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Yorodumi- EMDB-24497: Yeast CTP Synthase (URA8) tetramer bound to ATP/UTP at neutral pH -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24497 | |||||||||
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Title | Yeast CTP Synthase (URA8) tetramer bound to ATP/UTP at neutral pH | |||||||||
Map data | Yeast CTP Synthase (Ura8) tetramer bound to ATP and UTP at neutral pH. | |||||||||
Sample |
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Keywords | glutaminase / amido-ligase / nucleotide metabolism / PROTEIN FIBRIL | |||||||||
Function / homology | Function and homology information cytoophidium / CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / glutamine metabolic process / ATP binding / identical protein binding / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Hansen JM / Lynch EM | |||||||||
Funding support | United States, 2 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_24497.map.gz | 4.4 MB | EMDB map data format | |
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Header (meta data) | emd-24497-v30.xml emd-24497.xml | 12.9 KB 12.9 KB | Display Display | EMDB header |
Images | emd_24497.png | 161.9 KB | ||
Filedesc metadata | emd-24497.cif.gz | 6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24497 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24497 | HTTPS FTP |
-Validation report
Summary document | emd_24497_validation.pdf.gz | 364.3 KB | Display | EMDB validaton report |
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Full document | emd_24497_full_validation.pdf.gz | 363.9 KB | Display | |
Data in XML | emd_24497_validation.xml.gz | 6.6 KB | Display | |
Data in CIF | emd_24497_validation.cif.gz | 7.6 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24497 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24497 | HTTPS FTP |
-Related structure data
Related structure data | 7rkhMC 7rl0C 7rl5C 7rmcC 7rmfC 7rmkC 7rmoC 7rmvC 7rnlC 7rnrC 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_24497.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Yeast CTP Synthase (Ura8) tetramer bound to ATP and UTP at neutral pH. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Yeast CTP Synthase (URA8) tetramer bound to ATP/UTP at neutral pH
Entire | Name: Yeast CTP Synthase (URA8) tetramer bound to ATP/UTP at neutral pH |
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Components |
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-Supramolecule #1: Yeast CTP Synthase (URA8) tetramer bound to ATP/UTP at neutral pH
Supramolecule | Name: Yeast CTP Synthase (URA8) tetramer bound to ATP/UTP at neutral pH type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 256 kDa/nm |
-Macromolecule #1: CTP synthase
Macromolecule | Name: CTP synthase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: CTP synthase (glutamine hydrolysing) |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Molecular weight | Theoretical: 62.439168 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MKYVVVSGGV ISGIGKGVLA SSTGMLLKTL GLKVTSIKID PYMNIDAGTM SPLEHGECFV LDDGGETDLD LGNYERYLGI TLSRDHNIT TGKIYSHVIS RERRGDYLGK TVQIVPHLTN AIQDWIQRVS KIPVDDTGLE PDVCIIELGG TVGDIESAPF V EALRQFQF ...String: MKYVVVSGGV ISGIGKGVLA SSTGMLLKTL GLKVTSIKID PYMNIDAGTM SPLEHGECFV LDDGGETDLD LGNYERYLGI TLSRDHNIT TGKIYSHVIS RERRGDYLGK TVQIVPHLTN AIQDWIQRVS KIPVDDTGLE PDVCIIELGG TVGDIESAPF V EALRQFQF EVGRENFALI HVSLVPVIHG EQKTKPTQAA IKDLRSLGLI PDMIACRCSE ELNRSTIDKI AMFCHVGPEQ VV NVHDVNS TYHVPLLLLK QHMIDYLHSR LKLGEVPLTL EDKERGSQLL TNWENMTKNL DDSDDVVKIA LVGKYTNLKD SYL SVTKSL EHASMKCRRQ LEILWVEASN LEPETQEVDK NKFHDSWNKL SSADGILVPG GFGTRGIEGM ILAAKWARES GVPF LGVCL GLQVAAIEFA RNVIGRPNSS STEFLDETLL APEDQVVITM RLGLRPTIFQ PNSEWSNIRK LYGEVNEVHE RHRHR YEIN PKIVNDMESR GFIFVGKDET GQRCEIFELK GHPYYVGTQY HPEYTSKVLE PSRPFWGLVA AASGTLGEVI KDINL UniProtKB: CTP synthase |
-Macromolecule #2: URIDINE 5'-TRIPHOSPHATE
Macromolecule | Name: URIDINE 5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: UTP |
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Molecular weight | Theoretical: 484.141 Da |
Chemical component information | ChemComp-UTP: |
-Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 4 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Macromolecule #4: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 8 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: C-flat / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 90.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 5.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Applied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: OTHER / Software - Name: RELION / Details: FSCref0.5 (Phenix Density modification) / Number images used: 76963 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1) |