3D reconstruction of the 50s ribosomal subunit of escherichia coli

1986 ◽  
Vol 44 ◽  
pp. 40-41
Author(s):  
M. Radermacher ◽  
T. Wagenknecht ◽  
A. Verschoor ◽  
J. Frank
Keyword(s):  
3D Reconstruction ◽  
3D Structure ◽  
Three Dimensional ◽  
Ribosomal Subunit ◽  
Main Body ◽  
Large Ribosomal Subunit ◽  
E Coli ◽  
Reconstruction Scheme ◽  
Particle Preparation ◽  
Electron Microscopical

The three-dimensional (3D) structure of the large ribosomal subunit from E. coli was determined from micrographs of a negatively stained 50S particle preparation using our new reconstruction scheme. The 50S subunit occurs in electron microscopical preparations mainly in the crown-view orientation with the interface side of the main body situated parallel to the specimen plane, but in random in plane orientations. An image of such a specimen tilted by a large tilt angle, which inherently contains a conical tilt series of the particle, was used to calculate a 3D reconstruction.

Detection, Averaging, and 3D Reconstruction of Biological Specimens on Hypercubes (Transputer-based) Computers

1990 ◽  
Vol 48 (1) ◽  
pp. 454-455
Author(s):  
Jose-Maria Carazo ◽  
I. Benavides ◽  
S. Marco ◽  
J.L. Carrascosa ◽  
E.L. Zapata
Keyword(s):  
3D Reconstruction ◽  
3D Structure ◽  
Three Dimensional ◽  
Software Tools ◽  
Mapping Method ◽  
Computer Architectures ◽  
Parallel Computer ◽  
Reconstruction Process ◽  
Computing Power ◽  
Order Of Magnitude

Obtaining the three-dimensional (3D) structure of negatively stained biological specimens at a resolution of, typically, 2 - 4 nm is becoming a relatively common practice in an increasing number of laboratories. A combination of new conceptual approaches, new software tools, and faster computers have made this situation possible. However, all these 3D reconstruction processes are quite computer intensive, and the middle term future is full of suggestions entailing an even greater need of computing power. Up to now all published 3D reconstructions in this field have been performed on conventional (sequential) computers, but it is a fact that new parallel computer architectures represent the potential of order-of-magnitude increases in computing power and should, therefore, be considered for their possible application in the most computing intensive tasks.We have studied both shared-memory-based computer architectures, like the BBN Butterfly, and local-memory-based architectures, mainly hypercubes implemented on transputers, where we have used the algorithmic mapping method proposed by Zapata el at. In this work we have developed the basic software tools needed to obtain a 3D reconstruction from non-crystalline specimens (“single particles”) using the so-called Random Conical Tilt Series Method. We start from a pair of images presenting the same field, first tilted (by ≃55°) and then untilted. It is then assumed that we can supply the system with the image of the particle we are looking for (ideally, a 2D average from a previous study) and with a matrix describing the geometrical relationships between the tilted and untilted fields (this step is now accomplished by interactively marking a few pairs of corresponding features in the two fields). From here on the 3D reconstruction process may be run automatically.

A compact three-dimensional crystal form of the large ribosomal subunit from Bacillus stearothermophilus

FEBS Letters ◽  
1983 ◽  
Vol 163 (1) ◽  
pp. 69-72 ◽  
Author(s):  
A. Yonath ◽  
J. Piefke ◽  
J. Müssig ◽  
H.-S. Gewitz ◽  
H.G. Wittmann
Keyword(s):  
Bacillus Stearothermophilus ◽  
Three Dimensional ◽  
Ribosomal Subunit ◽  
Crystal Form ◽  
Large Ribosomal Subunit ◽  
Dimensional Crystal

scholarly journals An in silico structural insights into Plasmodium LytB protein and its inhibition

