Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Biological assembly 3 assigned by authors.

Macromolecule Content

• Total Structure Weight: 28.21 kDa 
• Atom Count: 2,243 
• Modelled Residue Count: 169 
• Deposited Residue Count: 178 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 1DI2

CRYSTAL STRUCTURE OF A DSRNA-BINDING DOMAIN COMPLEXED WITH DSRNA: MOLECULAR BASIS OF DOUBLE-STRANDED RNA-PROTEIN INTERACTIONS

• PDB DOI: 10.2210/pdb1DI2/pdb
• NDB: PR0020

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Xenopus laevis
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 1999-11-28 Released: 1999-12-02 
• Deposition Author(s): Ryter, J.M., Schultz, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.258 
• R-Value Work: 0.228 
• R-Value Observed: 0.231 

Literature

Molecular basis of double-stranded RNA-protein interactions: structure of a dsRNA-binding domain complexed with dsRNA.

Ryter, J.M., Schultz, S.C.

(1998) EMBO J 17: 7505-7513

• PubMed: 9857205 
• DOI: 10.1093/emboj/17.24.7505
• Primary Citation of Related Structures:  
  1DI2


• PubMed Abstract: 
  

Protein interactions with double-stranded RNA (dsRNA) are critical for many cell processes; however, in contrast to protein-dsDNA interactions, surprisingly little is known about the molecular basis of protein-dsRNA interactions. A large and diverse class of proteins that bind dsRNA do so by utilizing an approximately 70 amino acid motif referred to as the dsRNA-binding domain (dsRBD). We have determined a 1.9 A resolution crystal structure of the second dsRBD of Xenopus laevis RNA-binding protein A complexed with dsRNA. The structure shows that the protein spans 16 bp of dsRNA, interacting with two successive minor grooves and across the intervening major groove on one face of a primarily A-form RNA helix. The nature of these interactions explains dsRBD specificity for dsRNA (over ssRNA or dsDNA) and the apparent lack of sequence specificity. Interestingly, the dsRBD fold resembles a portion of the conserved core structure of a family of polynucleotidyl transferases that includes RuvC, MuA transposase, retroviral integrase and RNase H. Structural comparisons of the dsRBD-dsRNA complex and models proposed for polynucleotidyl transferase-nucleic acid complexes suggest that similarities in nucleic acid binding also exist between these families of proteins.

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Organizational Affiliation: 

Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309-0215, USA.

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DOUBLE STRANDED RNA BINDING PROTEIN A	E [auth A], F [auth B]	69	Xenopus laevis	Mutation(s): 1  Gene Names: prkra-b, rbpa
UniProt
Find proteins for Q91836 (Xenopus laevis) Explore Q91836  Go to UniProtKB:  Q91836

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*CP*GP*CP*GP*CP*GP*CP*C)-3')	A [auth C], B [auth D], C [auth E], D [auth G]	10	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.258 
• R-Value Work: 0.228 
• R-Value Observed: 0.231 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.4	α = 90
b = 58.5	β = 105.2
c = 58.9	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-12-02 
Deposition Author(s): Ryter, J.M., Schultz, S.C.

Revision History  

• Version 1.0: 1999-12-02
  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: 2021-11-03
  Changes: Database references