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- EMDB-24578: Yeast CTP Synthase (Ura7) H360R Filament bound to Substrates -

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Basic information

Entry
Database: EMDB / ID: EMD-24578
TitleYeast CTP Synthase (Ura7) H360R Filament bound to Substrates
Map dataYeast CTPS (Ura7) H360R filament bound to substrates at low pH
Sample
  • Complex: CTP Synthase Bundle assembled with Substrates
    • Protein or peptide: CTP synthaseCTP synthetase
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: URIDINE 5'-TRIPHOSPHATE
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
Biological speciesSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsHansen JM / Lynch EM / Farrell DP / DiMaio F / Quispe J / Kollman JM
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 28, 2021-
Header (metadata) releaseNov 24, 2021-
Map releaseNov 24, 2021-
UpdateNov 24, 2021-
Current statusNov 24, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0158
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0158
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7rmv
  • Surface level: 0.0158
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7rmv
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_24578.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationYeast CTPS (Ura7) H360R filament 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 320 pix.
= 336. Å
1.05 Å/pix.
x 320 pix.
= 336. Å
1.05 Å/pix.
x 320 pix.
= 336. 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
Contour LevelBy AUTHOR: 0.0158 / Movie #1: 0.0158
Minimum - Maximum-0.0022490183 - 0.03022319
Average (Standard dev.)0.00020241864 (±0.0022138339)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z336.000336.000336.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ320320320
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0020.0300.000

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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 synthaseCTP synthetase
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • 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 (baker's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: CTP synthase

MacromoleculeName: CTP synthase / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO / EC number: CTP synthase (glutamine hydrolysing)
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Molecular weightTheoretical: 61.898977 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKYVVVSGGV ISGIGKGVLA SSTGMLMKTL GLKVTSIKID PYMNIDAGTM SPLEHGECFV LDDGGETDLD LGNYERYLGV TLTKDHNIT TGKIYSHVIA KERKGDYLGK TVQIVPHLTN AIQDWIERVA KIPVDDTGME PDVCIIELGG TVGDIESAPF V EALRQFQF ...String:
MKYVVVSGGV ISGIGKGVLA SSTGMLMKTL GLKVTSIKID PYMNIDAGTM SPLEHGECFV LDDGGETDLD LGNYERYLGV TLTKDHNIT TGKIYSHVIA KERKGDYLGK TVQIVPHLTN AIQDWIERVA KIPVDDTGME PDVCIIELGG TVGDIESAPF V EALRQFQF KVGKENFALI HVSLVPVIHG EQKTKPTQAA IKGLRSLGLV PDMIACRCSE TLDKPTIDKI AMFCHVGPEQ VV NVHDVNS TYHVPLLLLE QKMIDYLHAR LKLDEISLTE EEELLSKWKA TTGNFDETVK IALVGKYTNL KDSYLSVIKA LEH SSMKCR RKLDIKWVEA TDLEPEAQES NKTKFREAWN MVSTADGILI PGGFGVRGTE GMVLAARWAR ENHIPFLGVC LGLQ IATIE FTRSVLGRKD SHSAEFYPDI DEKNHVVVFM MRLGLRPTFF QNETEWSQIK KLYGDVSEVH ERHRHRYEIN PKMVD ELEN NGLIFVGKDD TGKRCEILEL KNHPYYIATQ YHPEYTSKVL DPSKPFLGLV AASAGILQDV IEGKYDLEA

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 8 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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Macromolecule #3: URIDINE 5'-TRIPHOSPHATE

MacromoleculeName: URIDINE 5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 8 / Formula: UTP
Molecular weightTheoretical: 484.141 Da
Chemical component information

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

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

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 54928

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