1B7F | pdb_00001b7f

SXL-LETHAL PROTEIN/RNA COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1B7F/pdb
• NAKB: 1B7F

• Classification: RNA-BINDING PROTEIN/RNA
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 1999-01-23 Released: 1999-05-03 
• Deposition Author(s): Handa, N., Nureki, O., Kurimoto, K., Kim, I., Sakamoto, H., Shimura, Y., Muto, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.294 (Depositor) 
• R-Value Work: 
  0.201 (Depositor) 

Literature

Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein.

Handa, N., Nureki, O., Kurimoto, K., Kim, I., Sakamoto, H., Shimura, Y., Muto, Y., Yokoyama, S.

(1999) Nature 398: 579-585

• PubMed: 10217141 
• DOI: https://doi.org/10.1038/19242
• Primary Citation Related Structures: 
  1B7F


• PubMed Abstract: 
  

  The Sex-lethal (Sxl) protein of Drosophila melanogaster regulates alternative splicing of the transformer (tra) messenger RNA precursor by binding to the tra polypyrimidine tract during the sex-determination process. The crystal structure has now been determined at 2.6 A resolution of the complex formed between two tandemly arranged RNA-binding domains of the Sxl protein and a 12-nucleotide, single-stranded RNA derived from the tra polypyrimidine tract. The two RNA-binding domains have their beta-sheet platforms facing each other to form a V-shaped cleft. The RNA is characteristically extended and bound in this cleft, where the UGUUUUUUU sequence is specifically recognized by the protein. This structure offers the first insight, to our knowledge, into how a protein binds specifically to a cognate RNA without any intramolecular base-pairing.

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Organizational Affiliation: 
• Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Japan.

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: 45.36 kDa 
• Atom Count: 3,236 
• Modeled Residue Count: 358 
• Deposited Residue Count: 360 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (SXL-LETHAL PROTEIN)	C [auth A], D [auth B]	168	Drosophila melanogaster	Mutation(s): 1
UniProt
Find proteins for P19339 (Drosophila melanogaster) Explore P19339  Go to UniProtKB:  P19339

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*GP*UP*UP*GP*UP*UP*UP*UP*UP*UP*UP*U)-3')	A [auth P], B [auth Q]	12	N/A

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.294 (Depositor) 
• R-Value Work:  0.201 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.9	α = 90
b = 86.8	β = 90
c = 160.4	γ = 90

Software Package:

Software Name	Purpose
MLPHARE	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-05-03 
Deposition Author(s): Handa, N., Nureki, O., Kurimoto, K., Kim, I., Sakamoto, H., Shimura, Y., Muto, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 1999-05-03
  Type: Initial release
  
• Version 1.1: 2008-04-26
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-12-28
  Changes: Advisory
• Version 1.4: 2021-11-03
  Changes: Database references
• Version 1.5: 2023-12-27
  Changes: Data collection