PDBsum entry: 1mhn

RNA binding protein

PDB id: 1mhn

Contents

Protein chain

59 a.a. *

Waters ×65

* Residue conservation analysis

PDB id:

1mhn

Name:

RNA binding protein

Title:

High resolution crystal structure of the smn tudor domain

Structure:

Survival motor neuron protein. Chain: a. Fragment: tudor domain. Synonym: smn, component of gems 1, gemin1. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: smn1. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.

Resolution:

1.80Å R-factor: 0.147 R-free: 0.187

Authors:

R.Sprangers,M.R.Groves,I.Sinning,M.Sattler

Key ref:

R.Sprangers et al. (2003). High-resolution X-ray and NMR structures of the SMN Tudor domain: conformational variation in the binding site for symmetrically dimethylated arginine residues. J Mol Biol, 327, 507-520. PubMed id: 12628254 DOI: 10.1016/S0022-2836(03)00148-7

Date:

20-Aug-02 Release date: 25-Mar-03

Protein chain

Q16637  (SMN_HUMAN) -  Survival motor neuron protein

Seq: 294 a.a.

Struc: 59 a.a.

 Gene Ontology (GO) functional annotation 

• Biochemical function: nucleic acid binding (1 term)

DOI no: 10.1016/S0022-2836(03)00148-7

J Mol Biol 327:507-520 (2003)

PubMed id: 12628254

High-resolution X-ray and NMR structures of the SMN Tudor domain: conformational variation in the binding site for symmetrically dimethylated arginine residues.

R.Sprangers, M.R.Groves, I.Sinning, M.Sattler.

ABSTRACT

The SMN protein, which is linked to spinal muscular atrophy (SMA), plays an important role in the assembly of the spliceosomal small nuclear ribonucleoprotein complexes. This function requires binding of SMN to the arginine-glycine (RG) rich C-terminal tails of the Sm proteins, which contain symmetrically dimethylated arginine residues (sDMA) in vivo. Using NMR titrations, we show that the SMN Tudor domain recognizes these sDMAs in the methylated RG repeats. Upon complex formation a cluster of conserved aromatic residues in the SMN Tudor domain interacts with the sDMA methyl groups. We present two high resolution structures of the uncomplexed SMN Tudor domain, a 1.8A crystal structure and an NMR structure that has been refined against a large number of backbone and side-chain residual dipolar couplings. The backbone conformation of both structures is very similar, however, differences are observed for the cluster of conserved aromatic side-chains in the sDMA binding pocket. In order to validate these variations we introduce a novel application of residual dipolar couplings for aromatic rings. We show that structural information can be derived from aromatic ring residual dipolar couplings, even in the presence of internal motions such as ring flipping. These residual dipolar couplings and ring current shifts independently confirm that the SMN Tudor domain adopts two different conformations in the sDMA binding pocket. The observed structural variations may play a role for the recognition of sDMAs.

Selected figure(s)

Figure 5.
Figure 5. Deviation from experimental restraints. Observed versus Back-calculated residual dipolar couplings. Left: ensemble of NMR structures; right: crystal structure. Top: residual dipolar couplings used in the structure calculations (HN-N, Ha-C^a, N-C', HN-C', C-CH[3], H-C[aromatic] (Trp), C^b-C^g, H epsilon 1-N epsilon 1). Bottom: residual dipolar couplings used for the calculation of the Q-factor (HN(i) -Ha(i) and HN(i) -Ha(i -1)).

Figure 7.
Figure 7. Aromatic ring residual dipolar couplings. The vectors for which residual dipolar couplings have been measured are indicated in black. As a result of the reorientation around x[2] and of the geometry of the ring only one residual dipolar coupling for the aromatic ring is measured (D[ring]).

The above figures are reprinted by permission from Elsevier: J Mol Biol (2003, 327, 507-520) copyright 2003.

Figures were selected by an automated process.