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- EMDB-35102: Closed conformation of CTPS with dATP dUTP dGTP and DON -

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Basic information

Entry
Database: EMDB / ID: EMD-35102
TitleClosed conformation of CTPS with dATP dUTP dGTP and DON
Map data
Sample
  • Organelle or cellular component: Drosophila substrate-bound CTP synthase
    • Protein or peptide: CTP synthase
  • Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
  • Ligand: DEOXYURIDINE-5'-TRIPHOSPHATE
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsfilament / 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 / glutamine metabolic process / ATP 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 / glutamine metabolic 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 class-I / Glutamine amidotransferase / 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: 3.4 Å
AuthorsLiu JL / Guo CJ
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Structural basis of bifunctional CTP/dCTP synthase
Authors: Guo CJ / Zhang Z / Zhong J / Liu JL
History
DepositionJan 11, 2023-
Header (metadata) releaseJul 17, 2024-
Map releaseJul 17, 2024-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35102.png

Downloads & links

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Map

FileDownload / File: emd_35102.map.gz / Format: CCP4 / Size: 59.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 250 pix.
= 265. Å		1.06 Å/pix.
x 250 pix.
= 265. Å		1.06 Å/pix.
x 250 pix.
= 265. Å

Surface

Projections

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.3019406 - 0.6238438
Average (Standard dev.)0.0012064371 (±0.02699969)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions250250250
Spacing250250250
CellA=B=C: 265.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_35102_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Half map: #1

Fileemd_35102_half_map_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_35102_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

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Sample components

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Entire : Drosophila substrate-bound CTP synthase

EntireName: Drosophila substrate-bound CTP synthase
Components
  • Organelle or cellular component: Drosophila substrate-bound CTP synthase
    • Protein or peptide: CTP synthase
  • Ligand: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE
  • Ligand: DEOXYURIDINE-5'-TRIPHOSPHATE
  • Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Drosophila substrate-bound CTP synthase

SupramoleculeName: Drosophila substrate-bound CTP synthase / type: organelle_or_cellular_component / 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: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

MacromoleculeName: 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 1 / Formula: DTP
Molecular weightTheoretical: 491.182 Da
Chemical component information

ChemComp-DTP:
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE

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Macromolecule #3: DEOXYURIDINE-5'-TRIPHOSPHATE

MacromoleculeName: DEOXYURIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: DUT
Molecular weightTheoretical: 468.142 Da
Chemical component information

ChemComp-DUT:
DEOXYURIDINE-5'-TRIPHOSPHATE

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Macromolecule #4: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 1 / Formula: DGT
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-DGT:
2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: DARK FIELD / Nominal defocus max: 20.0 µm / Nominal defocus min: 5.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 434720
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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