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 

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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: https://doi.org/10.1038/s41467-018-04561-6
  • Primary Citation of Related Structures:  
    6F4G, 6F4H, 6F4I, 6F4J

  • 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 auxiliary U2A' protein ...

    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

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Probable U2 small nuclear ribonucleoprotein A'
A, D
176Drosophila melanogasterMutation(s): 3 
Gene Names: U2A, CG1406
UniProt
Find proteins for Q9V4Q8 (Drosophila melanogaster)
Explore Q9V4Q8 
Go to UniProtKB:  Q9V4Q8
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UniProt GroupQ9V4Q8
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
U1 small nuclear ribonucleoprotein A
B, E
98Drosophila melanogasterMutation(s): 0 
Gene Names: snf, D25, fs(1)1621, liz, CG4528
UniProt
Find proteins for P43332 (Drosophila melanogaster)
Explore P43332 
Go to UniProtKB:  P43332
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UniProt GroupP43332
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsLengthOrganismImage
U2-SL4
C, F
25Drosophila melanogaster
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
H [auth D],
I [auth D]		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
G [auth B],
J [auth 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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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