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Yorodumi- PDB-8r2h: Cryo-EM structure of 1-deoxy-D-xylulose 5-phosphate synthase (DXP... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8r2h | |||||||||
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Title | Cryo-EM structure of 1-deoxy-D-xylulose 5-phosphate synthase (DXPS) from Plasmodium falciparum | |||||||||
Components | 1-deoxy-D-xylulose-5-phosphate synthase | |||||||||
Keywords | TRANSFERASE / 1-deoxy-D-xylulose 5-phosphate synthase / thiamin di-phosphate complex / transketolase | |||||||||
Function / homology | Function and homology information 1-deoxy-D-xylulose-5-phosphate synthase / 1-deoxy-D-xylulose 5-phosphate biosynthetic process / 1-deoxy-D-xylulose-5-phosphate synthase activity / 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 | |||||||||
Biological species | Plasmodium falciparum (malaria parasite P. falciparum) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.42 Å | |||||||||
Authors | Gawriljuk, V.O. / Godoy, A.S. / Oerlemans, R. / Groves, M.R. | |||||||||
Funding support | European Union, United Kingdom, 2items
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Citation | Journal: Nat Commun / Year: 2024 Title: Cryo-EM structure of 1-deoxy-D-xylulose 5-phosphate synthase DXPS from Plasmodium falciparum reveals a distinct N-terminal domain. Authors: Victor O Gawriljuk / Andre S Godoy / Rick Oerlemans / Luise A T Welker / Anna K H Hirsch / Matthew R Groves / Abstract: Plasmodium falciparum is the main causative agent of malaria, a deadly disease that mainly affects children under five years old. Artemisinin-based combination therapies have been pivotal in ...Plasmodium falciparum is the main causative agent of malaria, a deadly disease that mainly affects children under five years old. Artemisinin-based combination therapies have been pivotal in controlling the disease, but resistance has arisen in various regions, increasing the risk of treatment failure. The non-mevalonate pathway is essential for the isoprenoid synthesis in Plasmodium and provides several under-explored targets to be used in the discovery of new antimalarials. 1-deoxy-D-xylulose-5-phosphate synthase (DXPS) is the first and rate-limiting enzyme of the pathway. Despite its importance, there are no structures available for any Plasmodium spp., due to the complex sequence which contains large regions of high disorder, making crystallisation a difficult task. In this manuscript, we use cryo-electron microscopy to solve the P. falciparum DXPS structure at a final resolution of 2.42 Å. Overall, the structure resembles other DXPS enzymes but includes a distinct N-terminal domain exclusive to the Plasmodium genus. Mutational studies show that destabilization of the cap domain interface negatively impacts protein stability and activity. Additionally, a density for the co-factor thiamine diphosphate is found in the active site. Our work highlights the potential of cryo-EM to obtain structures of P. falciparum proteins that are unfeasible by means of crystallography. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8r2h.cif.gz | 301.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8r2h.ent.gz | 230.7 KB | Display | PDB format |
PDBx/mmJSON format | 8r2h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8r2h_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 8r2h_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 8r2h_validation.xml.gz | 58.9 KB | Display | |
Data in CIF | 8r2h_validation.cif.gz | 85.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r2/8r2h ftp://data.pdbj.org/pub/pdb/validation_reports/r2/8r2h | HTTPS FTP |
-Related structure data
Related structure data | 18842MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 105953.609 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum) Gene: dxs / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O96694 #2: Chemical | #3: Chemical | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Dimer of 1-deoxy-D-xylulose 5-phosphate synthase with Thiamin diphosphate bound. Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Plasmodium falciparum (malaria parasite P. falciparum) |
Source (recombinant) | Organism: Escherichia coli BL21(DE3) (bacteria) |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 800 nm |
Image recording | Electron dose: 44.47 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.42 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 97205 / Algorithm: FOURIER SPACE / Num. of class averages: 2 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||
Atomic model building | Accession code: O96694 / Source name: AlphaFold / Type: in silico model | ||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE |