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Related Concept Videos

Ribosome Profiling02:24

Ribosome Profiling

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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
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Ribosomes01:27

Ribosomes

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Ribosomes translate genetic information encoded by messenger RNA (mRNA) into proteins. Both prokaryotic and eukaryotic cells have ribosomes. Cells that synthesize large quantities of protein—such as secretory cells in the human pancreas—can contain millions of ribosomes.
Ribosome Structure and Assembly
Ribosomes are composed of ribosomal RNA (rRNA) and proteins. In eukaryotes, rRNA is transcribed from genes in the nucleolus—a part of the nucleus that specializes in ribosome...
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Ribosomes01:27

Ribosomes

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Ribosomes translate genetic information encoded by messenger RNA (mRNA) into proteins. Both prokaryotic and eukaryotic cells have ribosomes. Cells that synthesize large quantities of protein—such as secretory cells in the human pancreas—can contain millions of ribosomes.
Ribosome Structure and Assembly
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Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

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Ribosome synthesis is a highly complex and coordinated process involving more than 200 assembly factors. The synthesis and processing of ribosomal components occurs not only in the nucleolus but also in the nucleoplasm and the cytoplasm of eukaryotic cells.
Ribosome biogenesis begins with the synthesis of 5S and 45S pre-rRNAs by distinct RNA polymerases. The primary transcripts are extensively processed and modified before they are bound and folded by ribosomal proteins and assembly factors,...
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Ribosomal RNA Synthesis02:53

Ribosomal RNA Synthesis

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Termination of Translation01:44

Termination of Translation

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The large ribosomal subunit has several important structures essential to translation. These include the peptidyl transferase center (PTC) - which is the site where the peptide bond is formed - and a large, internal, water-filled tube through which the nascent polypeptide moves. This latter structure is called the Peptide Exit Tunnel, and it begins at the PTC and spans the body of the large ribosomal subunit. During translation, as the nascent polypeptide chain is synthesized, it passes through...
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RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing
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RIBO-seq in Bacteria: a Sample Collection and Library Preparation Protocol for NGS Sequencing

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The PDB and the ribosome.

Peter B Moore1

  • 1Department of Chemistry, Yale University, New Haven, Connecticut, USA.

The Journal of Biological Chemistry
|March 21, 2021
PubMed
Summary
This summary is machine-generated.

The Protein Data Bank, established 50 years ago, provides crucial structural data. Early ribosome structure determination was challenging, with cryo-electron microscopy now surpassing X-ray crystallography.

Keywords:
PDBcryo-EMcrystallographymodelribosomestructure

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Area of Science:

  • Structural Biology
  • Biochemistry
  • Molecular Biology

Background:

  • The Protein Data Bank (PDB) was established 50 years ago to archive and disseminate macromolecular structural data.
  • The PDB provides essential services for scientists studying the structure and function of biological molecules.
  • This essay commemorates the PDB's anniversary and reflects on its impact.

Purpose of the Study:

  • To commemorate the 50th anniversary of the Protein Data Bank.
  • To discuss the historical context and challenges in determining early ribosome structures.
  • To highlight the evolution of techniques used in ribosome structure determination.

Main Methods:

  • Historical account of the establishment of the Protein Data Bank.
  • Description of the determination of the crystal structure of the large ribosomal subunit from Haloarcula marismortui.
  • Review of the challenges faced by the PDB in handling early ribosome structures.

Main Results:

  • The determination of the first ribosome crystal structures presented significant challenges for the Protein Data Bank.
  • Subsequent developments have led to advancements in ribosome structure determination.
  • Cryo-electron microscopy (cryo-EM) has emerged as the preferred method over X-ray crystallography for ribosome structure studies.

Conclusions:

  • The Protein Data Bank has played a vital role in advancing structural biology over the past 50 years.
  • The field of ribosome structure determination has evolved significantly, with cryo-EM now being the dominant technique.
  • Continued innovation in structural biology methods is crucial for future discoveries.