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- EMDB-18842: Cryo-EM structure of 1-deoxy-D-xylulose 5-phosphate synthase (DXP... -

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Basic information

Entry
Database: EMDB / ID: EMD-18842
TitleCryo-EM structure of 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Plasmodium falciparum
Map data
Sample
  • Complex: Dimer of 1-deoxy-D-xylulose 5-phosphate synthase with Thiamin diphosphate bound.
    • Protein or peptide: 1-deoxy-D-xylulose-5-phosphate synthase
  • Ligand: MAGNESIUM ION
  • Ligand: THIAMINE DIPHOSPHATE
Keywords1-deoxy-D-xylulose 5-phosphate synthase / thiamin di-phosphate complex / transketolase / TRANSFERASE
Function / homology
Function and homology information


1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase activity / 1-deoxy-D-xylulose 5-phosphate biosynthetic process / chlorophyll biosynthetic process / thiamine biosynthetic process / isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway / terpenoid biosynthetic process / chloroplast / membrane / metal ion binding / cytosol
Similarity search - Function
Deoxyxylulose-5-phosphate synthase / 1-deoxy-D-xylulose-5-phosphate synthase / Transketolase binding site / Transketolase signature 2. / Transketolase, C-terminal domain / Transketolase, C-terminal domain / Transketolase-like, pyrimidine-binding domain / Transketolase, pyrimidine binding domain / Transketolase, pyrimidine binding domain / Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II / Thiamin diphosphate-binding fold
Similarity search - Domain/homology
1-deoxy-D-xylulose-5-phosphate synthase
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.42 Å
AuthorsGawriljuk VO / Godoy AS / Oerlemans R / Groves MR
Funding supportEuropean Union, United Kingdom, 2 items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission860816European Union
Medical Research Council (MRC, United Kingdom)218785/Z/19/Z United Kingdom
CitationJournal: To Be Published
Title: Cryo-EM structure of 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Plasmodium falciparum
Authors: Gawriljuk VO / Godoy AS / Oerlemans R / Groves MR
History
DepositionNov 6, 2023-
Header (metadata) releaseJun 12, 2024-
Map releaseJun 12, 2024-
UpdateJun 12, 2024-
Current statusJun 12, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18842.png

Downloads & links

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Map

FileDownload / File: emd_18842.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.74 Å
Density
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.059852377 - 2.205356
Average (Standard dev.)0.0009618149 (±0.021254776)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 296.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_18842_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: #1

Fileemd_18842_additional_1.map
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18842_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_18842_half_map_2.map
Projections & Slices
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Sample components

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Entire : Dimer of 1-deoxy-D-xylulose 5-phosphate synthase with Thiamin dip...

EntireName: Dimer of 1-deoxy-D-xylulose 5-phosphate synthase with Thiamin diphosphate bound.
Components
  • Complex: Dimer of 1-deoxy-D-xylulose 5-phosphate synthase with Thiamin diphosphate bound.
    • Protein or peptide: 1-deoxy-D-xylulose-5-phosphate synthase
  • Ligand: MAGNESIUM ION
  • Ligand: THIAMINE DIPHOSPHATE

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Supramolecule #1: Dimer of 1-deoxy-D-xylulose 5-phosphate synthase with Thiamin dip...

SupramoleculeName: Dimer of 1-deoxy-D-xylulose 5-phosphate synthase with Thiamin diphosphate bound.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)

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Macromolecule #1: 1-deoxy-D-xylulose-5-phosphate synthase

MacromoleculeName: 1-deoxy-D-xylulose-5-phosphate synthase / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Plasmodium falciparum (malaria parasite P. falciparum)
Molecular weightTheoretical: 105.953609 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MYDIGKYFKQ INTFINIDEY KTIYGDEIYK EIYELYVERN IPEYYERKYF SEDIKKSVLF DIDKYNDVE FEKAIKEEFI NNGVYINNID NTYYKKENIL IMKKILHYFP LLKLINNPSD LKKLKKQYLP LLAHELKIFL F FIVNITGG ...String:
MGSSHHHHHH SSGLVPRGSH MYDIGKYFKQ INTFINIDEY KTIYGDEIYK EIYELYVERN IPEYYERKYF SEDIKKSVLF DIDKYNDVE FEKAIKEEFI NNGVYINNID NTYYKKENIL IMKKILHYFP LLKLINNPSD LKKLKKQYLP LLAHELKIFL F FIVNITGG HFSSVLSSLE IQLLLLYIFN QPYDNVIYDI GHQAYVHKIL TGRKLLFLSL RNKKGISGFL NIFESIYDKF GA GHSSTSL SAIQGYYEAE WQVKNKEKYG NGDIEISDNA NVTNNERIFQ KGIHNDNNIN NNINNNNYIN PSDVVGRENT NVP NVRNDN HNVDKVHIAI IGDGGLTGGM ALEALNYISF LNSKILIIYN DNGQVSLPTN AVSISGNRPI GSISDHLHYF VSNI EANAG DNKLSKNAKE NNIFENLNYD YIGVVNGNNT EELFKVLNNI KENKLKRATV LHVRTKKSND FINSKSPISI LHSIK KNEI FPFDTTILNG NIHKENKIEE EKNVSSSTKY DVNNKNNKNN DNSEIIKYED MFSKETFTDI YTNEMLKYLK KDRNII FLS PAMLGGSGLV KISERYPNNV YDVGIAEQHS VTFAAAMAMN KKLKIQLCIY STFLQRAYDQ IIHDLNLQNI PLKVIIG RS GLVGEDGATH QGIYDLSYLG TLNNAYIISP SNQVDLKRAL RFAYLDKDHS VYIRIPRMNI LSDKYMKGYL NIHMKNES K NIDVNVDIND DVDKYSEEYM DDDNFIKSFI GKSRIIKMDN ENNNTNEHYS SRGDTQTKKK KVCIFNMGSM LFNVINAIK EIEKEQYISH NYSFSIVDMI FLNPLDKNMI DHVIKQNKHQ YLITYEDNTI GGFSTHFNNY LIENNYITKH NLYVHNIYLS NEPIEHASF KDQQEVVKMD KCSLVNRIKN YLKNNPT

UniProtKB: 1-deoxy-D-xylulose-5-phosphate synthase

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Macromolecule #2: MAGNESIUM ION

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

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Macromolecule #3: THIAMINE DIPHOSPHATE

MacromoleculeName: THIAMINE DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 2 / Formula: TPP
Molecular weightTheoretical: 425.314 Da
Chemical component information

ChemComp-TPP:
THIAMINE DIPHOSPHATE

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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

Concentration0.9 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 44.47 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF
Software: (Name: Coot (ver. 0.9.6), PHENIX (ver. 1.20.1-4487))
Number images used: 97205
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.1.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6694


Chain - Source name: AlphaFold / Chain - Initial model type: in silico model
Output model

PDB-8r2h:
Cryo-EM structure of 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Plasmodium falciparum

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