2N7C

Solution structure of Plasmodium falciparum SR1-RRM1 in complex with ACAUCA RNA

Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

The N-terminal RNA Recognition Motif of PfSR1 Confers Semi-specificity for Pyrimidines during RNA Recognition.

Ganguly, A.K., Verma, G., Bhavesh, N.S.

(2019) J Mol Biol 431: 498-510

  • DOI: 10.1016/j.jmb.2018.11.020
  • Primary Citation of Related Structures:  
    2N3L, 2N7C

  • PubMed Abstract: 

    • Alternative splicing confers a complexity to the mRNA landscape of apicomplexans, resulting in a high proteomic diversity. The Plasmodium falciparum Ser/Arg-rich protein 1 (PfSR1) is the first protein to be confirmed as an alternative splicing factor in this class of parasitic protists [1] ...

    Alternative splicing confers a complexity to the mRNA landscape of apicomplexans, resulting in a high proteomic diversity. The Plasmodium falciparum Ser/Arg-rich protein 1 (PfSR1) is the first protein to be confirmed as an alternative splicing factor in this class of parasitic protists [1]. A recent study [2] showed a purine bias in RNA binding among cognate RNA substrates of PfSR1. Here, we have investigated the role played by the amino-terminal RNA recognition motif (RRM1) of PfSR1 from the solution structure of its complex with ACAUCA RNA hexamer to understand how its mechanism of RNA recognition compares to human orthologs and to the C-terminal RRM. RNA binding by RRM1 is mediated through specific recognition of a cytosine base situated 5' of one or more pyrimidine bases by a conserved tyrosine residue on β 1 and a glutamate residue on the β 4 strand. Affinity is conferred through insertion of a 3' pyrimidine into a positively charged pocket. Retention of fast dynamics and ITC binding constants indicate the complex to be of moderate affinity. Using calorimetry and mapping of NMR chemical shift perturbations, we have also ascertained the purine preference of PfSR1 to be a property of the carboxy terminal pseudo-RRM (RRM2), which binds RNA non-canonically and with greater affinity compared to RRM1. Our findings show conclusive evidence of complementary RNA sequence recognition by the two RRMs, which may potentially aid PfSR1 in binding RNA with a high sequence specificity.

    Organizational Affiliation: 

    Transcription Regulation group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Aruna Asaf Ali Marg, New Delhi 110067, India. Electronic address: neelsb@icgeb.res.in.



Macromolecules

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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
putative splicing factorA89Plasmodium falciparum 3D7Mutation(s): 0 
Gene Names: PFE0865c, PF3D7_0517300
UniProt
Find proteins for Q8I3T5 (Plasmodium falciparum (isolate 3D7))
Explore Q8I3T5 
Go to UniProtKB:  Q8I3T5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8I3T5
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsLengthOrganismImage
RNA_(5'-R(*AP*CP*AP*UP*CP*A)-3')B6synthetic construct
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 200 
  • Conformers Submitted: 20 
  • Selection Criteria: structures with the least restraint violations 

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-12
    Type: Initial release
  • Version 1.1: 2019-04-17
    Changes: Data collection, Database references