1H, 13C, and 15N Chemical Shift Assignments for Ribosomal Protein S4 delta 41

The solution structure of ribosomal protein S4 delta41 reveals two subdomains
and a positively charged surface that may interact with RNA.

Prokaryotic protein S4 initiates assembly of the small ribosomal subunit by
binding to 16 S rRNA. Residues 43-200 of S4 from Bacillus stearothermophilus
(S4 Delta41) bind to both 16 S rRNA and to a mRNA pseudoknot. In order to
obtain structure-based insights regarding RNA binding, we previously determined
the solution structure of S4 Delta41 using NOE, hydrogen bond, and torsion
angle restraints. S4 Delta41 is elongated, with two distinct subdomains, one
all helical, the other including a beta-sheet. In contrast to the high
resolution structures obtained for each individual subdomain, their relative
orientation was not precisely defined because only 17 intersubdomain NOE
restraints were determined. Compared to the 1.7 A crystal structure, when the
sheet-containing subdomains are superimposed, the helical subdomain is twisted
by almost 45 degrees about the long axis of the molecule in the solution
structure. Because variations in subdomain orientation may explain how the
protein recognizes multiple RNA targets, our current goal is to determine the
orientation of the subdomains in solution with high precision. To this end, NOE
assignments were re-examined. NOESY experiments on a specifically labeled
sample revealed that one of the intersubdomain restraints had been misassigned.
However, the revised set of NOE restraints produces solution structures that
still have imprecisely defined subdomain orientations and that lie between the
original NMR structure and the crystal structure. In contrast, augmenting the
NOE restraints with N-H dipolar couplings, measured in uniaxial liquid
crystalline phases, clearly establishes the relative orientation of the
subdomains. Data obtained from two independent liquid crystalline milieux,
DMPC/DHPC bicelles and the filamentous bacteriophage Pf1, show that the
relative orientation of the subdomains in solution is quite similar to the
subdomain orientation in the crystal structure. The solution structure, refined
with dipolar data, is presented and its implications for S4's RNA binding
activity are discussed.

Journal of Molecular Biology (1999) 292: 375-387
Refining the overall structure and subdomain orientation of ribosomal protein S4 delta41 with dipolar couplings measured by NMR in uniaxial liquid crystalline phases.

Resdiues 1 and 43-200 of the Bacillus stearothermophilus sequence for ribosomal
protein S4

Solution Structure Of Ribosomal Protein S4 Delta 41, Refined With Dipolar Couplings (Minimized Average Structure)

Solution Structure Of Ribosomal Protein S4 Delta 41, Refined With Dipolar Couplings (Ensemble Of 16 Structures)

Fitting Of Components With Known Structure Into An 11.5 A Cryo-Em Map Of The E.Coli 70s Ribosome

30S ribosomal protein S4 [Geobacillus kaustophilus HTA426]

30S ribosomal protein S4 [Geobacillus kaustophilus GBlys]

30S ribosomal protein S4 [Geobacillus thermoleovorans B23]

ribosomal protein S4 [Bacillus stearothermophilus, Peptide, 198 aa]

ribosomal protein S4 [Geobacillus sp. Y412MC61]

ribosomal protein S4 [Geobacillus sp. C56-T3]

ribosomal protein S4 [Geobacillus sp. Y412MC52]

30S ribosomal protein S4 [Geobacillus thermoleovorans CCB_US3_UF5]

MULTISPECIES: 30S ribosomal protein S4 [Geobacillus]

30S ribosomal protein S4 [Geobacillus vulcani]

30S ribosomal protein S4 [Geobacillus stearothermophilus]

RecName: Full=30S ribosomal protein S4; AltName: Full=BS5

Residues 2-42 of the naturally occurring Bacillus stearothermophilus ribosomal
S4 sequence were deleted to create the delta 41 protein.

hybrid DGSA protocol without the dipolar coupling restraints followed by additional SA with the dipolar coupling restraints add

residue specific labelling as follows: proline: deuterated at beta, gamma,
and delta positions; methionine: uniformly 15N and 13C labelled (also
protonated); tyrosine: 13C labelled at the epsilon position of the ring (also
protonated)

conditions refer to samples 15N_sample, 15N13C_sample_1 and 15N13C_sample_2

conditions refer to sample bicelle_sample

spectrometer operation and preliminary processing