1EC6

CRYSTAL STRUCTURE OF NOVA-2 KH3 K-HOMOLOGY RNA-BINDING DOMAIN BOUND TO 20-MER RNA HAIRPIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.215 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Sequence-specific RNA binding by a Nova KH domain: implications for paraneoplastic disease and the fragile X syndrome.

Lewis, H.A.Musunuru, K.Jensen, K.B.Edo, C.Chen, H.Darnell, R.B.Burley, S.K.

(2000) Cell 100: 323-332

  • DOI: 10.1016/s0092-8674(00)80668-6
  • Primary Citation of Related Structures:  
    1EC6

  • PubMed Abstract: 
  • The structure of a Nova protein K homology (KH) domain recognizing single-stranded RNA has been determined at 2.4 A resolution. Mammalian Nova antigens (1 and 2) constitute an important family of regulators of RNA metabolism in neurons, first identified using sera from cancer patients with the autoimmune disorder paraneoplastic opsoclonus-myoclonus ataxia (POMA) ...

    The structure of a Nova protein K homology (KH) domain recognizing single-stranded RNA has been determined at 2.4 A resolution. Mammalian Nova antigens (1 and 2) constitute an important family of regulators of RNA metabolism in neurons, first identified using sera from cancer patients with the autoimmune disorder paraneoplastic opsoclonus-myoclonus ataxia (POMA). The structure of the third KH domain (KH3) of Nova-2 bound to a stem loop RNA resembles a molecular vise, with 5'-Ura-Cyt-Ade-Cyt-3' pinioned between an invariant Gly-X-X-Gly motif and the variable loop. Tetranucleotide recognition is supported by an aliphatic alpha helix/beta sheet RNA-binding platform, which mimics 5'-Ura-Gua-3' by making Watson-Crick-like hydrogen bonds with 5'-Cyt-Ade-3'. Sequence conservation suggests that fragile X mental retardation results from perturbation of RNA binding by the FMR1 protein.


    Organizational Affiliation

    Laboratories of Molecular Biophysics, The Rockefeller University, New York, New York 10021, USA.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
RNA-BINDING PROTEIN NOVA-2C [auth A], D [auth B]87Homo sapiensMutation(s): 0 
Gene Names: NOVA2ANOVANOVA3
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNW9 (Homo sapiens)
Explore Q9UNW9 
Go to UniProtKB:  Q9UNW9
PHAROS:  Q9UNW9
Protein Feature View
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  • Reference Sequence

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Entity ID: 1
MoleculeChainsLengthOrganismImage
20-MER RNA HAIRPINA [auth C], B [auth D]20N/A
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.215 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 47.85α = 90
b = 51.21β = 90
c = 128.6γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
CCP4data scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2000-02-21
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-02-03
    Changes: Database references