2KYD

RDC and RCSA refinement of an A-form RNA: Improvements in Major Groove Width

Summary for 2KYD

• Entry DOI: 10.2210/pdb2kyd/pdb
• NMR Information: BMRB: 16980
• Descriptor: RNA (5'-R(*CP*UP*AP*GP*UP*UP*AP*GP*CP*UP*AP*AP*CP*UP*AP*G)-3') (1 entity in total)
• Functional Keywords: a-form rna, slb duplex, moloney murine leukemia virus dimerization signal, rdc and rcsa refinement, rna
• Total number of polymer chains: 2
• Total formula weight: 10166.13

Authors

Tolbert, B.S.,Summers, M.F.,Miyazaki, Y.,Barton, S.,Kinde, B.,Stark, P.,Singh, R.,Bax, A.,Case, D. (deposition date: 2010-05-24, release date: 2010-07-07, Last modification date: 2024-05-01)

Primary citation

Tolbert, B.S.,Miyazaki, Y.,Barton, S.,Kinde, B.,Starck, P.,Singh, R.,Bax, A.,Case, D.A.,Summers, M.F.
Major groove width variations in RNA structures determined by NMR and impact of 13C residual chemical shift anisotropy and 1H-13C residual dipolar coupling on refinement.
J.Biomol.Nmr, 47:205-219, 2010

PubMed Abstract: Ribonucleic acid structure determination by NMR spectroscopy relies primarily on local structural restraints provided by (1)H- (1)H NOEs and J-couplings. When employed loosely, these restraints are broadly compatible with A- and B-like helical geometries and give rise to calculated structures that are highly sensitive to the force fields employed during refinement. A survey of recently reported NMR structures reveals significant variations in helical parameters, particularly the major groove width. Although helical parameters observed in high-resolution X-ray crystal structures of isolated A-form RNA helices are sensitive to crystal packing effects, variations among the published X-ray structures are significantly smaller than those observed in NMR structures. Here we show that restraints derived from aromatic (1)H- (13)C residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs) can overcome NMR restraint and force field deficiencies and afford structures with helical properties similar to those observed in high-resolution X-ray structures.

PubMed: 20549304
DOI: 10.1007/s10858-010-9424-x

Experimental method

SOLUTION NMR