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Open data
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Basic information
Entry | Database: PDB / ID: 7rmk | |||||||||
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Title | Yeast CTP Synthase (Ura7) Bundle bound to substrates at low pH | |||||||||
![]() | CTP synthase | |||||||||
![]() | PROTEIN FIBRIL / glutaminase and amino-ligase | |||||||||
Function / homology | ![]() CTP synthase (glutamine hydrolysing) / CTP synthase activity / cytoophidium / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / glutamine metabolic process / ATP binding / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.6 Å | |||||||||
Model details | cryo-EM D2 reconstruction | |||||||||
![]() | Hansen, J.M. / Lynch, E.M. / Farrell, D.P. / DiMaio, F. / Quispe, J. / Kollman, J.M. | |||||||||
Funding support | 2items
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![]() | ![]() 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 in vitro polymerization and investigate in vivo 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. | |||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 8.2 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 24575MC ![]() 7rkhC ![]() 7rl0C ![]() 7rl5C ![]() 7rmcC ![]() 7rmfC ![]() 7rmoC ![]() 7rmvC ![]() 7rnlC ![]() 7rnrC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 61879.922 Da / Num. of mol.: 28 Source method: isolated from a genetically manipulated source Details: 6XHIS c-ter Source: (gene. exp.) ![]() ![]() Gene: PACBIOSEQ_LOCUS169, PACBIOSEQ_LOCUS176, PACBIOSEQ_LOCUS177, PACBIOSEQ_LOCUS179 Plasmid: pET28b / Production host: ![]() ![]() References: UniProt: A0A7I9CFN1, CTP synthase (glutamine hydrolysing) #2: Chemical | ChemComp-ATP / #3: Chemical | ChemComp-UTP / 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
Component | Name: CTP Synthase Bundle assembled with substrates / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Source (natural) | Organism: ![]() ![]() |
Source (recombinant) | Organism: ![]() ![]() |
Buffer solution | pH: 6 |
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: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 90 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
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Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: C2 (2 fold cyclic) |
3D reconstruction | Resolution: 6.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 24059 / Symmetry type: POINT |