3SXL | pdb_00003sxl

SEX-LETHAL RNA RECOGNITION DOMAINS 1 AND 2 FROM DROSOPHILA MELANOGASTER

• PDB DOI: https://doi.org/10.2210/pdb3SXL/pdb

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


• Deposited: 1999-04-04 Released: 1999-04-27 
• Deposition Author(s): Crowder, S.M., Kanaar, R., Rio, D.C., Alber, T.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.264 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.218 (DCC) 

Literature

Absence of interdomain contacts in the crystal structure of the RNA recognition motifs of Sex-lethal.

Crowder, S.M., Kanaar, R., Rio, D.C., Alber, T.

(1999) Proc Natl Acad Sci U S A 96: 4892-4897

• PubMed: 10220389 
• DOI: https://doi.org/10.1073/pnas.96.9.4892
• Primary Citation Related Structures: 
  3SXL


• PubMed Abstract: 
  

  By binding specific RNA transcripts, the Sex-lethal protein (SXL) governs sexual differentiation and dosage compensation in Drosophila melanogaster. To investigate the basis for RNA binding specificity, we determined the crystal structure of the tandem RNA recognition motifs (RRMs) of SXL. Both RRMs adopt the canonical RRM fold, and the 10-residue, interdomain linker shows significant disorder. In contrast to the previously determined structure of the two-RRM fragment of heterogeneous nuclear ribonucleoprotein Al, SXL displays no interdomain contacts between RRMs. These results suggest that the SXL RRMs are flexibly tethered in solution, and RNA binding restricts the orientation of RRMs. Therefore, the observed specificity for single-stranded, U-rich sequences does not arise from a predefined, rigid architecture of the isolated SXL RRMs.

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Organizational Affiliation: 
• Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, 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.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 63.09 kDa 
• Atom Count: 3,696 
• Modeled Residue Count: 471 
• Deposited Residue Count: 552 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEIN (SEX-LETHAL)	A, B, C	184	Drosophila melanogaster	Mutation(s): 4
UniProt
Find proteins for P19339 (Drosophila melanogaster) Explore P19339  Go to UniProtKB:  P19339

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B, C	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.264 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.218 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.91	α = 90
b = 124.47	β = 120
c = 50.93	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1999-04-27 
Deposition Author(s): Crowder, S.M., Kanaar, R., Rio, D.C., Alber, T.C.

Revision History  

• Version 1.0: 1999-04-27
  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: 2021-11-03
  Changes: Database references, Derived calculations
• Version 1.4: 2023-12-27
  Changes: Data collection
• Version 1.5: 2024-10-09
  Changes: Structure summary