6HCT

Crystal structure of Archeoglobus fulgidus L7Ae bound to its cognate UTR k-turn


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.091 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.187 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

The role of RNA structure in translational regulation by L7Ae protein in archaea.

Huang, L.Ashraf, S.Lilley, D.M.J.

(2018) RNA --: --

  • DOI: 10.1261/rna.068510.118

  • PubMed Abstract: 
  • A recent study has shown that archaeal L7Ae binds to a putative k-turn structure in the 5'-leader of the mRNA of its structural gene to regulate translation. To function as a regulator the RNA should be unstructured in the absence of protein, but it ...

    A recent study has shown that archaeal L7Ae binds to a putative k-turn structure in the 5'-leader of the mRNA of its structural gene to regulate translation. To function as a regulator the RNA should be unstructured in the absence of protein, but it should adopt a k-turn-containing stem-loop on binding L7Ae. Sequence analysis of UTR sequences indicates that their k-turn elements will be unable to fold in the absence of L7Ae, and we have demonstrated this experimentally in solution using FRET for the Archeoglobus fulgidus sequence. We have solved the X-ray crystal structure of the complex of the A. fulgidus RNA bound to its cognate L7Ae protein. The RNA adopts a standard k-turn conformation, that is specifically recognized by the L7Ae protein so stabilizing the stem-loop. In-line probing of the natural-sequence UTR shows that the RNA is unstructured in the absence of L7Ae binding, but folds on binding the protein such that the ribosome binding site is occluded. Thus L7Ae regulates its own translation by switching the conformation of the RNA to alter accessibility.


    Organizational Affiliation

    University of Dundee.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L7Ae
C, D, G
117Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)Mutation(s): 0 
Gene Names: rpl7ae
Find proteins for O29494 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Go to UniProtKB:  O29494
Entity ID: 1
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*CP*CP*GP*AP*UP*GP*AP*AP*UP*GP*CP*AP*UP*GP*AP*AP*GP*C)-3')A,B19Archaeoglobus fulgidus DSM 4304
Entity ID: 3
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*CP*CP*GP*AP*UP*GP*AP*AP*UP*G)-3')E11Archaeoglobus fulgidus DSM 4304
Entity ID: 4
MoleculeChainsLengthOrganism
RNA (5'-R(P*CP*AP*UP*GP*AP*AP*GP*C)-3')F8Archaeoglobus fulgidus DSM 4304
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, D
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.091 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.187 
  • Space Group: I 4 2 2
Unit Cell:
Length (Å)Angle (°)
a = 142.140α = 90.00
b = 142.140β = 90.00
c = 166.798γ = 90.00
Software Package:
Software NamePurpose
xia2data reduction
PHENIXrefinement
PHASERphasing
xia2data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Cancer Research UKUnited KingdomA18604

Revision History 

  • Version 1.0: 2018-10-31
    Type: Initial release