5OGW | pdb_00005ogw

Cryo-EM structure of jasplakinolide-stabilized malaria parasite F-actin at near-atomic resolution


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 5OGW

This is version 1.5 of the entry. See complete history

Literature

Near-atomic structure of jasplakinolide-stabilized malaria parasite F-actin reveals the structural basis of filament instability.

Pospich, S.Kumpula, E.P.von der Ecken, J.Vahokoski, J.Kursula, I.Raunser, S.

(2017) Proc Natl Acad Sci U S A 114: 10636-10641

  • DOI: https://doi.org/10.1073/pnas.1707506114
  • Primary Citation Related Structures: 
    5OGW

  • PubMed Abstract: 

    During their life cycle, apicomplexan parasites, such as the malaria parasite Plasmodium falciparum , use actomyosin-driven gliding motility to move and invade host cells. For this process, actin filament length and stability are temporally and spatially controlled. In contrast to canonical actin, P. falciparum actin 1 ( Pf Act1) does not readily polymerize into long, stable filaments. The structural basis of filament instability, which plays a pivotal role in host cell invasion, and thus infectivity, is poorly understood, largely because high-resolution structures of Pf Act1 filaments were missing. Here, we report the near-atomic structure of jasplakinolide (JAS)-stabilized Pf Act1 filaments determined by electron cryomicroscopy. The general filament architecture is similar to that of mammalian F-actin. The high resolution of the structure allowed us to identify small but important differences at inter- and intrastrand contact sites, explaining the inherent instability of apicomplexan actin filaments. JAS binds at regular intervals inside the filament to three adjacent actin subunits, reinforcing filament stability by hydrophobic interactions. Our study reveals the high-resolution structure of a small molecule bound to F-actin, highlighting the potential of electron cryomicroscopy for structure-based drug design. Furthermore, our work serves as a strong foundation for understanding the structural design and evolution of actin filaments and their function in motility and host cell invasion of apicomplexan parasites.


  • Organizational Affiliation
    • Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227 Dortmund, Germany.

Macromolecule Content 

  • Total Structure Weight: 214.62 kDa 
  • Atom Count: 14,736 
  • Modeled Residue Count: 1,850 
  • Deposited Residue Count: 1,890 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Actin-1
A, B, C, D, E
378Plasmodium falciparum HB3Mutation(s): 0 
EC: 3.6.4
UniProt
Find proteins for Q8I4X0 (Plasmodium falciparum (isolate 3D7))
Explore Q8I4X0 
Go to UniProtKB:  Q8I4X0
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8I4X0
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
9UE

Query on 9UE



Download:Ideal Coordinates CCD File
H [auth A],
M [auth C],
R [auth E]
Jasplakinolide
C36 H45 Br N4 O6
GQWYWHOHRVVHAP-DHKPLNAMSA-N
ADP

Query on ADP



Download:Ideal Coordinates CCD File
F [auth A],
I [auth B],
K [auth C],
N [auth D],
P [auth E]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG

Query on MG



Download:Ideal Coordinates CCD File
G [auth A],
J [auth B],
L [auth C],
O [auth D],
Q [auth E]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTCoot
MODEL REFINEMENTPHENIX
MODEL REFINEMENTREFMAC
RECONSTRUCTIONRELION1.4

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--
European Union615984
Academy of FinlandFinland257537, 265112, 292718
Emil Aaltonen, Sigrid Juselius, and Jane and Aatos Erkko foundations--

Revision History  (Full details and data files)

  • Version 1.0: 2017-09-27
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Data processing, Database references
  • Version 1.2: 2018-10-17
    Changes: Data collection, Refinement description
  • Version 1.3: 2019-10-23
    Changes: Data collection, Other
  • Version 1.4: 2022-11-09
    Changes: Database references, Refinement description
  • Version 1.5: 2024-07-10
    Changes: Data collection