[English] 日本語
Yorodumi
- EMDB-21458: Cryo-EM structure of Plasmodium vivax hexokinase (Open state) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-21458
TitleCryo-EM structure of Plasmodium vivax hexokinase (Open state)
Map dataPlasmodium vivax hexokinase (Open state)
Sample
  • Complex: Plasmodium vivax hexokinase
    • Protein or peptide: Phosphotransferase
KeywordsHexokinase / TRANSFERASE
Function / homology
Function and homology information


hexokinase activity / Transferases; Transferring phosphorus-containing groups; Phosphotransferases with an alcohol group as acceptor / glucose binding / intracellular glucose homeostasis / glycolytic process / ATP binding
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: 3.3 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-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-6vyf
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_21458.png

Downloads & links

-
Map

FileDownload / File: emd_21458.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPlasmodium vivax hexokinase (Open state)
Voxel sizeX=Y=Z: 0.8354 Å
Density
Contour LevelBy AUTHOR: 0.012 / Movie #1: 0.015
Minimum - Maximum-0.05453369 - 0.097699694
Average (Standard dev.)0.000060049322 (±0.0045265285)
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-0.0550.0980.000

-
Supplemental data

-
Sample components

-
Entire : Plasmodium vivax hexokinase

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

-
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)

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
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

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm 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

-
Image processing

Particle selectionNumber selected: 181611
Startup modelType of model: OTHER
Details: Initial model generated in RELION 3.0 using particles selected from 2D classification
Initial angle assignmentType: RANDOM ASSIGNMENT
Final 3D classificationNumber classes: 4 / Software - Name: RELION (ver. 3.0)
Details: Number of particles selected for 3D classification were 24390
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: D2 (2x2 fold dihedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 12604

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more