Characterization of crystals of small ribosomal subunits

Yonath, Ada; Glotz, Carola; Gewitz, H.S.; Bartels, Klaus; Böhlen, K. von; Makowski, I.; Wittmann, H. G.

doi:10.1016/0022-2836(88)90216-1

Cited by 61 publications

(32 citation statements)

References 18 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Over two decades ago, the 50S subunit was crystallized by Yonath, Wittmann, and their coworkers (108). Crystals of the 30S subunit and the whole 70S ribosome were originally reported by the Puschino group (109) and subsequently similar crystals of the 30S subunit were obtained by Yonath and coworkers (110,111). Almost a decade of work by Yonath and coworkers resulted in improved crystals of the 50S subunit that diffracted to 3Å resolution, raising the possibility that an atomic structure of it might one day be obtained (112).…”

Section: Crystallography Of the Ribosomementioning

confidence: 99%

Structural Insights Into Translational Fidelity

Ogle

Ramakrishnan

2005

Annu. Rev. Biochem.

555

538

View full text Add to dashboard Cite

■ Abstract The underlying basis for the accuracy of protein synthesis has been the subject of over four decades of investigation. Recent biochemical and structural data make it possible to understand at least in outline the structural basis for tRNA selection, in which codon recognition by cognate tRNA results in the hydrolysis of GTP by EF-Tu over 75Å away. The ribosome recognizes the geometry of codonanticodon base pairing at the first two positions but monitors the third, or wobble position, less stringently. Part of the additional binding energy of cognate tRNA is used to induce conformational changes in the ribosome that stabilize a transition state for GTP hydrolysis by EF-Tu and subsequently result in accelerated accommodation of tRNA into the peptidyl transferase center. The transition state for GTP hydrolysis is characterized, among other things, by a distorted tRNA. This picture explains a large body of data on the effect of antibiotics and mutations on translational fidelity. However, many fundamental questions remain, such as the mechanism of activation of GTP hydrolysis by EF-Tu, and the relationship between decoding and frameshifting. CONTENTS

show abstract

Section: Crystallography Of the Ribosomementioning

confidence: 99%

Structural Insights Into Translational Fidelity

Ogle

Ramakrishnan

2005

Annu. Rev. Biochem.

555

538

View full text Add to dashboard Cite

show abstract

“…In contrast to the marked tendency of large ribosomal subunits to crystallize, only one crystal form has beem obtained so far from the small ribosomal subunit (Trakhanov et al, 1987;Yonath et al, 1988). For almost a decade, this crystal form (T30S) yielded satisfactory data only to 12±15 A Ê (Schlu È nzen et al, 1995), although re¯ections were observed up to 7.3 A Ê .…”

Section: Resolution Versus Diffraction Qualitymentioning

confidence: 99%

Crystallographic Studies on the Ribosome, a Large Macromolecular Assembly Exhibiting Severe Nonisomorphism, Extreme Beam Sensitivity and No Internal Symmetry

Yonath¹,

Harms²,

Hansen³

et al. 1998

Acta Cryst Sect A

Self Cite

View full text Add to dashboard Cite

Crystals, diffracting best to around 3 A Ê , have been grown from intact large and small ribosomal subunits. The bright synchrotron radiation necessary for the collection of the higher-resolution X-ray diffraction data introduces signi®cant decay even at cryo temperatures. Nevertheless, owing to the reasonable isomorphism of the recently improved crystals of the small ribosomal subunits, reliable phases have been extracted at medium resolution (5±6 A Ê ) and an interpretable ®ve-derivative MIR map has been constructed. For the crystals of the large subunits, however, the situation is more complicated because at higher resolution (2.7±7 A Ê ) they suffer from substantial radiation sensitivity, a low level of isomorphism, instability of the longest unit-cell axis and nonisotropic mosaicity. The 8 A Ê MIR map, constructed to gain insight into this unusual system, may provide feasible reasoning for the odd combination of the properties of these crystals as well as hints for future improvement. Parallel efforts, in which electron-microscopy-reconstructed images are being exploited for molecular-replacement studies, are also discussed.

