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Related Concept Videos

Ribozymes02:47

Ribozymes

The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can be...
Ribozymes02:47

Ribozymes

The term ribozyme is used for RNA that can act as an enzyme. Ribozymes are mainly found in selected viruses, bacteria, plant organelles, and lower eukaryotes. Ribozymes were first discovered in 1982 when Tom Cech’s laboratory observed Group I introns acting as enzymes. This was shortly followed by the discovery of another ribozyme, Ribonulcease P, by Sid Altman’s laboratory. Both Cech and Altman received the Nobel Prize in chemistry in 1989 for their work on ribozymes.
Ribozymes can be...
Ribosome Profiling02:24

Ribosome Profiling

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 helps...
X-ray Diffraction of Biological Samples01:10

X-ray Diffraction of Biological Samples

X-ray diffraction or XRD is an analytical tool that utilizes X-rays to study ordered structures such as crystalline organic and inorganic samples, polycrystalline materials, proteins, carbohydrates, and drugs.
According to Bragg's law, when X-rays strike the sample positioned on a stage, the rays are  scattered by the electron clouds around the sample atoms. The  X-ray diffraction or scattering is caused by constructive interference of the X-ray waves that reflect off the internal crystal...
Ribosomes01:27

Ribosomes

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 AssemblyRibosomes 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 production. Within the...
X-ray Crystallography02:18

X-ray Crystallography

The size of the unit cell and the arrangement of atoms in a crystal may be determined from measurements of the diffraction of X-rays by the crystal, termed X-ray crystallography.
Diffraction
Diffraction is the change in the direction of travel experienced by an electromagnetic wave when it encounters a physical barrier whose dimensions are comparable to those of the wavelength of the light. X-rays are electromagnetic radiation with wavelengths about as long as the distance between neighboring...

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Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae
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Combining X-Ray Crystallography with Small Angle X-Ray Scattering to Model Unstructured Regions of Nsa1 from S. Cerevisiae

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The complete VS ribozyme in solution studied by small-angle X-ray scattering.

Jan Lipfert1, Jonathan Ouellet, David G Norman

  • 1Department of Physics, Geballe Laboratory of Advanced Materials, Stanford University, Stanford, CA 94305, USA.

Structure (London, England : 1993)
|September 13, 2008
PubMed
Summary
This summary is machine-generated.

Small-angle X-ray scattering reveals the VS ribozyme

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Small and Wide Angle X-Ray Scattering Studies of Biological Macromolecules in Solution
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Small and Wide Angle X-Ray Scattering Studies of Biological Macromolecules in Solution

Published on: January 8, 2013

Area of Science:

  • Biochemistry and Molecular Biology
  • Structural Biology
  • RNA Catalysis

Background:

  • Ribozymes are RNA molecules with catalytic activity.
  • Understanding the three-dimensional structure of ribozymes is crucial for elucidating their catalytic mechanisms.
  • The VS ribozyme is a key model system for studying RNA folding and catalysis.

Purpose of the Study:

  • To determine the ab initio shape reconstruction of the complete VS ribozyme.
  • To visualize the overall architecture and arrangement of helical elements within the ribozyme.
  • To provide structural insights into the catalytic mechanism of the VS ribozyme.

Main Methods:

  • Small-angle X-ray solution scattering (SAXS) was employed to obtain low-resolution structural information.
  • Ab initio shape reconstruction was performed using SAXS data to model the ribozyme's envelope.
  • Helical segments were fitted into the reconstructed electron density envelope to build an atomic model.

Main Results:

  • The VS ribozyme adopts an irregular, complex three-dimensional shape.
  • A core structure consisting of a near-coaxial stack of three helices organized by two three-way junctions was identified.
  • An auxiliary helix forms an additional three-way junction, positioning the substrate stem-loop for catalysis.

Conclusions:

  • The determined structure provides a framework for understanding VS ribozyme folding and function.
  • The structural arrangement supports a model where interacting loops, including adenine and guanine nucleobases, facilitate general acid-base catalysis.
  • This study enhances our comprehension of RNA-based catalysis and the structural basis of enzymatic activity in ribozymes.