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- PDB-7rmc: Yeast CTP Synthase (Ura7) filament bound to CTP at low pH -

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Basic information

Entry
Database: PDB / ID: 7rmc
TitleYeast CTP Synthase (Ura7) filament bound to CTP at low pH
ComponentsCTP synthase 1
KeywordsPROTEIN FIBRIL / glutaminase and amino-ligase
Function / homology
Function and homology information


Interconversion of nucleotide di- and triphosphates / cytoophidium / CTP synthase activity / CTP synthase (glutamine hydrolysing) / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / fungal-type vacuole / phospholipid biosynthetic process / CTP biosynthetic process / glutamine metabolic process ...Interconversion of nucleotide di- and triphosphates / cytoophidium / CTP synthase activity / CTP synthase (glutamine hydrolysing) / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / fungal-type vacuole / phospholipid biosynthetic process / CTP biosynthetic process / glutamine metabolic process / ATP binding / identical protein binding / cytoplasm
Similarity search - Function
CTP synthase N-terminus / CTP synthase GATase domain / CTP synthase, N-terminal / CTP synthase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Glutamine amidotransferase / Class I glutamine amidotransferase-like / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
CYTIDINE-5'-TRIPHOSPHATE / CTP synthase 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (baker's yeast)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
Model detailscryo-EM D2 reconstruction
AuthorsHansen, J.M. / Lynch, E.M. / Farrell, D.P. / DiMaio, F. / Quispe, J. / Kollman, J.M.
Funding support2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM118396
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM007270
CitationJournal: 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.
History
DepositionJul 27, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release

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Assembly

Deposited unit
V: CTP synthase 1
D: CTP synthase 1
E: CTP synthase 1
F: CTP synthase 1
g: CTP synthase 1
Q: CTP synthase 1
S: CTP synthase 1
U: CTP synthase 1
h: CTP synthase 1
R: CTP synthase 1
T: CTP synthase 1
W: CTP synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)765,34036
Polymers753,74412
Non-polymers11,59624
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, cryoEM and SDS PAGE
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
CTP synthase 1 / / CTP synthetase 1 / UTP--ammonia ligase 1


Mass: 62812.035 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Details: 6XHIS c-ter
Source: (gene. exp.) Saccharomyces cerevisiae (baker's yeast)
Gene: URA7, YBL039C, YBL0410 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL
References: UniProt: P28274, CTP synthase (glutamine hydrolysing)
#2: Chemical...
ChemComp-CTP / CYTIDINE-5'-TRIPHOSPHATE / Cytidine triphosphate


Mass: 483.156 Da / Num. of mol.: 24 / Source method: obtained synthetically / Formula: C9H16N3O14P3
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CTP synthase 1 with bound CTP / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 256 kDa/nm / Experimental value: YES
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 90 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 3.5 Å / Resolution method: OTHER / Num. of particles: 64010 / Details: FSCref0.5 (Phenix Density modification) / Symmetry type: POINT

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