|Entry||Database: PDB / ID: 7rl5|
|Title||Yeast CTP Synthase (URA8) filament bound to CTP at low pH|
|Components||CTP synthaseCTP synthetase|
|Keywords||PROTEIN FIBRIL / glutaminase and amino-ligase|
|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
CYTIDINE-5'-TRIPHOSPHATE / CTP synthase
Similarity search - Component
|Biological species||Saccharomyces cerevisiae (baker's yeast)|
|Method||ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 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|| United States, 2items |
|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||Molecule: |
Downloads & links
A: CTP synthase
B: CTP synthase
C: CTP synthase
D: CTP synthase
E: CTP synthase
M: CTP synthase
P: CTP synthase
R: CTP synthase
L: CTP synthase
O: CTP synthase
Q: CTP synthase
S: CTP synthase
Mass: 62439.168 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: PACBIOSEQ_LOCUS3439, SCNYR20_0009027000 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE3)-RIL
References: UniProt: A0A6A5PYW3, CTP synthase (glutamine hydrolysing)
|Has ligand of interest||N|
|Experiment||Method: ELECTRON MICROSCOPY|
|EM experiment||Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction|
|Component||Name: Yeast CTP Synthase filament with CTP bound / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT|
|Molecular weight||Value: 256 kDa/nm / Experimental value: YES|
|Source (natural)||Organism: Saccharomyces cerevisiae (baker'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
Model: Titan Krios / Image courtesy: FEI Company
|Microscopy||Model: FEI TITAN KRIOS|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM|
|Electron lens||Mode: BRIGHT FIELDBright-field microscopy|
|Image recording||Electron dose: 90 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)|
|EM imaging optics||Energyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV|
|EM software||Name: cryoSPARC / Version: 3 / Category: final Euler assignment|
|CTF correction||Type: PHASE FLIPPING AND AMPLITUDE CORRECTION|
|Symmetry||Point symmetry: D2 (2x2 fold dihedral)|
|3D reconstruction||Resolution: 3.8 Å / Resolution method: OTHER / Num. of particles: 181136 / Details: FSCref0.5 (phenix density modification) / Symmetry type: POINT|
-Aug 12, 2020. Covid-19 info
New page: Covid-19 featured information page in EM Navigator.
Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data
-Mar 5, 2020. Novel coronavirus structure data
Novel coronavirus structure data
- International Committee on Taxonomy of Viruses (ICTV) defined the short name of the 2019 coronavirus as "SARS-CoV-2".
- The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2 - nature microbiology
- In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info
+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
- The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
- The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
+Jul 12, 2017. Major update of PDB
Major update of PDB
- wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
- This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
- In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
- Now, EM Navigator and Yorodumi are based on the updated data.
+Jun 16, 2017. Omokage search with filter
Omokage search with filter
Result of Omokage search can be filtered by keywords and the database types
Related info.:Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
- The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi