6F4G

'Crystal structure of the Drosophila melanogaster SNF/U2A'/U2-SL4 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

wwPDB Validation 3D Report Full Report



Literature

Molecular principles underlying dual RNA specificity in the Drosophila SNF protein.

Weber, G.DeKoster, G.T.Holton, N.Hall, K.B.Wahl, M.C.

(2018) Nat Commun 9: 2220-2220

  • DOI: 10.1038/s41467-018-04561-6
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The first RNA recognition motif of the Drosophila SNF protein is an example of an RNA binding protein with multi-specificity. It binds different RNA hairpin loops in spliceosomal U1 or U2 small nuclear RNAs, and only in the latter case requires the a ...

    The first RNA recognition motif of the Drosophila SNF protein is an example of an RNA binding protein with multi-specificity. It binds different RNA hairpin loops in spliceosomal U1 or U2 small nuclear RNAs, and only in the latter case requires the auxiliary U2A' protein. Here we investigate its functions by crystal structures of SNF alone and bound to U1 stem-loop II, U2A' or U2 stem-loop IV and U2A', SNF dynamics from NMR spectroscopy, and structure-guided mutagenesis in binding studies. We find that different loop-closing base pairs and a nucleotide exchange at the tips of the loops contribute to differential SNF affinity for the RNAs. U2A' immobilizes SNF and RNA residues to restore U2 stem-loop IV binding affinity, while U1 stem-loop II binding does not require such adjustments. Our findings show how U2A' can modulate RNA specificity of SNF without changing SNF conformation or relying on direct RNA contacts.


    Organizational Affiliation

    Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Albert-Einstein-Straße 15, D-12489, Berlin, Germany. mwahl@zedat.fu-berlin.de.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Probable U2 small nuclear ribonucleoprotein A'A, D176Drosophila melanogasterMutation(s): 3 
Gene Names: U2ACG1406
Find proteins for Q9V4Q8 (Drosophila melanogaster)
Explore Q9V4Q8 
Go to UniProtKB:  Q9V4Q8
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
U1 small nuclear ribonucleoprotein AB, E98Drosophila melanogasterMutation(s): 0 
Gene Names: snfD25fs(1)1621lizCG4528
Find proteins for P43332 (Drosophila melanogaster)
Explore P43332 
Go to UniProtKB:  P43332
Protein Feature View
 ( Mouse scroll to zoom / Hold left click to move )
  • Reference Sequence

Find similar nucleic acids by: Sequence   |  Structure

Entity ID: 3
MoleculeChainsLengthOrganism
U2-SL4C, F25Drosophila melanogaster
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

Download CCD File 
B, E
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.045α = 90
b = 103.914β = 90
c = 116.35γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-06-20
    Type: Initial release