PDBsum entry 1aud

RNA binding protein/RNA

PDB id: 1aud

Contents

Protein chain

101 a.a. *

DNA/RNA

* Residue conservation analysis

PDB id:

1aud

Name:

RNA binding protein/RNA

Title:

U1a-utrrna, nmr, 31 structures

Structure:

RNA 3utr. Chain: b. Synonym: uucg tetraloop, only box 1 of 3'utr RNA. Engineered: yes. U1a 102. Chain: a. Fragment: residues 1 - 102 of u1a. Synonym: u1 small nuclear ribonucleoprotein a. Engineered: yes.

Source:

Synthetic: yes. Homo sapiens. Human. Organism_taxid: 9606. Strain: bl21 (de3). Cell_line: bl21. Gene: u1a 1-102. Expressed in: escherichia coli. Expression_system_taxid: 562.

NMR struc:

31 models

Authors:

F.H.-T.Allain,C.C.Gubser,P.W.A.Howe,K.Nagai,D.Neuhaus,G.Varani

Key ref:

F.H.Allain et al. (1997). Structural basis of the RNA-binding specificity of human U1A protein. EMBO J, 16, 5764-5772. PubMed id: 9312034 DOI: 10.1093/emboj/16.18.5764

Date:

22-Aug-97 Release date: 25-Feb-98

Supersedes:

1num

Protein chain

P09012  (SNRPA_HUMAN) -  U1 small nuclear ribonucleoprotein A from Homo sapiens

Seq: 282 a.a.

Struc: 101 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DNA/RNA chain

G-G-C-A-G-A-G-U-C-C-U-U-C-G-G-G-A-C-A-U-U-G-C-A-C-C-U-G-C-C 30 bases

Enzyme reactions

• Enzyme class: E.C.?

DOI no: 10.1093/emboj/16.18.5764

EMBO J 16:5764-5772 (1997)

PubMed id: 9312034

Structural basis of the RNA-binding specificity of human U1A protein.

F.H.Allain, P.W.Howe, D.Neuhaus, G.Varani.

ABSTRACT

The RNP domain is a very common eukaryotic protein domain involved in recognition of a wide range of RNA structures and sequences. Two structures of human U1A in complex with distinct RNA substrates have revealed important aspects of RNP-RNA recognition, but have also raised intriguing questions concerning the origin of binding specificity. The beta-sheet of the domain provides an extensive RNA-binding platform for packing aromatic RNA bases and hydrophobic protein side chains. However, many interactions between functional groups on the single-stranded nucleotides and residues on the beta-sheet surface are potentially common to RNP proteins with diverse specificity and therefore make only limited contribution to molecular discrimination. The refined structure of the U1A complex with the RNA polyadenylation inhibition element reported here clarifies the role of the RNP domain principal specificity determinants (the variable loops) in molecular recognition. The most variable region of RNP proteins, loop 3, plays a crucial role in defining the global geometry of the intermolecular interface. Electrostatic interactions with the RNA phosphodiester backbone involve protein side chains that are unique to U1A and are likely to be important for discrimination. This analysis provides a novel picture of RNA-protein recognition, much closer to our current understanding of protein-protein recognition than that of DNA-protein recognition.

Selected figure(s)

Figure 3.
Figure 3 (A) Global view of a converged structure of the U1A -PIE complex. The RNA bases are splayed out across the surface of the -sheet of U1A to form extensive intermolecular interactions, while the phosphates (dark blue) remain exposed to solvent. (B) The superposition of 31 converged structures highlights the excellent definition of the intermolecular interface. The backbone at the C-terminus of U1A N-terminal RNP domain is highlighted in yellow.

Figure 5.
Figure 5 (A) The surface representation of the complex shows loop 3 of U1A (white) protruding through the hole in the RNA internal loop (light blue); interactions involving Leu49, Ser46 and Ser48 (dark blue) and Arg52 (hidden in this orientation) are critical to dock the protein against the RNA. (B) Surface representation of free and bound protein structures. The red surface identifies residues involved in intermolecular stacking interactions that become exposed upon the rearrangement of helix C; dark blue identifies loop 3 residues that interact with the RNA by rigid fit; light blue identifies the location of the remaining sites of intermolecular contact.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (1997, 16, 5764-5772) copyright 1997.

Figures were selected by an automated process.