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- EMDB-63990: CTP synthase DON-state -

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Basic information

Entry
Database: EMDB / ID: EMD-63990
TitleCTP synthase DON-state
Map data
Sample
  • Complex: DON-state CTP synthase
    • Protein or peptide: CTP synthase
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(2-oxidanyl-4-phosphonooxy-pyrimidin-1-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: 5-OXO-L-NORLEUCINE
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsCTP synthase / CTPS / LIGASE
Function / homology
Function and homology information


Interconversion of nucleotide di- and triphosphates / larval lymph gland hemopoiesis / CTP synthase (glutamine hydrolysing) / CTP synthase activity / cytoophidium / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / CTP biosynthetic process / ATP binding / identical protein binding ...Interconversion of nucleotide di- and triphosphates / larval lymph gland hemopoiesis / CTP synthase (glutamine hydrolysing) / CTP synthase activity / cytoophidium / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / CTP biosynthetic process / ATP binding / identical protein binding / cytoplasm / 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
Biological speciesDrosophila melanogaster (fruit fly)
Methodsingle particle reconstruction / cryo EM / Resolution: 1.99 Å
AuthorsGuo CJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: CTP synthase DON-state
Authors: Guo CJ
History
DepositionApr 1, 2025-
Header (metadata) releaseApr 8, 2026-
Map releaseApr 8, 2026-
UpdateApr 8, 2026-
Current statusApr 8, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_63990.png

Downloads & links

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Map

FileDownload / File: emd_63990.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.71 Å/pix.
x 384 pix.
= 271.488 Å		0.71 Å/pix.
x 384 pix.
= 271.488 Å		0.71 Å/pix.
x 384 pix.
= 271.488 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.707 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-1.0611299 - 1.8410017
Average (Standard dev.)0.00042369266 (±0.022872658)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 271.488 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63990_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_63990_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_63990_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : DON-state CTP synthase

EntireName: DON-state CTP synthase
Components
  • Complex: DON-state CTP synthase
    • Protein or peptide: CTP synthase
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(2-oxidanyl-4-phosphonooxy-pyrimidin-1-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
  • Ligand: GUANOSINE-5'-TRIPHOSPHATE
  • Ligand: 5-OXO-L-NORLEUCINE
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: DON-state CTP synthase

SupramoleculeName: DON-state CTP synthase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Drosophila melanogaster (fruit fly)

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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: Drosophila melanogaster (fruit fly)
Molecular weightTheoretical: 62.443656 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: MKYILVTGGV ISGVGKGVIA SSFGTLLKSC GLDVTSIKID PYINIDAGTF SPYEHGEVYV LDDGAEVDLD LGNYERFLDV TLHRDNNIT TGKIYKLVIE KERTGEYLGK TVQVVPHITD AIQEWVERVA QTPVQGSSKP QVCIVELGGT IGDIEGMPFV E AFRQFQFR ...String:
MKYILVTGGV ISGVGKGVIA SSFGTLLKSC GLDVTSIKID PYINIDAGTF SPYEHGEVYV LDDGAEVDLD LGNYERFLDV TLHRDNNIT TGKIYKLVIE KERTGEYLGK TVQVVPHITD AIQEWVERVA QTPVQGSSKP QVCIVELGGT IGDIEGMPFV E AFRQFQFR VKRENFCLAH VSLVPLPKAT GEPKTKPTQS SVRELRGCGL SPDLIVCRSE KPIGLEVKEK ISNFCHVGPD QV ICIHDLN SIYHVPLLME QNGVIEYLNE RLQLNIDMSK RTKCLQQWRD LARRTETVRR EVCIAVVGKY TKFTDSYASV VKA LQHAAL AVNRKLELVF IESCLLEEET LHSEPSKYHK EWQKLCDSHG ILVPGGFGSR GMEGKIRACQ WARENQKPLL GICL GLQAA VIEFARNKLG LKDANTTEID PNTANALVID MPEHHTGQLG GTMRLGKRIT VFSDGPSVIR QLYGNPKSVQ ERHRH RYEV NPKYVHLLEE QGMRFVGTDV DKTRMEIIEL SGHPYFVATQ YHPEYLSRPL KPSPPFLGLI LASVDRLNQY IQ

UniProtKB: CTP synthase

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Macromolecule #2: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 4 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #3: [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(2-oxidanyl-4-pho...

MacromoleculeName: [[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(2-oxidanyl-4-phosphonooxy-pyrimidin-1-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate
type: ligand / ID: 3 / Number of copies: 4 / Formula: 5ZL
Molecular weightTheoretical: 565.129 Da
Chemical component information

ChemComp-5ZL:
[[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(2-oxidanyl-4-phosphonooxy-pyrimidin-1-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate

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Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 4 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM

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Macromolecule #5: 5-OXO-L-NORLEUCINE

MacromoleculeName: 5-OXO-L-NORLEUCINE / type: ligand / ID: 5 / Number of copies: 4 / Formula: ONL
Molecular weightTheoretical: 145.156 Da
Chemical component information

ChemComp-ONL:
5-OXO-L-NORLEUCINE

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Macromolecule #6: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 6 / Number of copies: 16 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #7: water

MacromoleculeName: water / type: ligand / ID: 7 / Number of copies: 888 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7dpt

Final reconstructionResolution.type: BY AUTHOR / Resolution: 1.99 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 894213
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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