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- EMDB-21459: Cryo-EM structure of Plasmodium vivax hexokinase (Closed state) -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-21459 | |||||||||
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Title | Cryo-EM structure of Plasmodium vivax hexokinase (Closed state) | |||||||||
![]() | Plasmodium vivax hexokinase (Closed state) | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Srivastava SS / Darling JE / Suryadi J / Morris JC / Drew ME / Subramaniam S | |||||||||
Funding support | ![]()
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![]() | ![]() Title: and human hexokinases share similar active sites but display distinct quaternary architectures. Authors: Shanti Swaroop Srivastava / Joseph E Darling / Jimmy Suryadi / James C Morris / Mark E Drew / Sriram Subramaniam / ![]() ![]() Abstract: Malaria is a devastating disease caused by a protozoan parasite. It affects over 300 million individuals and results in over 400 000 deaths annually, most of whom are young children under the age ...Malaria is a devastating disease caused by a protozoan parasite. It affects over 300 million individuals and results in over 400 000 deaths annually, most of whom are young children under the age of five. Hexokinase, the first enzyme in glucose metabolism, plays an important role in the infection process and represents a promising target for therapeutic intervention. Here, cryo-EM structures of two conformational states of hexokinase (PvHK) are reported at resolutions of ∼3 Å. It is shown that unlike other known hexokinase structures, PvHK displays a unique tetrameric organization (∼220 kDa) that can exist in either open or closed quaternary conformational states. Despite the resemblance of the active site of PvHK to its mammalian counterparts, this tetrameric organization is distinct from that of human hexokinases, providing a foundation for the structure-guided design of parasite-selective antimalarial drugs. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.6 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 11.9 KB 11.9 KB | Display Display | ![]() |
Images | ![]() | 178.5 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6vygMC ![]() 6vyfC C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Plasmodium vivax hexokinase (Closed state) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.8354 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Plasmodium vivax hexokinase
Entire | Name: Plasmodium vivax hexokinase |
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Components |
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-Supramolecule #1: Plasmodium vivax hexokinase
Supramolecule | Name: Plasmodium vivax hexokinase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: ![]() ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() ![]() |
-Macromolecule #1: Phosphotransferase
Macromolecule | Name: Phosphotransferase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO EC number: ![]() |
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Source (natural) | Organism: ![]() ![]() ![]() |
Molecular weight | Theoretical: 56.851543 KDa |
Recombinant expression | Organism: ![]() ![]() ![]() |
Sequence | String: MRGSHHHHHH GSMSYYNLEK DDTVYYKLDT IKCDIPINEE LQARINKHVN QLRITYSTLE EFVDNFVYEL KKGLEAHRRH PNLWIPHEC SFKMLDSCIA DIPTGQEKGT YYAIDFGGTN FRAVRASLDG NGKIKRDQET YSLKFTGTFS HEKGLLDKHA T ASQLFDHF ...String: MRGSHHHHHH GSMSYYNLEK DDTVYYKLDT IKCDIPINEE LQARINKHVN QLRITYSTLE EFVDNFVYEL KKGLEAHRRH PNLWIPHEC SFKMLDSCIA DIPTGQEKGT YYAIDFGGTN FRAVRASLDG NGKIKRDQET YSLKFTGTFS HEKGLLDKHA T ASQLFDHF AERIKYIMGE FKDLDNPEGK NVGFTFSFPC TSPSINCSIL IDWTKGFETG RATNDPVEGR DVCKLMNDAF VR SEVPAKV CCVVNDAVGT LMSCAYQKGK TTPPCYIGII LGTGSNGCYY EPEWKKYKYS GKIINIELGN FDKDLPLSPI DLV MDWHSA NRSRQLFEKM ISGAYLGEIV RRFMVNVLQS ASSEKMWKSD SFNSELGSVV LNDTSPNFEE SRKVAKDAWD MDFT DEQIY ALRKICESVY NRSAALAAAA IAAIAKRIKI IEHSKFSCGV DGSLFVKNAW YCKRLQEHLK VILADKAENL IIIPA DDGS GKGAAITAAV VSQSSSIKQL P |
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.5 / Details: 20 mM Tris, pH 7.5, 50 mM NaCl, 1 mM TCEP |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.32 e/Å2 |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Particle selection | Number selected: 181611 |
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Startup model | Type of model: OTHER Details: Initial model generated in RELION 3.0 using particles selected from 2D classification |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final 3D classification | Number classes: 4 / Software - Name: RELION (ver. 3.0) Details: Number of particles selected for 3D classification were 24390 |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral![]() |