6PUN

Crystal structure of a ternary complex of FBF-2 with LST-1 (site B) and compact FBE RNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.099 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A crystal structure of a collaborative RNA regulatory complex reveals mechanisms to refine target specificity.

Qiu, C.Bhat, V.D.Rajeev, S.Zhang, C.Lasley, A.E.Wine, R.N.Campbell, Z.T.Tanaka Hall, T.M.T.

(2019) Elife 8: --

  • DOI: 10.7554/eLife.48968

  • PubMed Abstract: 
  • In the <i>Caenorhabditis elegans </i> germline, <i>fem-3 </i> Binding Factor (FBF) partners with LST-1 to maintain stem cells. A crystal structure of an FBF-2/LST-1/RNA complex revealed that FBF-2 recognizes a short RNA motif different from the cha ...

    In the Caenorhabditis elegans germline, fem-3 Binding Factor (FBF) partners with LST-1 to maintain stem cells. A crystal structure of an FBF-2/LST-1/RNA complex revealed that FBF-2 recognizes a short RNA motif different from the characteristic 9-nt FBF binding element, and compact motif recognition coincided with curvature changes in the FBF-2 scaffold. Previously, we engineered FBF-2 to favor recognition of shorter RNA motifs without curvature change (Bhat et al., 2019). In vitro selection of RNAs bound by FBF-2 suggested sequence specificity in the central region of the compact element. This bias, reflected in the crystal structure, was validated in RNA-binding assays. FBF-2 has the intrinsic ability to bind to this shorter motif. LST-1 weakens FBF-2 binding affinity for short and long motifs, which may increase target selectivity. Our findings highlight the role of FBF scaffold flexibility in RNA recognition and suggest a new mechanism by which protein partners refine target site selection.


    Organizational Affiliation

    Department of Biological Sciences, University of Texas at Dallas, Richardson, United States.,Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fem-3 mRNA-binding factor 2
A, C
413Caenorhabditis elegansMutation(s): 0 
Gene Names: fbf-2
Find proteins for Q09312 (Caenorhabditis elegans)
Go to UniProtKB:  Q09312
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
LST-1
E, F
29Caenorhabditis elegansMutation(s): 0 
Find proteins for Q86RT0 (Caenorhabditis elegans)
Go to UniProtKB:  Q86RT0
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*CP*UP*GP*UP*GP*AP*AP*U)-3')B,D8Caenorhabditis elegans
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
EDO
Query on EDO

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Download CCD File 
A, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.099 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.198 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 42.751α = 107.17
b = 74.380β = 104.40
c = 81.547γ = 101.76
Software Package:
Software NamePurpose
SERGUIdata collection
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-08-21
    Type: Initial release