U1A RNA binding domain at 1.8 angstrom resolution reveals a pre-organized C-terminal helix

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 

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This is version 1.6 of the entry. See complete history


U1A RNA-binding domain at 1.8 A resolution.

Rupert, P.B.Xiao, H.Ferre-D'Amare, A.R.

(2003) Acta Crystallogr D Biol Crystallogr 59: 1521-1524

  • DOI: https://doi.org/10.1107/s0907444903011338
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The human U1A RNA-binding domain (RBD1) adopts one of the most common protein folds, the RNA-recognition motif, and is a paradigm for understanding RNA-protein interactions. A 2.8 A resolution structure of the unbound RBD1 has previously been determined [Nagai et al. (1990). Nature (London), 348, 515-520] and revealed a well defined alpha/beta core with disordered termini. Using a longer construct, a 1.8 A resolution structure of the unbound domain was determined that reveals an ordered C-terminal helix. The presence of this helix is consistent with a solution structure of the free domain [Avis et al. (1996). J. Mol. Biol. 257, 398-411]; however, in the solution structure the helix occludes the RNA-binding surface. In the present structure, the helix occupies a position similar to that seen in a 1.9 A resolution RNA-RBD1 complex structure [Oubridge et al. (1994). Nature (London), 372, 432-438]. The crystals in this study were grown from 2.2 M sodium malonate. It is possible that the high salt concentration helps to orient the C-terminal helix in the RNA-bound conformation by strengthening hydrophobic interactions between the buried face of the helix and the alpha/beta core of the protein. Alternatively, the malonate (several molecules of which are bound in the vicinity of the RNA-binding surface) may mimic RNA.

  • Organizational Affiliation

    Fred Hutchinson Cancer Research Center, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
U1A RNA binding domain
A, B
97Homo sapiensMutation(s): 2 
UniProt & NIH Common Fund Data Resources
Find proteins for P09012 (Homo sapiens)
Explore P09012 
Go to UniProtKB:  P09012
PHAROS:  P09012
GTEx:  ENSG00000077312 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09012
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on MLA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
C3 H4 O4
Query on MG

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
K [auth B],
L [auth B],
M [auth B]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.203 
  • Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 91.819α = 90
b = 91.819β = 90
c = 120.448γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-02-14
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2011-11-16
    Changes: Atomic model
  • Version 1.4: 2015-04-29
    Changes: Non-polymer description
  • Version 1.5: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.6: 2023-08-16
    Changes: Data collection, Refinement description