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- EMDB-8476: human CTP synthase 1 - mutant H355A -

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Basic information

Entry
Database: EMDB / ID: 8476
Titlehuman CTP synthase 1 - mutant H355A
Map datahuman CTP synthase 1 - mutant H355A
SamplehCTPS1-H355A tetramer
  • hCTPS1-H355A
Function/homologyCTP synthase / CTP synthase activity / CTP synthase GATase domain / CTP synthase, N-terminal / CTP synthase / CTP synthase N-terminus / 'de novo' CTP biosynthetic process / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / B cell proliferation ...CTP synthase / CTP synthase activity / CTP synthase GATase domain / CTP synthase, N-terminal / CTP synthase / CTP synthase N-terminus / 'de novo' CTP biosynthetic process / Glutamine amidotransferase / Glutamine amidotransferase type 1 domain profile. / B cell proliferation / CTP biosynthetic process / Glutamine amidotransferase class-I / nucleobase-containing compound metabolic process / Interconversion of nucleotide di- and triphosphates / glutamine metabolic process / T cell proliferation / nucleobase-containing small molecule interconversion / Class I glutamine amidotransferase-like / response to drug / P-loop containing nucleoside triphosphate hydrolase / membrane / ATP binding / identical protein binding / cytosol / | / CTP synthase 1
Function and homology information
SourceHomo sapiens / / human
Methodsingle particle reconstruction / 17 Å resolution
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.
DateDeposition: Nov 22, 2016 / Header (metadata) release: Feb 8, 2017 / Map release: Apr 26, 2017 / Last update: Jun 21, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.2
  • Imaged by UCSF CHIMERA
  • Download
3D viewer
Supplemental images

Downloads & links

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Map

Fileemd_8476.map.gz (map file in CCP4 format, 5620 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
112 pix
2.07 Å/pix.
= 231.84 Å
112 pix
2.07 Å/pix.
= 231.84 Å
112 pix
2.07 Å/pix.
= 231.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.07 Å
Density
Contour Level:0.2 (by author), 0.2 (movie #1):
Minimum - Maximum-0.012666393 - 0.38952807
Average (Standard dev.)0.015670443 (0.05302331)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions112112112
Origin-56-56-56
Limit555555
Spacing112112112
CellA=B=C: 231.84 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.072.072.07
M x/y/z112112112
origin x/y/z0.0000.0000.000
length x/y/z231.840231.840231.840
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-56-56-56
NC/NR/NS112112112
D min/max/mean-0.0130.3900.016

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Supplemental data

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Sample components

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Entire hCTPS1-H355A tetramer

EntireName: hCTPS1-H355A tetramer / Number of components: 2

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Component #1: protein, hCTPS1-H355A tetramer

ProteinName: hCTPS1-H355A tetramer / Recombinant expression: No
SourceSpecies: Homo sapiens / / human
Source (engineered)Expression System: Saccharomyces cerevisiae / / yeast / / Vector: pDO105-hCTPS1-H355A

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Component #2: protein, hCTPS1-H355A

ProteinName: hCTPS1-H355A / Recombinant expression: No
Source (engineered)Expression System: Homo sapiens / / human

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle
Sample solutionpH: 7.9
VitrificationCryogen name: NONE

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI SPIRIT
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 120 kV / Electron dose: 40 e/Å2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: D2 (2*2 fold dihedral) / Number of projections: 4413
3D reconstructionSoftware: RELION / Resolution: 17 Å / Resolution method: FSC 0.143 CUT-OFF

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