5FJ4

Structure of the standard kink turn HmKt-7 as stem loop bound with U1A and L7Ae proteins

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

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Literature

A Critical Base Pair in K-Turns Determines the Conformational Class Adopted, and Correlates with Biological Function.

Huang, L., Wang, J., Lilley, D.M.J.

(2016) Nucleic Acids Res 44: 5390

  • DOI: https://doi.org/10.1093/nar/gkw201
  • Primary Citation of Related Structures:  
    5FJ0, 5FJ1, 5FJ4, 5FJC, 5FK1, 5FK2, 5FK3, 5FK4, 5FK5, 5FK6, 5FKD, 5FKE, 5FKF, 5FKG, 5FKH

  • PubMed Abstract: 

    • k-turns are commonly-occurring motifs that introduce sharp kinks into duplex RNA, thereby facilitating tertiary contacts. Both the folding and conformation of k-turns are determined by their local sequence. k-turns fall into two conformational classes, called N3 and N1, that differ in the pattern of hydrogen bonding in the core ...

    k-turns are commonly-occurring motifs that introduce sharp kinks into duplex RNA, thereby facilitating tertiary contacts. Both the folding and conformation of k-turns are determined by their local sequence. k-turns fall into two conformational classes, called N3 and N1, that differ in the pattern of hydrogen bonding in the core. We show here that this is determined by the basepair adjacent to the critical G•A pairs. We determined crystal structures of a series of Kt-7 variants in which this 3b,3n position has been systematically varied, showing that this leads to a switch in the conformation. We have previously shown that the 3b,3n position also determines the folding characteristics of the k-turn, i.e. whether or not the k-turn can fold in the presence of metal ions alone. We have analyzed the distribution of 3b,3n sequences from four classes of k-turns from ribosomes, riboswitches and U4 snRNA, finding a strong conservation of properties for a given k-turn type. We thus demonstrate a strong association between biological function, 3b,3n sequence and k-turn folding and conformation. This has strong predictive power, and can be applied to the modeling of large RNA architectures.

    Organizational Affiliation: 

    Cancer Research UK Nucleic Acid Structure Research Group, MSI/WTB Complex, The University of Dundee, Dow Street, Dundee DD1 5EH, UK d.m.j.lilley@dundee.ac.uk.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
U1 SMALL NUCLEAR RIBONUCLEOPROTEIN AA, B, E, F102Homo sapiensMutation(s): 0 
Gene Names: SNRPA
UniProt & NIH Common Fund Data Resources
Find proteins for P09012 (Homo sapiens)
Explore P09012 
Go to UniProtKB:  P09012
PHAROS:  P09012
Entity Groups  
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UniProt GroupP09012
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
50S RIBOSOMAL PROTEIN L7AEC, G123Archaeoglobus fulgidus DSM 4304Mutation(s): 0 
Gene Names: rpl7ae, AF_0764
UniProt
Find proteins for O29494 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O29494 
Go to UniProtKB:  O29494
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UniProt GroupO29494
Protein Feature View
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Entity ID: 3
MoleculeChainsLengthOrganismImage
HMKT-7D, H35Haloarcula marismortui
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.853α = 90
b = 161.226β = 90
c = 149.899γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-07-06
    Changes: Database references