4C4W

Structure of a rare, non-standard sequence k-turn bound by L7Ae protein

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

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Literature

Structure of a Rare, Non-Standard Sequence K-Turn Bound by L7Ae Protein

Huang, L., Lilley, D.M.J.

(2014) Nucleic Acids Res 42: 4734

  • DOI: 10.1093/nar/gku087
  • Primary Citation of Related Structures:  
    4C4W

  • PubMed Abstract: 

    • Kt-23 from Thelohania solenopsae is a rare RNA kink turn (k-turn) where an adenine replaces the normal guanine at the 2n position. L7Ae is a member of a strongly conserved family of proteins that bind a range of k-turn structures in the ribosome, box C/D and H/ACA small nucleolar RNAs and U4 small nuclear RNA ...

    Kt-23 from Thelohania solenopsae is a rare RNA kink turn (k-turn) where an adenine replaces the normal guanine at the 2n position. L7Ae is a member of a strongly conserved family of proteins that bind a range of k-turn structures in the ribosome, box C/D and H/ACA small nucleolar RNAs and U4 small nuclear RNA. We have solved the crystal structure of T. solenopsae Kt-23 RNA bound to Archeoglobus fulgidus L7Ae protein at a resolution of 2.95 Å. The protein binds in the major groove displayed on the outer face of the k-turn, in a manner similar to complexes with standard k-turn structures. The k-turn adopts a standard N3 class conformation, with a single hydrogen bond from A2b N6 to A2n N3. This contrasts with the structure of the same sequence located in the SAM-I riboswitch, where it adopts an N1 structure, showing the inherent plasticity of k-turn structure. This potentially can affect any tertiary interactions in which the RNA participates.

    Organizational Affiliation: 

    Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
U1 SMALL NUCLEAR RIBONUCLEOPROTEIN A A, B, E, F102Homo sapiensMutation(s): 0 
Gene Names: SNRPA
Find proteins for P09012 (Homo sapiens)
Explore P09012 
Go to UniProtKB:  P09012
NIH Common Fund Data Resources
PHAROS:  P09012
GTEx:  ENSG00000077312
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L7AE C, G123Archaeoglobus fulgidus DSM 4304Mutation(s): 0 
Gene Names: rpl7ae, AF_0764
Find proteins for O29494 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Explore O29494 
Go to UniProtKB:  O29494
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsLengthOrganismImage
TSKT-23D, H35Kneallhazia solenopsae
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
2HP
Query on 2HP
Download Ideal Coordinates CCD File 
D, H
DIHYDROGENPHOSPHATE ION
H2 O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-M		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.892α = 90
b = 155.545β = 90
c = 146.874γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-02-12
    Type: Initial release
  • Version 1.1: 2014-04-30
    Changes: Database references