+Open data
-Basic information
Entry | Database: PDB / ID: 7rmc | |||||||||
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Title | Yeast CTP Synthase (Ura7) filament bound to CTP at low pH | |||||||||
Components | CTP synthase 1 | |||||||||
Keywords | PROTEIN FIBRIL / glutaminase and amino-ligase | |||||||||
Function / homology | Function and homology information Interconversion of nucleotide di- and triphosphates / cytoophidium / CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / phospholipid biosynthetic process / pyrimidine nucleobase biosynthetic process / fungal-type vacuole / CTP biosynthetic process / glutamine metabolic process ...Interconversion of nucleotide di- and triphosphates / cytoophidium / CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / phospholipid biosynthetic process / pyrimidine nucleobase biosynthetic process / fungal-type vacuole / CTP biosynthetic process / glutamine metabolic process / ATP binding / identical protein binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Model details | cryo-EM D2 reconstruction | |||||||||
Authors | Hansen, J.M. / Lynch, E.M. / Farrell, D.P. / DiMaio, F. / Quispe, J. / Kollman, J.M. | |||||||||
Funding support | 2items
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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 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
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7rmc.cif.gz | 3.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7rmc.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7rmc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7rmc_validation.pdf.gz | 2.1 MB | Display | wwPDB validaton report |
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Full document | 7rmc_full_validation.pdf.gz | 2.1 MB | Display | |
Data in XML | 7rmc_validation.xml.gz | 156.6 KB | Display | |
Data in CIF | 7rmc_validation.cif.gz | 245.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rm/7rmc ftp://data.pdbj.org/pub/pdb/validation_reports/rm/7rmc | HTTPS FTP |
-Related structure data
Related structure data | 24560MC 7rkhC 7rl0C 7rl5C 7rmfC 7rmkC 7rmoC 7rmvC 7rnlC 7rnrC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 (brewer'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 / 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 |
-Sample preparation
Component | Name: CTP synthase 1 with bound CTP / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Value: 256 kDa/nm / Experimental value: YES |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 6 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 90 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Symmetry | Point symmetry: D2 (2x2 fold dihedral) |
3D reconstruction | Resolution: 3.5 Å / Resolution method: OTHER / Num. of particles: 64010 / Details: FSCref0.5 (Phenix Density modification) / Symmetry type: POINT |