6UKJ

Single-Particle Cryo-EM Structure of Plasmodium falciparum Chloroquine Resistance Transporter (PfCRT) 7G8 Isoform


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure and drug resistance of the Plasmodium falciparum transporter PfCRT.

Kim, J.Tan, Y.Z.Wicht, K.J.Erramilli, S.K.Dhingra, S.K.Okombo, J.Vendome, J.Hagenah, L.M.Giacometti, S.I.Warren, A.L.Nosol, K.Roepe, P.D.Potter, C.S.Carragher, B.Kossiakoff, A.A.Quick, M.Fidock, D.A.Mancia, F.

(2019) Nature 576: 315-320

  • DOI: https://doi.org/10.1038/s41586-019-1795-x
  • Primary Citation of Related Structures:  
    6UKJ

  • PubMed Abstract: 

    The emergence and spread of drug-resistant Plasmodium falciparum impedes global efforts to control and eliminate malaria. For decades, treatment of malaria has relied on chloroquine (CQ), a safe and affordable 4-aminoquinoline that was highly effective against intra-erythrocytic asexual blood-stage parasites, until resistance arose in Southeast Asia and South America and spread worldwide 1 . Clinical resistance to the chemically related current first-line combination drug piperaquine (PPQ) has now emerged regionally, reducing its efficacy 2 . Resistance to CQ and PPQ has been associated with distinct sets of point mutations in the P. falciparum CQ-resistance transporter PfCRT, a 49-kDa member of the drug/metabolite transporter superfamily that traverses the membrane of the acidic digestive vacuole of the parasite 3-9 . Here we present the structure, at 3.2 Å resolution, of the PfCRT isoform of CQ-resistant, PPQ-sensitive South American 7G8 parasites, using single-particle cryo-electron microscopy and antigen-binding fragment technology. Mutations that contribute to CQ and PPQ resistance localize primarily to moderately conserved sites on distinct helices that line a central negatively charged cavity, indicating that this cavity is the principal site of interaction with the positively charged CQ and PPQ. Binding and transport studies reveal that the 7G8 isoform binds both drugs with comparable affinities, and that these drugs are mutually competitive. The 7G8 isoform transports CQ in a membrane potential- and pH-dependent manner, consistent with an active efflux mechanism that drives CQ resistance 5 , but does not transport PPQ. Functional studies on the newly emerging PfCRT F145I and C350R mutations, associated with decreased PPQ susceptibility in Asia and South America, respectively 6,9 , reveal their ability to mediate PPQ transport in 7G8 variant proteins and to confer resistance in gene-edited parasites. Structural, functional and in silico analyses suggest that distinct mechanistic features mediate the resistance to CQ and PPQ in PfCRT variants. These data provide atomic-level insights into the molecular mechanism of this key mediator of antimalarial treatment failures.


  • Organizational Affiliation

    Department of Physiology and Cellular Biophysics, Columbia University Irving Medical Center, New York, NY, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Chloroquine resistance transporter464Plasmodium falciparum 7G8Mutation(s): 0 
Gene Names: PFBG_01689
Membrane Entity: Yes 
UniProt
Find proteins for W7FI62 (Plasmodium falciparum (isolate 7G8))
Explore W7FI62 
Go to UniProtKB:  W7FI62
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupW7FI62
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fab Heavy ChainB [auth H]241Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fab Light ChainC [auth L]215Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y01 (Subject of Investigation/LOI)
Query on Y01

Download Ideal Coordinates CCD File 
D [auth A]CHOLESTEROL HEMISUCCINATE
C31 H50 O4
WLNARFZDISHUGS-MIXBDBMTSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcisTEM1

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM111980
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR37 AI50234
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 AI124678
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM119396
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 AI506312
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesAI111962
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32 HL120826
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41 GM103310
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP41 GM116799

Revision History  (Full details and data files)

  • Version 1.0: 2019-12-04
    Type: Initial release
  • Version 1.1: 2019-12-11
    Changes: Database references
  • Version 1.2: 2019-12-25
    Changes: Database references, Structure summary
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence