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

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Basic information

Entry
Database: PDB / ID: 5u03
TitleCryo-EM structure of the human CTP synthase filament
ComponentsCTP synthase 1CTP synthetase
KeywordsLIGASE / PROTEIN FIBRIL / nucleotide metabolism / enzyme / filament
Function / homologyCTP synthase N-terminus / Glutamine amidotransferase type 1 domain profile. / Glutamine amidotransferase class-I / Interconversion of nucleotide di- and triphosphates / CTP synthase GATase domain / Class I glutamine amidotransferase-like / P-loop containing nucleoside triphosphate hydrolase / Glutamine amidotransferase / CTP synthase, N-terminal / CTP synthase ...CTP synthase N-terminus / Glutamine amidotransferase type 1 domain profile. / Glutamine amidotransferase class-I / Interconversion of nucleotide di- and triphosphates / CTP synthase GATase domain / Class I glutamine amidotransferase-like / P-loop containing nucleoside triphosphate hydrolase / Glutamine amidotransferase / CTP synthase, N-terminal / CTP synthase / CTP synthase activity / CTP synthase / 'de novo' CTP biosynthetic process / B cell proliferation / CTP biosynthetic process / nucleobase-containing compound metabolic process / glutamine metabolic process / T cell proliferation / nucleobase-containing small molecule interconversion / response to drug / membrane / ATP binding / identical protein binding / cytosol / CTP synthase 1
Function and homology information
Specimen sourceHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / 6.1 Å resolution
AuthorsLynch, E.M. / Kollman, J.M.
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Nov 22, 2016 / Release: Apr 26, 2017
RevisionDateData content typeGroupCategoryItemProviderType
1.0Apr 26, 2017Structure modelrepositoryInitial release
1.1May 17, 2017Structure modelDatabase references
1.2Jun 21, 2017Structure modelDatabase referencescitation_citation.country / _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

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  • Biological unit as representative helical assembly
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  • Deposited structure unit
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  • Superimposition on EM map
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Structure viewerMolecule:
MolmilJmol/JSmol

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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
Helical symmetryCircular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Number of operations: 4 / Rise per n subunits: 104.1 Å / Rotation per n subunits: 60.6 deg.

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Components

#1: Protein/peptide
CTP synthase 1 / CTP synthetase / CTP synthetase 1 / UTP--ammonia ligase 1


Mass: 66777.297 Da / Num. of mol.: 4 / Source: (gene. exp.) Homo sapiens (human) / Gene: CTPS1, CTPS / Production host: Saccharomyces cerevisiae (baker's yeast) / References: UniProt: P17812, CTP synthase
#2: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 4 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#3: Chemical
ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE


Mass: 484.141 Da / Num. of mol.: 4 / Formula: C9H15N2O15P3 / Uridine triphosphate / Comment: UTP *YM

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / Reconstruction method: helical reconstruction

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Sample preparation

ComponentName: human CTP synthase 1 filament / Type: COMPLEX
Details: hCTPS1 filaments assembled in the presence of UTP, ATP, and GTP
Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Saccharomyces cerevisiae (baker's yeast) / Plasmid: pDO105-hCTPS1
Buffer solutionpH: 7.9
SpecimenConc.: 0.3 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 45 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
13SPIDER3D reconstruction
14hsearch_lorentz3D reconstruction
15ctffind3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
Helical symmertyAngular rotation/subunit: 60.6 deg. / Axial rise/subunit: 104.1 Å / Axial symmetry: C1
3D reconstructionResolution: 6.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 24880 / Symmetry type: HELICAL

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