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- EMDB-21459: Cryo-EM structure of Plasmodium vivax hexokinase (Closed state) -

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Basic information

Entry
Database: EMDB / ID: EMD-21459
TitleCryo-EM structure of Plasmodium vivax hexokinase (Closed state)
Map dataPlasmodium vivax hexokinase (Closed state)
Sample
  • Complex: Plasmodium vivax hexokinase
    • Protein or peptide: Phosphotransferase
KeywordsHexokinase / TRANSFERASE
Function / homology
Function and homology information


Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / fructokinase activity / glucokinase activity / D-glucose binding / intracellular glucose homeostasis / glycolytic process / glucose metabolic process / mitochondrion / ATP binding / cytosol
Similarity search - Function
Hexokinase / Hexokinase, binding site / Hexokinase, N-terminal / Hexokinase, C-terminal / Hexokinase / Hexokinase / Hexokinase domain signature. / Hexokinase domain profile. / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Phosphotransferase / Phosphotransferase
Similarity search - Component
Biological speciesPlasmodium vivax (malaria parasite P. vivax)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSrivastava SS / Darling JE
Funding support Canada, 1 items
OrganizationGrant numberCountry
Canada Excellence Research Chair Award Canada
CitationJournal: IUCrJ / Year: 2020
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
DepositionFeb 26, 2020-
Header (metadata) releaseMar 11, 2020-
Map releaseMay 6, 2020-
UpdateJun 4, 2025-
Current statusJun 4, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.016
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6vyg
  • Surface level: 0.016
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21459.png

Downloads & links

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Map

FileDownload / File: emd_21459.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPlasmodium vivax hexokinase (Closed state)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 256 pix.
= 213.862 Å		0.84 Å/pix.
x 256 pix.
= 213.862 Å		0.84 Å/pix.
x 256 pix.
= 213.862 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8354 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.014 / Movie #1: 0.016
Minimum - Maximum-0.04880109 - 0.085877515
Average (Standard dev.)0.000054009528 (±0.004156583)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 213.8624 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.83539843750.83539843750.8353984375
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z213.862213.862213.862
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0490.0860.000

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Supplemental data

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Sample components

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Entire : Plasmodium vivax hexokinase

EntireName: Plasmodium vivax hexokinase
Components
  • Complex: Plasmodium vivax hexokinase
    • Protein or peptide: Phosphotransferase

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Supramolecule #1: Plasmodium vivax hexokinase

SupramoleculeName: Plasmodium vivax hexokinase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Plasmodium vivax (malaria parasite P. vivax)

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Macromolecule #1: Phosphotransferase

MacromoleculeName: Phosphotransferase / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
EC number: Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor
Source (natural)Organism: Plasmodium vivax (malaria parasite P. vivax)
Molecular weightTheoretical: 56.851543 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

UniProtKB: Phosphotransferase

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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: 7.5 / Details: 20 mM Tris, pH 7.5, 50 mM NaCl, 1 mM TCEP
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 200 / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 60.32 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 181611
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Details: Initial model generated in RELION 3.0 using particles selected from 2D classification
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 6623
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.0)
Details: Number of particles selected for 3D classification were 24390

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