1EC6

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

• PDB DOI: https://doi.org/10.2210/pdb1EC6/pdb
• NAKB: 1EC6

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-01-25 Released: 2000-02-21 
• Deposition Author(s): Lewis, H.A., Musunuru, K., Jensen, K.B., Edo, C., Chen, H.

---

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 

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

• PubMed: 10676814 
• DOI: https://doi.org/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 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 31.56 kDa 
• Atom Count: 2,294 
• Modelled Residue Count: 211 
• Deposited Residue Count: 214 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
RNA-BINDING PROTEIN NOVA-2	C [auth A], D [auth B]	87	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNW9 (Homo sapiens) Explore Q9UNW9  Go to UniProtKB:  Q9UNW9
PHAROS:  Q9UNW9 GTEx:  ENSG00000104967

Entity ID: 1
Molecule	Chains	Length	Organism	Image
20-MER RNA HAIRPIN	A [auth C], B [auth D]	20	N/A

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 = 47.85	α = 90
b = 51.21	β = 90
c = 128.6	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
CCP4	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-02-21 
Deposition Author(s): Lewis, H.A., Musunuru, K., Jensen, K.B., Edo, C., Chen, H.

Revision History  

• 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
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references