7NB8

Plasmodium falciparum kinesin-5 motor domain without nucleotide, complexed with 14 protofilament microtubule.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of a microtubule-bound parasite kinesin motor and implications for its mechanism and inhibition.

Cook, A.D.Roberts, A.J.Atherton, J.Tewari, R.Topf, M.Moores, C.A.

(2021) J Biol Chem 297: 101063-101063

  • DOI: 10.1016/j.jbc.2021.101063
  • Primary Citation of Related Structures:  
    7NB8, 7NBA

  • PubMed Abstract: 
  • Plasmodium parasites cause malaria and are responsible annually for hundreds of thousands of deaths. Kinesins are a superfamily of microtubule-dependent ATPases that play important roles in the parasite replicative machinery, which is a potential target for anti-parasite drugs ...

    Plasmodium parasites cause malaria and are responsible annually for hundreds of thousands of deaths. Kinesins are a superfamily of microtubule-dependent ATPases that play important roles in the parasite replicative machinery, which is a potential target for anti-parasite drugs. Kinesin-5, a molecular motor that crosslinks microtubules, is an established anti-mitotic targets in other disease contexts, but its mechanism in P. falciparum is unclear. Here, we characterised P. falciparum kinesin-5 (PfK5) using cryo-EM to determine the motor's nucleotide-dependent microtubule-bound structure, and introduced 3D classification of individual motors into our microtubule image processing pipeline to maximise our structural insights. Despite sequence divergence in PfK5, the motor exhibits classical kinesin mechanochemistry, including ATP-induced subdomain rearrangement and cover neck bundle formation, consistent with its plus-ended directed motility. We also observed that an insertion in loop5 of the PfK5 motor domain creates a different environment in the well characterised human kinesin-5 drug-binding site. Our data reveal the possibility for selective inhibition of PfK5 and can be used to inform future exploration of Plasmodium kinesins as anti-parasite targets.


    Organizational Affiliation

    Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck, University of London, London, UK. Electronic address: c.moores@mail.cryst.bbk.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha-1B chainA451Sus scrofaMutation(s): 0 
Gene Names: TUBA1B
UniProt
Find proteins for Q2XVP4 (Sus scrofa)
Explore Q2XVP4 
Go to UniProtKB:  Q2XVP4
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta chainB445Sus scrofaMutation(s): 0 
UniProt
Find proteins for P02554 (Sus scrofa)
Explore P02554 
Go to UniProtKB:  P02554
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Kinesin-5C [auth K]405Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PF3D7_0317500
UniProt
Find proteins for O77382 (Plasmodium falciparum (isolate 3D7))
Explore O77382 
Go to UniProtKB:  O77382
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
D [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
G2P (Subject of Investigation/LOI)
Query on G2P

Download Ideal Coordinates CCD File 
F [auth B]PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
C11 H18 N5 O13 P3
GXTIEXDFEKYVGY-KQYNXXCUSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A], G [auth B]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.40 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/J003867/1
Wellcome TrustUnited Kingdom101311-10
Wellcome TrustUnited Kingdom079605/Z/06/Z
Biotechnology and Biological Sciences Research Council (BBSRC)United KingdomBB/L014211/1

Revision History  (Full details and data files)

  • Version 1.0: 2021-10-13
    Type: Initial release
  • Version 1.1: 2021-10-27
    Changes: Data collection, Database references