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- EMDB-24581: Yeast CTP Synthase (Ura8) Bundle Bound to Substrates at Low pH -

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Basic information

Entry
Database: EMDB / ID: EMD-24581
TitleYeast CTP Synthase (Ura8) Bundle Bound to Substrates at Low pH
Map dataYeast CTP Synthase (Ura8) Bundle bound to substrates at low pH
Sample
  • Complex: CTP Synthase Bundle assembled with Substrates
    • Protein or peptide: CTP synthase
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: URIDINE 5'-TRIPHOSPHATE
Keywordsglutaminase and amido-ligase / 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
CTP synthase / CTP synthase, N-terminal / CTP synthase GATase domain / CTP synthase N-terminus / Glutamine amidotransferase / Glutamine amidotransferase class-I / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase-like / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHansen JM / Lynch EM
Funding support2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01 GM118396
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)T32 GM007270
CitationJournal: 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
DepositionJul 29, 2021-
Header (metadata) releaseNov 24, 2021-
Map releaseNov 24, 2021-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.8
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  • Surface view with fitted model
  • Atomic models: PDB-7rnr
  • Surface level: 0.8
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7rnr
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24581.png

Downloads & links

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Map

FileDownload / File: emd_24581.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationYeast CTP Synthase (Ura8) Bundle bound to substrates at low pH
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 512 pix.
= 537.6 Å		1.05 Å/pix.
x 512 pix.
= 537.6 Å		1.05 Å/pix.
x 512 pix.
= 537.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.8 / Movie #1: 0.8
Minimum - Maximum-6.069124 - 10.085661999999999
Average (Standard dev.)-0.000000000208925 (±0.119653895)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 537.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z537.600537.600537.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-6.06910.086-0.000

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Supplemental data

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Sample components

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Entire : CTP Synthase Bundle assembled with Substrates

EntireName: CTP Synthase Bundle assembled with Substrates
Components
  • Complex: CTP Synthase Bundle assembled with Substrates
    • Protein or peptide: CTP synthase
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: URIDINE 5'-TRIPHOSPHATE

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Supramolecule #1: CTP Synthase Bundle assembled with Substrates

SupramoleculeName: CTP Synthase Bundle assembled with Substrates / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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Macromolecule #1: CTP synthase

MacromoleculeName: CTP synthase / type: protein_or_peptide / ID: 1 / Number of copies: 20 / Enantiomer: LEVO / EC number: CTP synthase (glutamine hydrolysing)
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 62.439168 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 20 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 40 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: URIDINE 5'-TRIPHOSPHATE

MacromoleculeName: URIDINE 5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 20 / Formula: UTP
Molecular weightTheoretical: 484.141 Da
Chemical component information

ChemComp-UTP:
URIDINE 5'-TRIPHOSPHATE / UTP*YM

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 90.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: OTHER / Details: FSCref0.5 (Phenix Density Modification) / Number images used: 21220
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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