Crystal structure (II) of Nova-1 KH1/KH2 domain tandem with 25nt RNA hairpin

Experimental Data Snapshot

  • Resolution: 1.94 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 

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Protein-RNA and protein-protein recognition by dual KH1/2 domains of the neuronal splicing factor Nova-1.

Teplova, M.Malinina, L.Darnell, J.C.Song, J.Lu, M.Abagyan, R.Musunuru, K.Teplov, A.Burley, S.K.Darnell, R.B.Patel, D.J.

(2011) Structure 19: 930-944

  • DOI: https://doi.org/10.1016/j.str.2011.05.002
  • Primary Citation of Related Structures:  
    2ANN, 2ANR

  • PubMed Abstract: 

    Nova onconeural antigens are neuron-specific RNA-binding proteins implicated in paraneoplastic opsoclonus-myoclonus-ataxia (POMA) syndrome. Nova harbors three K-homology (KH) motifs implicated in alternate splicing regulation of genes involved in inhibitory synaptic transmission. We report the crystal structure of the first two KH domains (KH1/2) of Nova-1 bound to an in vitro selected RNA hairpin, containing a UCAG-UCAC high-affinity binding site. Sequence-specific intermolecular contacts in the complex involve KH1 and the second UCAC repeat, with the RNA scaffold buttressed by interactions between repeats. Whereas the canonical RNA-binding surface of KH2 in the above complex engages in protein-protein interactions in the crystalline state, the individual KH2 domain can sequence-specifically target the UCAC RNA element in solution. The observed antiparallel alignment of KH1 and KH2 domains in the crystal structure of the complex generates a scaffold that could facilitate target pre-mRNA looping on Nova binding, thereby potentially explaining Nova's functional role in splicing regulation.

  • Organizational Affiliation

    Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA.


Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
RNA-binding protein Nova-1B [auth A]178Mus musculusMutation(s): 1 
Gene Names: Nova1
UniProt & NIH Common Fund Data Resources
Find proteins for P51513 (Homo sapiens)
Explore P51513 
Go to UniProtKB:  P51513
GTEx:  ENSG00000139910 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51513
Sequence Annotations
  • Reference Sequence

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
Experimental Data & Validation

Experimental Data

  • Resolution: 1.94 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.230 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 159.453α = 90
b = 37.885β = 96.64
c = 38.523γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-10-24
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.3: 2011-11-02
    Changes: Database references
  • Version 1.4: 2017-10-11
    Changes: Refinement description
  • Version 1.5: 2021-02-03
    Changes: Database references, Derived calculations, Structure summary
  • Version 1.6: 2021-10-20
    Changes: Database references
  • Version 1.7: 2023-08-23
    Changes: Data collection, Refinement description
  • Version 1.8: 2023-11-15
    Changes: Data collection
  • Version 1.9: 2023-12-20
    Changes: Database references, Derived calculations, Source and taxonomy, Structure summary