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Yorodumi- EMDB-0876: Cryo-EM structure of the Drosophila CTP synthase product-bound fi... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0876 | |||||||||
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Title | Cryo-EM structure of the Drosophila CTP synthase product-bound filament | |||||||||
Map data | ||||||||||
Sample |
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Keywords | product-bound / filament / LIGASE | |||||||||
Function / homology | Function and homology information Interconversion of nucleotide di- and triphosphates / larval lymph gland hemopoiesis / cytoophidium / CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / CTP biosynthetic process / glutamine metabolic process / ATP binding ...Interconversion of nucleotide di- and triphosphates / larval lymph gland hemopoiesis / cytoophidium / CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / CTP biosynthetic process / glutamine metabolic process / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Drosophila melanogaster (fruit fly) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 9.58 Å | |||||||||
Authors | Ji-long L / Xian Z | |||||||||
Funding support | China, 1 items
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Citation | Journal: J Genet Genomics / Year: 2019 Title: Drosophila CTP synthase can form distinct substrate- and product-bound filaments. Authors: Xian Zhou / Chen-Jun Guo / Huan-Huan Hu / Jiale Zhong / Qianqian Sun / Dandan Liu / Shuang Zhou / Chia Chun Chang / Ji-Long Liu / Abstract: Intracellular compartmentation is a key strategy for the functioning of a cell. In 2010, several studies revealed that the metabolic enzyme CTP synthase (CTPS) can form filamentous structures termed ...Intracellular compartmentation is a key strategy for the functioning of a cell. In 2010, several studies revealed that the metabolic enzyme CTP synthase (CTPS) can form filamentous structures termed cytoophidia in prokaryotic and eukaryotic cells. However, recent structural studies showed that CTPS only forms inactive product-bound filaments in bacteria while forming active substrate-bound filaments in eukaryotic cells. In this study, using negative staining and cryo-electron microscopy, we demonstrate that Drosophila CTPS, whether in substrate-bound or product-bound form, can form filaments. Our results challenge the previous model and indicate that substrate-bound and product-bound filaments can coexist in the same species. We speculate that the ability to switch between active and inactive cytoophidia in the same cells provides an additional layer of metabolic regulation. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0876.map.gz | 226.4 MB | EMDB map data format | |
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Header (meta data) | emd-0876-v30.xml emd-0876.xml | 13.1 KB 13.1 KB | Display Display | EMDB header |
Images | emd_0876.png | 104.9 KB | ||
Filedesc metadata | emd-0876.cif.gz | 5.1 KB | ||
Others | emd_0876_half_map_1.map.gz emd_0876_half_map_2.map.gz | 28.7 MB 28.7 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0876 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0876 | HTTPS FTP |
-Related structure data
Related structure data | 6lfgMC 0840C 6l6zC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0876.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.06 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: #1
File | emd_0876_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_0876_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Drosophila product-bound CTP synthase
Entire | Name: Drosophila product-bound CTP synthase |
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Components |
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-Supramolecule #1: Drosophila product-bound CTP synthase
Supramolecule | Name: Drosophila product-bound CTP synthase / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
-Macromolecule #1: CTP synthase
Macromolecule | Name: CTP synthase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: CTP synthase (glutamine hydrolysing) |
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Source (natural) | Organism: Drosophila melanogaster (fruit fly) |
Molecular weight | Theoretical: 63.11848 KDa |
Recombinant expression | Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
Sequence | String: MKYILVTGGV ISGVGKGVIA SSFGTLLKSC GLDVTSIKID PYINIDAGTF SPYEHGEVYV LDDGAEVDLD LGNYERFLDV TLHRDNNIT TGKIYKLVIE KERTGEYLGK TVQVVPHITD AIQEWVERVA QTPVQGSSKP QVCIVELGGT IGDIEGMPFV E AFRQFQFR ...String: MKYILVTGGV ISGVGKGVIA SSFGTLLKSC GLDVTSIKID PYINIDAGTF SPYEHGEVYV LDDGAEVDLD LGNYERFLDV TLHRDNNIT TGKIYKLVIE KERTGEYLGK TVQVVPHITD AIQEWVERVA QTPVQGSSKP QVCIVELGGT IGDIEGMPFV E AFRQFQFR VKRENFCLAH VSLVPLPKAT GEPKTKPTQS SVRELRGCGL SPDLIVCRSE KPIGLEVKEK ISNFCHVGPD QV ICIHDLN SIYHVPLLME QNGVIEYLNE RLQLNIDMSK RTKCLQQWRD LARRTETVRR EVCIAVVGKY TKFTDSYASV VKA LQHAAL AVNRKLELVF IESCLLEEET LHSEPSKYHK EWQKLCDSHG ILVPGGFGSR GMEGKIRACQ WARENQKPLL GICL GLQAA VIEFARNKLG LKDANTTEID PNTANALVID MPEHHTGQLG GTMRLGKRIT VFSDGPSVIR QLYGNPKSVQ ERHRH RYEV NPKYVHLLEE QGMRFVGTDV DKTRMEIIEL SGHPYFVATQ YHPEYLSRPL KPSPPFLGLI LASVDRLNQY IQRGCR LS UniProtKB: CTP synthase |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: DARK FIELD |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 55.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Initial angle assignment | Type: OTHER |
Final angle assignment | Type: ANGULAR RECONSTITUTION |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 9.58 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 52273 |