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- PDB-7yzk: Structure of Mycobacterium tuberculosis adenylyl cyclase Rv1625c / Cya -
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Open data
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Basic information
Entry | Database: PDB / ID: 7yzk | ||||||||||||
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Title | Structure of Mycobacterium tuberculosis adenylyl cyclase Rv1625c / Cya | ||||||||||||
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![]() | MEMBRANE PROTEIN / Adenylyl cyclase / cyclic adenosine monophosphate / signal transduction / nanobody | ||||||||||||
Function / homology | ![]() cyclic nucleotide biosynthetic process / adenylate cyclase activity / membrane => GO:0016020 / intracellular signal transduction Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.57 Å | ||||||||||||
![]() | Mehta, V. / Khanppnavar, B. / Korkhov, V.M. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structure of Cya, an evolutionary ancestor of the mammalian membrane adenylyl cyclases. Authors: Ved Mehta / Basavraj Khanppnavar / Dina Schuster / Ilayda Kantarci / Irene Vercellino / Angela Kosturanova / Tarun Iype / Sasa Stefanic / Paola Picotti / Volodymyr M Korkhov / ![]() Abstract: adenylyl cyclase (AC) Rv1625c/Cya is an evolutionary ancestor of the mammalian membrane ACs and a model system for studies of their structure and function. Although the vital role of ACs in cellular ... adenylyl cyclase (AC) Rv1625c/Cya is an evolutionary ancestor of the mammalian membrane ACs and a model system for studies of their structure and function. Although the vital role of ACs in cellular signalling is well established, the function of their transmembrane (TM) regions remains unknown. Here, we describe the cryo-EM structure of Cya bound to a stabilizing nanobody at 3.6 Å resolution. The TM helices 1-5 form a structurally conserved domain that facilitates the assembly of the helical and catalytic domains. The TM region contains discrete pockets accessible from the extracellular and cytosolic side of the membrane. Neutralization of the negatively charged extracellular pocket Ex1 destabilizes the cytosolic helical domain and reduces the catalytic activity of the enzyme. The TM domain acts as a functional component of Cya, guiding the assembly of the catalytic domain and providing the means for direct regulation of catalytic activity in response to extracellular ligands. | ||||||||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 325.4 KB | Display | ![]() |
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PDB format | ![]() | 269.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 45.7 KB | Display | |
Data in CIF | ![]() | 64.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 14389MC ![]() 7yz9C ![]() 7yziC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
#1: Protein | Mass: 50386.613 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Gene: cya, E5M05_05660, E5M52_05085, FPJ30_08830, FPJ32_08830, FPJ34_08835, FPJ36_08825, FPJ37_08855, FPJ39_08835, FPJ40_08830, FPJ41_08840, FPJ43_08855, FPJ45_08835, FPJ46_08835, FPJ48_08825, FPJ49_ ...Gene: cya, E5M05_05660, E5M52_05085, FPJ30_08830, FPJ32_08830, FPJ34_08835, FPJ36_08825, FPJ37_08855, FPJ39_08835, FPJ40_08830, FPJ41_08840, FPJ43_08855, FPJ45_08835, FPJ46_08835, FPJ48_08825, FPJ49_08855, FPJ50_08825, FPJ51_08820, FPJ52_08850, FPJ53_08835, FPJ54_08845, FPJ56_08825, FPJ57_08830, FPJ58_08855, FPJ59_08830, FPJ60_08860, FPJ61_08825, FPJ62_08815, FPJ65_08830, FPJ66_08825, FPJ67_08870, FPJ69_08870, FPJ70_08870, FPJ71_08870, FPJ72_07615, FPJ73_08825, FPJ76_08785, FPJ77_13855, FPJ78_08840, FPJ79_08850, FPJ83_12765, FPJ84_08830, FPJ85_12755, FPJ86_12755, FPJ87_12750, FPJ89_08835, FPJ91_08835, FPJ93_08825, FPJ94_07605, FPJ95_08830, FPJ97_08845, FPJ99_08865, FPK00_08815, FPK01_08875, FPK03_08835, FPK04_08825, FPK05_08895, FPK10_07595, FPK12_08800, FPK21_08825, FPK22_08835, HRD52_08540, HRD53_08530 Production host: ![]() ![]() #2: Antibody | Mass: 13771.179 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Chemical | #4: Chemical | ChemComp-MN / Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 / Details: 50 mM Tris pH 7.5, 200 mM NaCl, 0.1 % digitonin | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: TFS KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm |
Image recording | Electron dose: 48 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.57 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 646042 / Symmetry type: POINT |