PDBsum entry: 1ekz

Cell cycle/RNA

PDB-id: 1ekz

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PROCHECK

Protein chain

76 a.a. *

DNA/RNA

* Residue conservation analysis

Tools

Clefts Calculation

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PDB id:

1ekz

Name:

Cell cycle/RNA

Title:

Nmr structure of the complex between the third dsrbd from drosophila staufen and a RNA hairpin

Structure:

Maternal effect protein (staufen). Chain: a. Synonym: dsrbdiii. Engineered: yes. Staufen double-stranded RNA binding domain. Chain: b. Engineered: yes

Source:

Drosophila melanogaster. Fruit fly. Organism_taxid: 7227. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes

UniProt:

P25159 (STAU_DROME)

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

Struc:

Seq:

1026 a.a.

Struc:

76 a.a.

Key:	PfamA domain	PfamB domain
Secondary structure	CATH domain

Resolution:

not givenÅ

NMR structure:

36 models

Authors:

A.Ramos,S.Grunert,M.Bycroft,D.St Johnston,G.Varani

Key ref:

A.Ramos et al. (2000). RNA recognition by a Staufen double-stranded RNA-binding domain.. EMBO J, 19, 997. [PubMed id: 10698941] [DOI: 10.1093/emboj/19.5.997]

Date:

11-Mar-00

Release date:

21-Aug-00

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Key reference

DOI no: 10.1093/emboj/19.5.997

EMBO J 19:997 (2000)

PubMed id: 10698941

RNA recognition by a Staufen double-stranded RNA-binding domain.

A.Ramos, S.Grünert, J.Adams, D.R.Micklem, M.R.Proctor, S.Freund, M.Bycroft, D.St Johnston, G.Varani.

ABSTRACT

The double-stranded RNA-binding domain (dsRBD) is a common RNA-binding motif found in many proteins involved in RNA maturation and localization. To determine how this domain recognizes RNA, we have studied the third dsRBD from Drosophila Staufen. The domain binds optimally to RNA stem-loops containing 12 uninterrupted base pairs, and we have identified the amino acids required for this interaction. By mutating these residues in a staufen transgene, we show that the RNA-binding activity of dsRBD3 is required in vivo for Staufen-dependent localization of bicoid and oskar mRNAs. Using high-resolution NMR, we have determined the structure of the complex between dsRBD3 and an RNA stem-loop. The dsRBD recognizes the shape of A-form dsRNA through interactions between conserved residues within loop 2 and the minor groove, and between loop 4 and the phosphodiester backbone across the adjacent major groove. In addition, helix alpha1 interacts with the single-stranded loop that caps the RNA helix. Interactions between helix alpha1 and single-stranded RNA may be important determinants of the specificity of dsRBD proteins.

Selected figure(s)

Figure 4.
Figure 4 Heteronuclear ^1H-^15N NOE for free (A) and RNA-bound (B) Staufen dsRBD3.

Figure 6.
Figure 6 Intermolecular interactions between dsRBD and the RNA stem–loop in the superposition of 10 converged structures; one structure is represented in orange for clarity. (A) Interaction between loop 2 and the minor groove of the double-helical stem; Ala27 and His28 from the conserved GPAH sequence and the Lys30 side chains are shown explicitly; 2'-OH groups in close proximity to amino acids side chains are highlighted in red. (B) Interactions between loop 4 and the N-terminus of helix 2 and RNA phosphates (in red). (C) Interaction between helix 1 and the UUCG tetraloop.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2000, 19, 997-0) copyright 2000.

Figures were selected by an automated process.