|Entry||Database: EMDB / ID: EMD-24512|
|Title||Yeast CTP Synthase (URA8) Filament bound to ATP/UTP at low pH|
|Sample||Yeast CTP Synthase (URA8) filament bound to ATP/UTP at low pH:|
CTP synthaseCTP synthetase / (ligand) x 3
|Function / homology|
Function and homology information
CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / glutamine metabolic process / ATP binding
Similarity search - Function
CTP synthase / CTP synthase, N-terminal / CTP synthase GATase domain / CTP synthase N-terminus / Glutamine amidotransferase class-I / Glutamine amidotransferase / Class I glutamine amidotransferase-like / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Similarity search - Component
|Biological species||Saccharomyces cerevisiae (baker's yeast)|
|Method||single particle reconstruction / cryo EM / Resolution: 2.8 Å|
|Authors||Hansen JM / Lynch EM / Farrell DP / DiMaio F / Quispe J / Kollman JM|
|Funding support|| United States, 2 items |
|Citation||Journal: Elife / Year: 2021|
Title: Cryo-EM structures of CTP synthase filaments reveal mechanism of pH-sensitive assembly during budding yeast starvation.
Authors: Jesse M Hansen / Avital Horowitz / Eric M Lynch / Daniel P Farrell / Joel Quispe / Frank DiMaio / Justin M Kollman /
Abstract: Many metabolic enzymes self-assemble into micron-scale filaments to organize and regulate metabolism. The appearance of these assemblies often coincides with large metabolic changes as in ...Many metabolic enzymes self-assemble into micron-scale filaments to organize and regulate metabolism. The appearance of these assemblies often coincides with large metabolic changes as in development, cancer, and stress. Yeast undergo cytoplasmic acidification upon starvation, triggering the assembly of many metabolic enzymes into filaments. However, it is unclear how these filaments assemble at the molecular level and what their role is in the yeast starvation response. CTP Synthase (CTPS) assembles into metabolic filaments across many species. Here, we characterize polymerization and investigate consequences of CTPS assembly in yeast. Cryo-EM structures reveal a pH-sensitive assembly mechanism and highly ordered filament bundles that stabilize an inactive state of the enzyme, features unique to yeast CTPS. Disruption of filaments in cells with non-assembly or pH-insensitive mutations decreases growth rate, reflecting the importance of regulated CTPS filament assembly in homeotstasis.
|Structure viewer||EM map: |
Downloads & links
|File||Download / File: emd_24512.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)|
|Projections & slices|
Images are generated by Spider.
|Voxel size||X=Y=Z: 1.05 Å|
|Symmetry||Space group: 1|
CCP4 map header:
+Entire Yeast CTP Synthase (URA8) filament bound to ATP/UTP at low pH
|Entire||Name: Yeast CTP Synthase (URA8) filament bound to ATP/UTP at low pH|
Number of Components: 5
+Component #1: protein, Yeast CTP Synthase (URA8) filament bound to ATP/UTP at low pH
|Protein||Name: Yeast CTP Synthase (URA8) filament bound to ATP/UTP at low pH|
Recombinant expression: No
|Mass||Experimental: 256 MDa|
|Source||Species: Saccharomyces cerevisiae (baker's yeast)|
|Source (engineered)||Expression System: Escherichia coli (E. coli) / Strain: BL21-CodonPlus (DE3)-RIL|
+Component #2: protein, CTP synthase
|Protein||Name: CTP synthaseCTP synthetase / Number of Copies: 12 / Recombinant expression: No|
|Mass||Theoretical: 62.439168 kDa|
|Source||Species: Saccharomyces cerevisiae (baker's yeast)|
|Source (engineered)||Expression System: Escherichia coli (E. coli)|
+Component #3: ligand, MAGNESIUM ION
|Ligand||Name: MAGNESIUM ION / Number of Copies: 24 / Recombinant expression: No|
|Mass||Theoretical: 2.430505 MDa|
+Component #4: ligand, ADENOSINE-5'-TRIPHOSPHATE
|Ligand||Name: ADENOSINE-5'-TRIPHOSPHATE / Number of Copies: 12 / Recombinant expression: No|
|Mass||Theoretical: 0.507181 kDa|
+Component #5: ligand, URIDINE 5'-TRIPHOSPHATE
|Ligand||Name: URIDINE 5'-TRIPHOSPHATE / Number of Copies: 12 / Recombinant expression: No|
|Mass||Theoretical: 0.484141 kDa|
|Specimen||Specimen State: Particle / Method: cryo EM|
|Sample solution||pH: 6|
|Vitrification||Instrument: FEI VITROBOT MARK IV / Cryogen Name: ETHANE / Temperature: 277 K / Humidity: 100 %|
-Electron microscopy imaging
Model: Titan Krios / Image courtesy: FEI Company
|Imaging||Microscope: FEI TITAN KRIOS|
|Electron gun||Electron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 90 e/Å2 / Illumination Mode: FLOOD BEAM|
|Lens||Magnification: 130000.0 X (nominal) / Cs: 2.7 mm / Imaging Mode: BRIGHT FIELD / Defocus: 400.0 - 1900.0 nm / Energy Filter: GIF Bioquantum|
|Specimen Holder||Model: FEI TITAN KRIOS AUTOGRID HOLDER|
|Camera||Detector: GATAN K2 SUMMIT (4k x 4k)|
|Processing||Method: single particle reconstruction / Applied Symmetry: D2 (2x2 fold dihedral) / Number of Projections: 40474|
|3D reconstruction||Software: RELION / Resolution: 2.8 Å / Resolution Method: OTHER / Details: FSCref0.5 (Phenix Density Modification)|
-Atomic model buiding
|Modeling #1||Overall BValue: 32|
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