X-ray structure of KH1-2 domain of IMP3

Experimental Data Snapshot

  • Resolution: 2.15 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.240 

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Combinatorial recognition of clustered RNA elements by the multidomain RNA-binding protein IMP3.

Schneider, T.Hung, L.H.Aziz, M.Wilmen, A.Thaum, S.Wagner, J.Janowski, R.Muller, S.Schreiner, S.Friedhoff, P.Huttelmaier, S.Niessing, D.Sattler, M.Schlundt, A.Bindereif, A.

(2019) Nat Commun 10: 2266-2266

  • DOI: https://doi.org/10.1038/s41467-019-09769-8
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    How multidomain RNA-binding proteins recognize their specific target sequences, based on a combinatorial code, represents a fundamental unsolved question and has not been studied systematically so far. Here we focus on a prototypical multidomain RNA-binding protein, IMP3 (also called IGF2BP3), which contains six RNA-binding domains (RBDs): four KH and two RRM domains. We establish an integrative systematic strategy, combining single-domain-resolved SELEX-seq, motif-spacing analyses, in vivo iCLIP, functional validation assays, and structural biology. This approach identifies the RNA-binding specificity and RNP topology of IMP3, involving all six RBDs and a cluster of up to five distinct and appropriately spaced CA-rich and GGC-core RNA elements, covering a >100 nucleotide-long target RNA region. Our generally applicable approach explains both specificity and flexibility of IMP3-RNA recognition, allows the prediction of IMP3 targets, and provides a paradigm for the function of multivalent interactions with multidomain RNA-binding proteins in gene regulation.

  • Organizational Affiliation

    Institute of Biochemistry, Justus-Liebig-University of Giessen, 35392, Giessen, Germany. albrecht.bindereif@chemie.bio.uni-giessen.de.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Insulin-like growth factor 2 mRNA-binding protein 3168Homo sapiensMutation(s): 2 
Find proteins for A0A0B8RZH0 (Sus scrofa domesticus)
Explore A0A0B8RZH0 
Go to UniProtKB:  A0A0B8RZH0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0B8RZH0
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.15 Å
  • R-Value Free: 0.293 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.2α = 90
b = 58.09β = 90
c = 60.87γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-04-24
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.2: 2019-06-05
    Changes: Data collection, Database references
  • Version 1.3: 2019-08-14
    Changes: Data collection