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- EMDB-42605: M. tuberculosis CTP synthase filament bound to substrates -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-42605
TitleM. tuberculosis CTP synthase filament bound to substrates
Map data
Sample
  • Complex: CTP synthase filament
    • 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: MAGNESIUM ION
Keywordsmetabolic enzyme / filament / 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: 3.2 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: To Be Published
Title: M. tuberculosis CTP synthase filament bound to substrates
Authors: Lynch EM / Kollman JM
History
DepositionNov 2, 2023-
Header (metadata) releaseJul 2, 2025-
Map releaseJul 2, 2025-
UpdateJul 2, 2025-
Current statusJul 2, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42605.png

Downloads & links

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Map

FileDownload / File: emd_42605.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: 1.0
Minimum - Maximum-10.557053 - 16.989155
Average (Standard dev.)-0.000000000004214 (±0.45318317)
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: #2

Fileemd_42605_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_42605_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 : CTP synthase filament

EntireName: CTP synthase filament
Components
  • Complex: CTP synthase filament
    • 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: MAGNESIUM ION

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Supramolecule #1: CTP synthase filament

SupramoleculeName: CTP synthase filament / 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: 12 / 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: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 2 / Number of copies: 12 / 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: 12 / 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: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 24 / 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: 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: 2.4 µm / Nominal defocus min: 0.8 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: 3.2 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 106254
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-8uv4:
M. tuberculosis CTP synthase filament bound to substrates

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Atomic model buiding 2

RefinementProtocol: FLEXIBLE FIT
Output model

PDB-8uv4:
M. tuberculosis CTP synthase filament bound to substrates

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