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- PDB-5u03: Cryo-EM structure of the human CTP synthase filament -

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Entry
Database: PDB / ID: 5u03
TitleCryo-EM structure of the human CTP synthase filament
DescriptorCTP synthase 1 (E.C.6.3.4.2)
KeywordsLIGASE / PROTEIN FIBRIL / nucleotide metabolism / enzyme / filament
Specimen sourceHomo sapiens / human
MethodElectron microscopy (6.1 A resolution / Helical)
AuthorsLynch, E.M. / Kollman, J.M.
CitationNat. Struct. Mol. Biol., 2017

Nat. Struct. Mol. Biol., 2017 StrPapers
Human CTP synthase filament structure reveals the active enzyme conformation.
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

DateDeposition: Nov 22, 2016 / Release: Apr 26, 2017 / Last modification: May 17, 2017

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Assembly

Deposited unit
A: CTP synthase 1
B: CTP synthase 1
C: CTP synthase 1
D: CTP synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)271,07412
Polyers267,1094
Non-polymers3,9658
Water0
#1
A: CTP synthase 1
B: CTP synthase 1
C: CTP synthase 1
D: CTP synthase 1
hetero molecules

A: CTP synthase 1
B: CTP synthase 1
C: CTP synthase 1
D: CTP synthase 1
hetero molecules

A: CTP synthase 1
B: CTP synthase 1
C: CTP synthase 1
D: CTP synthase 1
hetero molecules

A: CTP synthase 1
B: CTP synthase 1
C: CTP synthase 1
D: CTP synthase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,084,29848
Polyers1,068,43716
Non-polymers15,86132
Water0
TypeNameSymmetry operationNumber
helical symmetry operation4
#2


  • idetical with deposited unit in distinct coordinate
  • helical asymmetric unit
TypeNameSymmetry operationNumber
helical symmetry operation1
#3


  • idetical with deposited unit in distinct coordinate
  • helical asymmetric unit, std helical frame
TypeNameSymmetry operationNumber
transform to helical frame1

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Components

#1: Polypeptide(L)
CTP synthase 1 / CTP synthetase 1 / UTP--ammonia ligase 1


Mass: 66777.297 Da / Num. of mol.: 4 / Source: (gene. exp.) Homo sapiens / human / References: UniProt: P17812, EC: 6.3.4.2
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / ATP (energy-carrying molecule) *YM


Mass: 507.181 Da / Num. of mol.: 4 / Formula: C10H16N5O13P3
#3: Chemical
ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / UTP *YM


Mass: 484.141 Da / Num. of mol.: 4 / Formula: C9H15N2O15P3

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentReconstruction method: HELICAL

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Sample preparation

ComponentName: human CTP synthase 1 filament
Details: hCTPS1 filaments assembled in the presence of UTP, ATP, and GTP
Type: COMPLEX
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyMicroscope model: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD

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Processing

EM helical entityAngular rotation per subunit: 60.6 deg. / Axial rise per subunit: 104.1 A / Axial symmetry: C1
3D reconstructionResolution: 6.1 A / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 24880

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