSIDR LRSEHVRKFL LTFREPDLEK KYSKQVDDRF GAYVACASLV FLFICFVQIT IVPHSIFMLS FYLTCSLLL TLVVFVSVIY SCVKLFPSPL QTLSRKIVRS KMNSTLVGVF TITLVFLAAF VNMFTCNSRD LLGCLAQEHN ISASQVNACH VAESAVNYS LGDEQGFCGS PWPNCNFPEY FTYSVLLSLL ACSVFLQISC IGKLVLMLAI ELIYVLIVEV PGVTLFDNAD L LVTANAID FFNNGTSQCP EHATKVALKV VTPIIISVFV LALYLHAQQV ESTARLDFLW KLQATEEKEE MEELQAYNRR LL HNILPKD VAAHFLARER RNDELYYQSC ECVAVMFASI ANFSEFYVEL EANNEGVECL RLLNEIIADF DEIISEDRFR QLE KIKTIG STYMAASGLN DSTYDKVGKT HIKALADFAM KLMDQMKYIN EHSFNNFQMK IGLNIGPVVA GVIGARKPQY DIWG NTVNV ASRMDSTGVP DRIQVTTDMY QVLAANTYQL ECRGVVKVKG KGEMMTYFLN GGPPLS

UniProtKB: Adenylate cyclase type 5

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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

Concentration0.2 mg/mL
BufferpH: 7.4
Component:
ConcentrationFormulaName
137.0 mMNaClSodium chlorideSodium Chloride
2.7 mMKClPotassium Chloride
8.0 mMNa2HPO4Sodium hydrogen Phosphate
2.0 mMKH2PO4Potassium dihydrogen phosphate
0.025 %C56H92O25glyco-diosgenin
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / 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 K3 (6k x 4k) / Average electron dose: 53.8 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: COMMON LINE / Software - Name: cryoSPARC
Final angle assignmentType: COMMON LINE / Software - Name: cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 102581

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