show abstract

“…The key to obtaining crystals was the use of ribosomes from robust bacteria, namely halophiles and thermophiles (79). These yielded suitable crystals from the large subunit from Haloarcula marismortui, 235 H50S (36, 61,74), and the small subunit from Thermus thermophilus, T30S (82). However, because H. marismortui is an archaeon sharing properties with prokaryotes as well as eukaryotes, the structural information obtained from its crystals is only partially relevant to the vast amount of functional knowledge accumulated over the years from the Escherichia coli ribosome.…”

Section: Introductionmentioning

confidence: 99%

Ribosomal Crystallography: Initiation, Peptide Bond Formation, and Amino Acid Polymerization are Hampered by Antibiotics

Yonath

Bashan

2004

Annu. Rev. Microbiol.

View full text Add to dashboard Cite

■ Abstract High-resolution structures of ribosomal complexes revealed that minute amounts of clinically relevant antibiotics hamper protein biosynthesis by limiting ribosomal mobility or perturbing its elaborate architecture, designed for navigating and controlling peptide bond formation and continuous amino acid polymerization. To accomplish this, the ribosome contributes positional rather than chemical catalysis, provides remote interactions governing accurate substrate alignment within the flexible peptidyl-transferase center (PTC) pocket, and ensures nascent-protein chirality through spatial limitations. Peptide bond formation is concurrent with aminoacylatedtRNA 3 end translocation and is performed by a rotatory motion around the axis of a sizable ribosomal symmetry-related region, which is located around the PTC in all known crystal structures. Guided by ribosomal-RNA scaffold along an exact pattern, the rotatory motion results in stereochemistry that is optimal for peptide bond formation and for nascent protein entrance into the exit tunnel, the main target of antibiotics targeting ribosomes. By connecting the PTC, the decoding center, and the tRNA entrance and exit regions, the symmetry-related region can transfer intraribosomal signals, guaranteeing smooth processivity of amino acid polymerization. CONTENTS INTRODUCTION . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . INTRODUCTIONRibosomes are the universal cellular riboprotein assemblies that catalyze amino acid polymerization into proteins. In this process, called protein biosynthesis, the ribosomes interact with the cellular environment, select the genetic frame to be translated, form the peptide bonds, and act as polymerases to ensure smooth and efficient elongation of the newly born protein chains. The ribosomes are composed of two riboprotein subunits of unequal size that associate upon the initiation of the process and dissociate at its termination. Protein biosynthesis is performed by a cooperative effort of both subunits, and the ribosome possesses features that facilitate transmission between its various functional sites, leading to efficient processivity of protein formation essential for cell vitality. The small ribosomal subunit facilitates the initiation of the translation process and is involved in selecting the frame to be translated, decoding the genetic message, and controlling the fidelity of codon-anticodon interactions. The large ribosomal subunit forms the peptide bond, ensures smooth amino acid polymerization, and channels the nascent proteins through their exit tunnel. Messenger RNA (mRNA) carries the genetic instructions to the ribosome, and aminoacylated transfer RNA (tRNA) molecules deliver the amino acids within a ternary complex containing GTP and the elongation factor Tu. The ribosome possesses three tRNA binding sites. The A-site hosts the aminoacylated-tRNA, the P-site hosts the peptidyl tRNA, and the E-site designates the location of the exiting free tRNA once a p...

show abstract

Characterization of crystals of small ribosomal subunits

Cited by 61 publications

References 18 publications

Structural Insights Into Translational Fidelity

Structural Insights Into Translational Fidelity

Crystallographic Studies on the Ribosome, a Large Macromolecular Assembly Exhibiting Severe Nonisomorphism, Extreme Beam Sensitivity and No Internal Symmetry

Ribosomal Crystallography: Initiation, Peptide Bond Formation, and Amino Acid Polymerization are Hampered by Antibiotics

Contact Info

Product

Resources

About