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

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Basic information

Entry
Database: EMDB / ID: EMD-8476
Titlehuman CTP synthase 1 - mutant H355A
Map datahuman CTP synthase 1 - mutant H355A
Sample
  • Complex: hCTPS1-H355A tetramer
    • Protein or peptide: hCTPS1-H355A
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 / identical protein binding / membrane / cytosol / cytoplasm
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
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / negative staining / Resolution: 17.0 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) releaseFeb 8, 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: 0.2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8476.png

Downloads & links

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Map

FileDownload / File: emd_8476.map.gz / Format: CCP4 / Size: 5.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationhuman CTP synthase 1 - mutant H355A
Projections & slices

Image control

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

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.2
Minimum - Maximum-0.012666393 - 0.38952807
Average (Standard dev.)0.015670443 (±0.05302331)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-56-56-56
Dimensions112112112
Spacing112112112
CellA=B=C: 231.84 Å
α=β=γ: 90.0 °

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-152-37
NX/NY/NZ998271
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
Components
  • Complex: hCTPS1-H355A tetramer
    • Protein or peptide: hCTPS1-H355A

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Supramolecule #1: hCTPS1-H355A tetramer

SupramoleculeName: hCTPS1-H355A tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant plasmid: pDO105-hCTPS1-H355A

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Macromolecule #1: hCTPS1-H355A

MacromoleculeName: hCTPS1-H355A / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: MKYILVTGGV ISGIGKGIIA SSVGTILKSC GLHVTSIKID PYINIDAGTF SPYEHGEVFV LDDGGEVDL DLGNYERFLD IRLTKDNNLT TGKIYQYVIN KERKGDYLGK TVQVVPHITD A IQEWVMRQ ALIPVDEDGL EPQVCVIELG GTVGDIESMP FIEAFRQFQF ...String:
MKYILVTGGV ISGIGKGIIA SSVGTILKSC GLHVTSIKID PYINIDAGTF SPYEHGEVFV LDDGGEVDL DLGNYERFLD IRLTKDNNLT TGKIYQYVIN KERKGDYLGK TVQVVPHITD A IQEWVMRQ ALIPVDEDGL EPQVCVIELG GTVGDIESMP FIEAFRQFQF KVKRENFCNI HV SLVPQPS STGEQKTKPT QNSVRELRGL GLSPDLVVCR CSNPLDTSVK EKISMFCHVE PEQ VICVHD VSSIYRVPLL LEEQGVVDYF LRRLDLPIER QPRKMLMKWK EMADRYDRLL ETCS IALVG KYTKFSDSYA SVIKALEHSA LAINHKLEIK YIDSADLEPI TSQEEPVRYA EAWQK LCSA HGVLVPGGFG VRGTEGKIQA IAWARNQKKP FLGVCLGMQL AVVEFSRNVL GWQDAN STE FDPTTSHPVV VDMPEHNPGQ MGGTMRLGKR RTLFQTKNSV MRKLYGDADY LEERHRH RF EVNPVWKKCL EEQGLKFVGQ DVEGERMEIV ELEDHPFFVG VQYHPEFLSR PIKPSPPY F GLLLASVGRL SHYLQKGCRL SPRDTYSDRS GSSSPDSEIT ELKFPSINHD

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.9
StainingType: NEGATIVE / Material: Uranyl Formate
Details20 mM Tris-HCl, pH 7.9, 2 mM UTP, 2 mM ATP, 0.2 mM GTP

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Electron microscopy

MicroscopeFEI TECNAI SPIRIT
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Tecnai Spirit / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: CTFFIND
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 17.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 4413
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION

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