2014 ◽  
Vol 70 (a1) ◽  
pp. C1791-C1791
Author(s):  
Rajabrata Bhunya ◽  
Suman Nandy ◽  
Alpana Seal
Keyword(s):  
In Silico ◽  
3D Structure ◽  
Three Dimensional ◽  
Comparative Modeling ◽  
Binding Energies ◽  
E Coli ◽  
Dimethylallyl Diphosphate ◽  
In Silico Study ◽  
Structural Insights ◽  
Insight Into

In most of the pathogenic organisms including Plasmodium falciparum, isoprenoids are synthesized via MEP (MethylErythritol 4-Phosphate) pathway. LytB is the last enzyme of this pathway which catalyzes the conversion of (E)-4-hydroxy-3-methylbut-2-en-1-yl diphosphate (HMBPP) into the two isoprenoid precursors: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). Since the MEP pathway is not used by humans, it represents an attractive target for the development of new antimalarial compounds or inhibitors. Here a systematic in-silico study has been conducted to get an insight into the structure of Plasmodium lytB as well as its affinities towards different inhibitors. We used comparative modeling technique to predict the three dimensional (3D) structure of Plasmodium LytB taking E. Coli LytB protein (PDB ID: 3KE8) as template and the model was subsequently refined through molecular dynamics (MD) simulation. A large ligand dataset containing diphospate group was subjected for virtual screening against the target using GOLD 5.2 program. Considering the mode of binding and affinities, 17 leads were selected on basis of binding energies in comparison to its substrate HMBPP (Gold.Chemscore.DG: -20.9734 kcal/mol). Among them, 5 were discarded because of their inhibitory activity towards other human enzymes. The rest 12 potential leads carry all the properties of any "drug like" molecule and the knowledge of Plasmodium LytB inhibitory mechanism which can provide valuable support for the antimalarial inhibitor design in future.

scholarly journals A NEW 3-D RECONSTRUCTION SCHEME APPLIED TO THE 50S RIBOSOMAL SUBUNIT OF E. COLI

1986 ◽  
Vol 141 (1) ◽  
pp. RP1-RP2 ◽  
Author(s):  
M. Radermacher ◽  
T. Wagenknecht ◽  
A. Verschoor ◽  
J. Frank
Keyword(s):  
Ribosomal Subunit ◽  
E Coli ◽  
Reconstruction Scheme

Three-Dimensional Image Reconstruction of the 50S Subunit from Escherichia Coli Ribosomes Lacking 5S-rRNA

1990 ◽  
Vol 48 (1) ◽  
pp. 284-285
Author(s):  
Michael Radermacher ◽  
Volker Nowotny ◽  
Robert Grassucci ◽  
Joachim Frank
Keyword(s):  
Three Dimensional ◽  
Ribosomal Subunit ◽  
5S Rrna ◽  
Scattering Data ◽  
23S Rrna ◽  
Reconstruction Technique ◽  
Electron Dose ◽  
E Coli ◽  
Phenol Extraction ◽  
Negative Stain

In earlier studies the structure of the 50S ribosomal subunit from E. coli has been determined from electron micrographs, using the single exposure random conical reconstruction technique. For the understanding of the function of ribosomes the single proteins and ribosomal RNAs need to be located within the ribosome structure. For localization of most proteins immunoelectron microscopy and neutron scattering data are available. The current study’s goal is the localization of the 5S rRNA from a comparison of the structures of complete 50S subunits with that of subunits reconstituted omitting the 5S rRNA.By Phenol extraction of purified 50S subunits the rRNA fraction was separated form the total protein fraction (TP50). This rRNA fraction was separated into 23S rRNA and 5S rRNA via HPLC on a DEAE-column. The total reconstitution of 23S rRNA and the equivalent amount of TP50 resulted in particles lacking the 5S rRNA. For electron microscopy the subunits were prepared in a negative stain sandwich preparation.Twenty tilt pairs at 50° tilt and 0° were recorded, with an electron dose of approximately 10el/A2 and a magnification of 49,000. A total of 983 particles were selected from these data. The 0° images were aligned using the procedure described in.

