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- EMDB-8475: Cryo-EM structure of the E. coli CTP synthase tetramer -

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Basic information

Entry
Database: EMDB / ID: EMD-8475
TitleCryo-EM structure of the E. coli CTP synthase tetramer
Map dataE. coli CTP synthase tetramer
Sample
  • Complex: E. coli CTP synthase tetramer
    • Protein or peptide: CTP synthase
Keywordsnucleotide metabolism / enzyme / active / LIGASE
Function / homology
Function and homology information


cytoophidium / CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / glutaminase activity / CTP biosynthetic process / glutamine metabolic process / protein homotetramerization / magnesium ion binding ...cytoophidium / CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / glutaminase activity / CTP biosynthetic process / glutamine metabolic process / protein homotetramerization / magnesium ion binding / protein-containing complex / ATP binding / identical protein binding / metal ion 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
CTP synthase / CTP synthase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.9 Å
AuthorsLynch EM / Hicks DR
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-
UpdateOct 23, 2024-
Current statusOct 23, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5u05
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8475.png

Downloads & links

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Map

FileDownload / File: emd_8475.map.gz / Format: CCP4 / Size: 20.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationE. coli CTP synthase tetramer
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.26 Å/pix.
x 176 pix.
= 221.76 Å		1.26 Å/pix.
x 176 pix.
= 221.76 Å		1.26 Å/pix.
x 176 pix.
= 221.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.26 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.3 / Movie #1: 1.3
Minimum - Maximum-1.5031044 - 3.2216463
Average (Standard dev.)-0.000000000875301 (±0.29334778)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-88-88-88
Dimensions176176176
Spacing176176176
CellA=B=C: 221.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.261.261.26
M x/y/z176176176
origin x/y/z0.0000.0000.000
length x/y/z221.760221.760221.760
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-88-88-88
NC/NR/NS176176176
D min/max/mean-1.5033.222-0.000

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Supplemental data

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Sample components

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Entire : E. coli CTP synthase tetramer

EntireName: E. coli CTP synthase tetramer
Components
  • Complex: E. coli CTP synthase tetramer
    • Protein or peptide: CTP synthase

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Supramolecule #1: E. coli CTP synthase tetramer

SupramoleculeName: E. coli CTP synthase tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: CTP synthase

MacromoleculeName: CTP synthase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: CTP synthase (glutamine hydrolysing)
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 60.44698 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTTNYIFVTG GVVSSLGKGI AAASLAAILE ARGLNVTIMK LDPYINVDPG TMSPIQHGEV FVTEDGAETD LDLGHYERFI RTKMSRRNN FTTGRIYSDV LRKERRGDYL GATVQVIPHI TNAIKERVLE GGEGHDVVLV EIGGTVGDIE SLPFLEAIRQ M AVEIGREH ...String:
MTTNYIFVTG GVVSSLGKGI AAASLAAILE ARGLNVTIMK LDPYINVDPG TMSPIQHGEV FVTEDGAETD LDLGHYERFI RTKMSRRNN FTTGRIYSDV LRKERRGDYL GATVQVIPHI TNAIKERVLE GGEGHDVVLV EIGGTVGDIE SLPFLEAIRQ M AVEIGREH TLFMHLTLVP YMAASGEVKT KPTQHSVKEL LSIGIQPDIL ICRSDRAVPA NERAKIALFC NVPEKAVISL KD VDSIYKI PGLLKSQGLD DYICKRFSLN CPEANLSEWE QVIFEEANPV SEVTIGMVGK YIELPDAYKS VIEALKHGGL KNR VSVNIK LIDSQDVETR GVEILKGLDA ILVPGGFGYR GVEGMITTAR FARENNIPYL GICLGMQVAL IDYARHVANM ENAN STEFV PDCKYPVVAL ITEWRDENGN VEVRSEKSDL GGTMRLGAQQ CQLVDDSLVR QLYNAPTIVE RHRHRYEVNN MLLKQ IEDA GLRVAGRSGD DQLVEIIEVP NHPWFVACQF HPEFTSTPRD GHPLFAGFVK AASEFQKRQA K

UniProtKB: CTP synthase

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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

Concentration0.3 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE
Details50 mM HEPES potassium, pH 8.0, 10 mM magnesium chloride, 0.6 mM UTP, 1.5 mM AMP-PNP, 0.2 mM GTP, 10 mM glutamine

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Electron microscopy

MicroscopeFEI TECNAI F20
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 68.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Startup modelType of model: PDB ENTRY
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 7.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 6407
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION

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