|Entry||Database: EMDB / ID: 8475|
|Title||Cryo-EM structure of the E. coli CTP synthase tetramer|
|Map data||E. coli CTP synthase tetramer|
|Sample||E. coli CTP synthase tetramer|
|Function/homology||CTP synthase / CTP synthase / CTP synthase GATase domain / CTP synthase activity / CTP synthase, N-terminal / CTP synthase N-terminus / 'de novo' CTP biosynthetic process / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / CTP biosynthetic process ...CTP synthase / CTP synthase / CTP synthase GATase domain / CTP synthase activity / CTP synthase, N-terminal / CTP synthase N-terminus / 'de novo' CTP biosynthetic process / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / CTP biosynthetic process / Glutamine amidotransferase class-I / glutamine metabolic process / Class I glutamine amidotransferase-like / P-loop containing nucleoside triphosphate hydrolase / ATP binding / identical protein binding / metal ion binding / cytosol / CTP synthase / CTP synthase|
Function and homology information
|Source||Escherichia coli / / bacteria /|
|Method||Cryo EM / single particle reconstruction / 7.9 Å resolution|
|Authors||Lynch EM / Hicks DR|
|Citation||Journal: Nat. Struct. Mol. Biol. / Year: 2017|
Title: Human CTP synthase filament structure reveals the active enzyme conformation.
Authors: Eric M Lynch / Derrick R Hicks / Matthew Shepherd / James A Endrizzi / Allison Maker / Jesse M Hansen / Rachael M Barry / Zemer Gitai / Enoch P Baldwin / Justin M Kollman
Abstract: The universally conserved enzyme CTP synthase (CTPS) forms filaments in bacteria and eukaryotes. In bacteria, polymerization inhibits CTPS activity and is required for nucleotide homeostasis. Here we ...The universally conserved enzyme CTP synthase (CTPS) forms filaments in bacteria and eukaryotes. In bacteria, polymerization inhibits CTPS activity and is required for nucleotide homeostasis. Here we show that for human CTPS, polymerization increases catalytic activity. The cryo-EM structures of bacterial and human CTPS filaments differ considerably in overall architecture and in the conformation of the CTPS protomer, explaining the divergent consequences of polymerization on activity. The structure of human CTPS filament, the first structure of the full-length human enzyme, reveals a novel active conformation. The filament structures elucidate allosteric mechanisms of assembly and regulation that rely on a conserved conformational equilibrium. The findings may provide a mechanism for increasing human CTPS activity in response to metabolic state and challenge the assumption that metabolic filaments are generally storage forms of inactive enzymes. Allosteric regulation of CTPS polymerization by ligands likely represents a fundamental mechanism underlying assembly of other metabolic filaments.
|Validation Report||PDB-ID: 5u05|
SummaryFull reportAbout validation report
|Date||Deposition: Nov 22, 2016 / Header (metadata) release: Apr 26, 2017 / Map release: Apr 26, 2017 / Last update: Jun 21, 2017|
Downloads & links
|File||emd_8475.map.gz (map file in CCP4 format, 21808 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.26 Å|
CCP4 map header:
-Entire E. coli CTP synthase tetramer
|Entire||Name: E. coli CTP synthase tetramer / Number of components: 2|
-Component #1: protein, E. coli CTP synthase tetramer
|Protein||Name: E. coli CTP synthase tetramer / Recombinant expression: No|
|Source||Species: Escherichia coli / / bacteria /|
|Source (engineered)||Expression System: Escherichia coli / / bacteria / / Vector: pET22|
-Component #2: protein, CTP synthase
|Protein||Name: CTP synthaseCTP synthetase / Recombinant expression: No|
|Mass||Theoretical: 60.44698 kDa|
|Source (engineered)||Expression System: Escherichia coli / / bacteria /|
|Specimen||Specimen state: particle / Method: Cryo EM|
|Sample solution||Specimen conc.: 0.3 mg/ml / pH: 8|
|Vitrification||Cryogen name: ETHANE|
-Electron microscopy imaging
Model: Tecnai F20 / Image courtesy: FEI Company
|Imaging||Microscope: FEI TECNAI F20|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 68 e/Å2 / Illumination mode: OTHER|
|Lens||Imaging mode: BRIGHT FIELD|
|Specimen Holder||Model: OTHER|
|Camera||Detector: GATAN K2 (4k x 4k)|
|Processing||Method: single particle reconstruction / Applied symmetry: D2 (2*2 fold dihedral) / Number of projections: 6407|
|3D reconstruction||Software: RELION / Resolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF|
-Atomic model buiding
-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. See below links for details.
- 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
+Sep 15, 2016. EM Navigator & Yorodumi renewed
EM Navigator & Yorodumi renewed
- New versions of EM Navigator and Yorodumi started
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)
+Aug 31, 2016. New EM Navigator & Yorodumi
New EM Navigator & Yorodumi
- In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
- Current version will continue as 'legacy version' for some time.
Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)
+Apr 13, 2016. Omokage search got faster
Omokage search got faster
- The computation time became ~1/2 compared to the previous version by re-optimization of data accession
- Enjoy "shape similarity" of biomolecules, more!
Related info.: Omokage search
Thousand views of thousand structures
- Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
- All the functionalities will be ported from the levgacy version.
- This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi