PDBsum entry: 3k5y

RNA/RNA binding protein

PDB-id: 3k5y

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Description

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References

PROCHECK

Protein chain

400 a.a. *

DNA/RNA

Waters ×97

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

3k5y

Name:

RNA/RNA binding protein

Title:

Crystal structure of fbf-2/gld-1 fbea complex

Structure:

Fem-3 mRNA-binding factor 2. Chain: a. Fragment: unp residues 164-575, RNA-binding domain. Engineered: yes. 5'-r( Up Gp Up Gp Cp Cp Ap Up A)-3'. Chain: b. Engineered: yes

Source:

Caenorhabditis elegans. Nematode. Organism_taxid: 6239. Gene: f21h12.5, fbf-2. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes

UniProt:

Q09312 (FBF2_CAEEL)

Seq:

Struc:

Seq:

Struc:

Seq:

632 a.a.

Struc:

400 a.a.

Key:	PfamA domain	PfamB domain
Secondary structure

Resolution:

2.30Å

R-factor:

0.171

R-free:

0.215

Authors:

Y.Wang,L.Opperman,M.Wickens,T.M.T.Hall

Key ref:

Y.Wang et al. (2009). Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein.. Proc Natl Acad Sci U S A, 106, 20186-20191. [PubMed id: 19901328] [DOI: 10.1073/pnas.0812076106]

Date:

08-Oct-09

Release date:

03-Nov-09

Related entries:

3k5q
3k5z
3k61
3k62
3k64

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Procheck

Clefts

Surface

Key reference

DOI no: 10.1073/pnas.0812076106

Proc Natl Acad Sci U S A 106:20186-20191 (2009)

PubMed id: 19901328

Structural basis for specific recognition of multiple mRNA targets by a PUF regulatory protein.

Y.Wang, L.Opperman, M.Wickens, T.M.Hall.

ABSTRACT

Caenorhabditis elegans fem-3 binding factor (FBF) is a founding member of the PUMILIO/FBF (PUF) family of mRNA regulatory proteins. It regulates multiple mRNAs critical for stem cell maintenance and germline development. Here, we report crystal structures of FBF in complex with 6 different 9-nt RNA sequences, including elements from 4 natural mRNAs. These structures reveal that FBF binds to conserved bases at positions 1-3 and 7-8. The key specificity determinant of FBF vs. other PUF proteins lies in positions 4-6. In FBF/RNA complexes, these bases stack directly with one another and turn away from the RNA-binding surface. A short region of FBF is sufficient to impart its unique specificity and lies directly opposite the flipped bases. We suggest that this region imposes a flattened curvature on the protein; hence, the requirement for the additional nucleotide. The principles of FBF/RNA recognition suggest a general mechanism by which PUF proteins recognize distinct families of RNAs yet exploit very nearly identical atomic contacts in doing so.

Selected figure(s)

Figure 3.
Three classes of RNA conformation in FBF-2 target RNAs. Interaction of FBF-2 repeats 4–6 with gld-1 FBEa (A), fem-3 PME (B), and gld-1 FBEa G4A mutant (C) RNAs are shown. Dashed lines indicate interacting atoms. Water molecules that mediate interactions are shown as red spheres. (D) Superposition of the RNA-interacting side chains of FBF-2 repeats 4–6 and gld-1 FBEa (gray), fem-3 PME (tan), and gld-1 FBEa G4A mutant (pale cyan) RNAs (rmsd of 0.15 Å over 130 CA atoms between PME and FBEa and rmsd of 0.28 Å over 130 CA atoms between PME and FBEa G4A mutant).

Figure 6.
Conservation and adaptation of PUF protein–RNA interactions. Schematic representations of interactions between PUF proteins and their RNA targets. Interactions and RNA base conformations unique to each protein are indicated by color: FBF-2 (red), PUM1 (gold), Puf4p (green), and Puf3p (orange).

Figures were selected by an automated process.