PDBsum entry 2k4c

RNA

PDB id: 2k4c

Contents

DNA/RNA

PDB id:

2k4c

Name:

RNA

Title:

Trnaphe-based homology model for trnaval refined against base n-h rdcs in two media and saxs data

Structure:

76-mer. Chain: a. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: sample is uniformly 15n labeled

NMR struc:

1 models

Authors:

A.Grishaev,J.Ying,M.D.Canny,A.Pardi,A.Bax

Key ref:

A.Grishaev et al. (2008). Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data. J Biomol Nmr, 42, 99. PubMed id: 18787959

Date:

04-Jun-08 Release date: 09-Dec-08

DNA/RNA chain

G-G-G-U-G-A-U-U-A-G-C-U-C-A-G-C-U-G-G-G-A-G-A-G-C-A-C-C-U-C-C-C-U-U-A-C-A-A-G- 76 bases

J Biomol Nmr 42:99 (2008)

PubMed id: 18787959

Solution structure of tRNAVal from refinement of homology model against residual dipolar coupling and SAXS data.

A.Grishaev, J.Ying, M.D.Canny, A.Pardi, A.Bax.

ABSTRACT

A procedure is presented for refinement of a homology model of E. coli tRNA(Val), originally based on the X-ray structure of yeast tRNA(Phe), using experimental residual dipolar coupling (RDC) and small angle X-ray scattering (SAXS) data. A spherical sampling algorithm is described for refinement against SAXS data that does not require a globbic approximation, which is particularly important for nucleic acids where such approximations are less appropriate. Substantially higher speed of the algorithm also makes its application favorable for proteins. In addition to the SAXS data, the structure refinement employed a sparse set of NMR data consisting of 24 imino N-H(N) RDCs measured with Pf1 phage alignment, and 20 imino N-H(N) RDCs obtained from magnetic field dependent alignment of tRNA(Val). The refinement strategy aims to largely retain the local geometry of the 58% identical tRNA(Phe) by ensuring that the atomic coordinates for short, overlapping segments of the ribose-phosphate backbone and the conserved base pairs remain close to those of the starting model. Local coordinate restraints are enforced using the non-crystallographic symmetry (NCS) term in the XPLOR-NIH or CNS software package, while still permitting modest movements of adjacent segments. The RDCs mainly drive the relative orientation of the helical arms, whereas the SAXS restraints ensure an overall molecular shape compatible with experimental scattering data. The resulting structure exhibits good cross-validation statistics (jack-knifed Q (free) = 14% for the Pf1 RDCs, compared to 25% for the starting model) and exhibits a larger angle between the two helical arms than observed in the X-ray structure of tRNA(Phe), in agreement with previous NMR-based tRNA(Val) models.