scholarly journals Time course of large ribosomal subunit assembly in E. coli cells overexpressing a helicase inactive DbpA protein

RNA ◽  
2016 ◽  
Vol 22 (7) ◽  
pp. 1055-1064 ◽  
Author(s):  
Riley C. Gentry ◽  
Jared J. Childs ◽  
Jirair Gevorkyan ◽  
Yulia V. Gerasimova ◽  
Eda Koculi
Keyword(s):  
Time Course ◽  
Ribosomal Subunit ◽  
Large Ribosomal Subunit ◽  
Subunit Assembly ◽  
E Coli

scholarly journals The Role of a Key Amino Acid Position in Species-Specific Proteinaceous dUTPase Inhibition

Biomolecules ◽  
2019 ◽  
Vol 9 (6) ◽  
pp. 221 ◽  
Author(s):  
András Benedek ◽  
Fanni Temesváry-Kis ◽  
Tamjidmaa Khatanbaatar ◽  
Ibolya Leveles ◽  
Éva Viola Surányi ◽  
...  
Keyword(s):  
Amino Acid ◽  
3D Structure ◽  
Three Dimensional ◽  
Amino Acid Position ◽  
Terminal Segment ◽  
Inhibition Mechanism ◽  
Structural Explanation ◽  
E Coli ◽  
Repair Enzymes ◽  
Species Specific

Protein inhibitors of key DNA repair enzymes play an important role in deciphering physiological pathways responsible for genome integrity, and may also be exploited in biomedical research. The staphylococcal repressor StlSaPIbov1 protein was described to be an efficient inhibitor of dUTPase homologues showing a certain degree of species-specificity. In order to provide insight into the inhibition mechanism, in the present study we investigated the interaction of StlSaPIbov1 and Escherichia coli dUTPase. Although we observed a strong interaction of these proteins, unexpectedly the E. coli dUTPase was not inhibited. Seeking a structural explanation for this phenomenon, we identified a key amino acid position where specific mutations sensitized E. coli dUTPase to StlSaPIbov1 inhibition. We solved the three-dimensional (3D) crystal structure of such a mutant in complex with the substrate analogue dUPNPP and surprisingly found that the C-terminal arm of the enzyme, containing the P-loop-like motif was ordered in the structure. This segment was never localized before in any other E. coli dUTPase crystal structures. The 3D structure in agreement with solution phase experiments suggested that ordering of the flexible C-terminal segment upon substrate binding is a major factor in defining the sensitivity of E. coli dUTPase for StlSaPIbov1 inhibition.

scholarly journals The rlmB Gene Is Essential for Formation of Gm2251 in 23S rRNA but Not for Ribosome Maturation inEscherichia coli

2001 ◽  
Vol 183 (23) ◽  
pp. 6957-6960 ◽  
Author(s):  
J. Mattias Lövgren ◽  
P. Mikael Wikström
Keyword(s):  
Type Strain ◽  
Wild Type Strain ◽  
Cell Mass ◽  
Ribosomal Subunit ◽  
23S Rrna ◽  
Ribosome Assembly ◽  
Large Ribosomal Subunit ◽  
Wild Type ◽  
Methyltransferase Activity ◽  
E Coli

ABSTRACT In Saccharomyces cerevisiae, the rRNA Gm2270 methyltransferase, Pet56p, has an essential role in the maturation of the mitochondrial large ribosomal subunit that is independent of its methyltransferase activity. Here we show that the proposedEscherichia coli ortholog, RlmB (formerly YjfH), indeed is essential for the formation of Gm in position 2251 of 23S rRNA. However, a ΔrlmB mutant did not show any ribosome assembly defects and was not outgrown by a wild-type strain even after 120 cell mass doublings. Thus, RlmB has no important role in ribosome assembly or function in E. coli.

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