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- EMDB-42611: M. tuberculosis CTP synthase tetramer bound to CTP -

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Basic information

Entry
Database: EMDB / ID: EMD-42611
TitleM. tuberculosis CTP synthase tetramer bound to CTP
Map data
Sample
  • Complex: CTP synthase tetramer
    • Protein or peptide: CTP synthase
  • Ligand: CYTIDINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION
Keywordsmetabolic enzyme / LIGASE
Function / homology
Function and homology information


cytoophidium / CTP synthase (glutamine hydrolysing) / CTP synthase activity / 'de novo' CTP biosynthetic process / pyrimidine nucleobase biosynthetic process / ATP binding / metal ion binding / identical protein 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
Biological speciesMycobacterium tuberculosis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsLynch EM / Kollman JM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35 GM149542 United States
CitationJournal: Nat Commun / Year: 2025
Title: Evolutionarily divergent Mycobacterium tuberculosis CTP synthase filaments are under selective pressure.
Authors: Eric M Lynch / Yao Lu / Jin Ho Park / Lin Shao / Justin M Kollman / E Hesper Rego /
Abstract: The final and rate-limiting enzyme in pyrimidine biosynthesis, cytidine triphosphate synthase (CTPS), is essential for the viability of Mycobacterium tuberculosis and other mycobacteria. Its product, ...The final and rate-limiting enzyme in pyrimidine biosynthesis, cytidine triphosphate synthase (CTPS), is essential for the viability of Mycobacterium tuberculosis and other mycobacteria. Its product, cytidine triphosphate (CTP), is critical for RNA, DNA, lipid and cell wall synthesis, and is involved in chromosome segregation. In various organisms across the tree of life, CTPS assembles into higher-order filaments, leading us to hypothesize that M. tuberculosis CTPS (mtCTPS) also forms higher-order structures. Here, we show that mtCTPS does assemble into filaments but with an unusual architecture not seen in other organisms. Through a combination of structural, biochemical, and cellular techniques, we show that polymerization stabilizes the active conformation of the enzyme and resists product inhibition, potentially allowing for the highly localized production of CTP within the cell. Indeed, CTPS filaments localize near the CTP-dependent complex needed for chromosome segregation, and cells expressing mutant enzymes unable to polymerize are altered in their ability to robustly form this complex. Intriguingly, mutants that inhibit filament formation are under positive selection in clinical isolates of M. tuberculosis, pointing to a critical role needed to withstand pressures imposed by the host and/or antibiotics. Taken together, our data reveal an unexpected mechanism for the spatially organized production of a critical nucleotide in M. tuberculosis, which may represent a vulnerability of the pathogen that can be exploited with chemotherapy.
History
DepositionNov 2, 2023-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42611.png

Downloads & links

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Map

FileDownload / File: emd_42611.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
1.16 Å/pix.
x 300 pix.
= 348. Å		1.16 Å/pix.
x 300 pix.
= 348. Å		1.16 Å/pix.
x 300 pix.
= 348. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.16 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.24
Minimum - Maximum-11.100705 - 16.189223999999999
Average (Standard dev.)-0.000000000000755 (±0.28577477)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 348.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_42611_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_42611_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : CTP synthase tetramer

EntireName: CTP synthase tetramer
Components
  • Complex: CTP synthase tetramer
    • Protein or peptide: CTP synthase
  • Ligand: CYTIDINE-5'-TRIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: CTP synthase tetramer

SupramoleculeName: CTP synthase tetramer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)

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Macromolecule #1: CTP synthase

MacromoleculeName: CTP synthase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Mycobacterium tuberculosis (bacteria)
Molecular weightTheoretical: 64.542797 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MRKHPQTATK HLFVSGGVAS SLGKGLTASS LGQLLTARGL HVTMQKLDPY LNVDPGTMNP FQHGEVFVTE DGAETDLDVG HYERFLDRN LPGSANVTTG QVYSTVIAKE RRGEYLGDTV QVIPHITDEI KRRILAMAQP DADGNRPDVV ITEIGGTVGD I ESQPFLEA ...String:
MRKHPQTATK HLFVSGGVAS SLGKGLTASS LGQLLTARGL HVTMQKLDPY LNVDPGTMNP FQHGEVFVTE DGAETDLDVG HYERFLDRN LPGSANVTTG QVYSTVIAKE RRGEYLGDTV QVIPHITDEI KRRILAMAQP DADGNRPDVV ITEIGGTVGD I ESQPFLEA ARQVRHYLGR EDVFFLHVSL VPYLAPSGEL KTKPTQHSVA ALRSIGITPD ALILRCDRDV PEALKNKIAL MC DVDIDGV ISTPDAPSIY DIPKVLHREE LDAFVVRRLN LPFRDVDWTE WDDLLRRVHE PHETVRIALV GKYVELSDAY LSV AEALRA GGFKHRAKVE ICWVASDGCE TTSGAAAALG DVHGVLIPGG FGIRGIEGKI GAIAYARARG LPVLGLCLGL QCIV IEAAR SVGLTNANSA EFDPDTPDPV IATMPDQEEI VAGEADLGGT MRLGSYPAVL EPDSVVAQAY QTTQVSERHR HRYEV NNAY RDKIAESGLR FSGTSPDGHL VEFVEYPPDR HPFVVGTQAH PELKSRPTRP HPLFVAFVGA AIDYKAGELL PVEIPE IPE HTPNGSSHRD GVGQPLPEPA SRGHHHHHH

UniProtKB: CTP synthase

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Macromolecule #2: CYTIDINE-5'-TRIPHOSPHATE

MacromoleculeName: CYTIDINE-5'-TRIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 8 / Formula: CTP
Molecular weightTheoretical: 483.156 Da
Chemical component information

ChemComp-CTP:
CYTIDINE-5'-TRIPHOSPHATE

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 4 / 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 stateparticle

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Sample preparation

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 65.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionApplied symmetry - Point group: D2 (2x2 fold dihedral) / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 31423
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-8uv8:
M. tuberculosis CTP synthase tetramer bound to CTP

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Atomic model buiding 2

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-8uv8:
M. tuberculosis CTP synthase tetramer bound to CTP

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