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- EMDB-8474: Cryo-EM structure of the human CTP synthase filament -

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Basic information

Entry
Database: EMDB / ID: EMD-8474
TitleCryo-EM structure of the human CTP synthase filament
Map dataHuman CTP synthase filament
Sample
  • Complex: human CTP synthase 1 filament
    • Protein or peptide: CTP synthase 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: URIDINE 5'-TRIPHOSPHATE
Function / homology
Function and homology information


cytoophidium / CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / Interconversion of nucleotide di- and triphosphates / CTP biosynthetic process / nucleobase-containing compound metabolic process / glutamine metabolic process / B cell proliferation ...cytoophidium / CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / Interconversion of nucleotide di- and triphosphates / CTP biosynthetic process / nucleobase-containing compound metabolic process / glutamine metabolic process / B cell proliferation / T cell proliferation / response to xenobiotic stimulus / ATP binding / membrane / identical protein binding / cytosol / cytoplasm
Similarity search - Function
CTP synthase / CTP synthase, N-terminal / CTP synthase GATase domain / CTP synthase N-terminus / Glutamine amidotransferase class-I / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / Class I glutamine amidotransferase-like / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Methodhelical reconstruction / cryo EM / Resolution: 6.1 Å
AuthorsLynch EM / Kollman JM
CitationJournal: 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.
History
DepositionNov 22, 2016-
Header (metadata) releaseApr 26, 2017-
Map releaseApr 26, 2017-
UpdateJul 18, 2018-
Current statusJul 18, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.8
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 3.8
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5u03
  • Surface level: 3.8
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_8474.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHuman CTP synthase filament
Voxel sizeX=Y=Z: 1.26 Å
Density
Contour LevelBy AUTHOR: 3.8 / Movie #1: 3.8
Minimum - Maximum-8.421113 - 15.893713
Average (Standard dev.)0.000000000169333 (±0.6589945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-192-192-192
Dimensions384384384
Spacing384384384
CellA=B=C: 483.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.261.261.26
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z483.840483.840483.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-192-192-192
NC/NR/NS384384384
D min/max/mean-8.42115.8940.000

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Supplemental data

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Sample components

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Entire : human CTP synthase 1 filament

EntireName: human CTP synthase 1 filament
Components
  • Complex: human CTP synthase 1 filament
    • Protein or peptide: CTP synthase 1
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: URIDINE 5'-TRIPHOSPHATE

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Supramolecule #1: human CTP synthase 1 filament

SupramoleculeName: human CTP synthase 1 filament / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: hCTPS1 filaments assembled in the presence of UTP, ATP, and GTP
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant plasmid: pDO105-hCTPS1

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Macromolecule #1: CTP synthase 1

MacromoleculeName: CTP synthase 1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: CTP synthase (glutamine hydrolysing)
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 66.777297 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MKYILVTGGV ISGIGKGIIA SSVGTILKSC GLHVTSIKID PYINIDAGTF SPYEHGEVFV LDDGGEVDLD LGNYERFLDI RLTKDNNLT TGKIYQYVIN KERKGDYLGK TVQVVPHITD AIQEWVMRQA LIPVDEDGLE PQVCVIELGG TVGDIESMPF I EAFRQFQF ...String:
MKYILVTGGV ISGIGKGIIA SSVGTILKSC GLHVTSIKID PYINIDAGTF SPYEHGEVFV LDDGGEVDLD LGNYERFLDI RLTKDNNLT TGKIYQYVIN KERKGDYLGK TVQVVPHITD AIQEWVMRQA LIPVDEDGLE PQVCVIELGG TVGDIESMPF I EAFRQFQF KVKRENFCNI HVSLVPQPSS TGEQKTKPTQ NSVRELRGLG LSPDLVVCRC SNPLDTSVKE KISMFCHVEP EQ VICVHDV SSIYRVPLLL EEQGVVDYFL RRLDLPIERQ PRKMLMKWKE MADRYDRLLE TCSIALVGKY TKFSDSYASV IKA LEHSAL AINHKLEIKY IDSADLEPIT SQEEPVRYHE AWQKLCSAHG VLVPGGFGVR GTEGKIQAIA WARNQKKPFL GVCL GMQLA VVEFSRNVLG WQDANSTEFD PTTSHPVVVD MPEHNPGQMG GTMRLGKRRT LFQTKNSVMR KLYGDADYLE ERHRH RFEV NPVWKKCLEE QGLKFVGQDV EGERMEIVEL EDHPFFVGVQ YHPEFLSRPI KPSPPYFGLL LASVGRLSHY LQKGCR LSP RDTYSDRSGS SSPDSEITEL KFPSINHD

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Macromolecule #2: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / 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: 4 / 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
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

Concentration0.3 mg/mL
BufferpH: 7.9
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: Cylinder
Final angle assignmentType: NOT APPLICABLE
Final reconstructionApplied symmetry - Helical parameters - Δz: 104.1 Å
Applied symmetry - Helical parameters - Δ&Phi: 60.6 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: SPIDER, hsearch_lorentz, CTFFIND) / Number images used: 24880

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