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RNA Structure

RNA Structure

The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...

RNA Structure

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...

RNA Structure

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...

The Nucleosome Core Particle

The Nucleosome Core Particle

Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their primary aim is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. On the other hand, they must allow polymerase enzymes to access histone-bound DNA during...

The Nucleosome Core Particle

The Nucleosome Core Particle

Nucleosomes are the DNA-histone complex, where the DNA strand is wound around the histone core. The histone core is an octamer containing two copies of H2A, H2B, H3, and H4 histone proteins.
The paradox
Nucleosomes, paradoxically, perform two opposite functions simultaneously. On the one hand, their main responsibility is to protect the delicate DNA strands from physical damage and help achieve a higher compaction ratio. While on the other hand, they must allow polymerase enzymes to access DNA...

Histone Modification

Histone Modification

The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
Acetylation
The enzyme histone acetyltransferase adds acetyl group to the histones. Another enzyme, histone deacetylase,...

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Related Experiment Video

Updated: May 15, 2026

Single-step Purification of Macromolecular Complexes Using RNA Attached to Biotin and a Photo-cleavable Linker

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Structure of histone mRNA stem-loop, human stem-loop binding protein, and 3'hExo ternary complex.

Dazhi Tan¹, William F Marzluff, Zbigniew Dominski

¹Department of Biological Sciences, Columbia University, New York, NY 10027, USA.

Science (New York, N.Y.)

|January 19, 2013

Summary

The crystal structure reveals how stem-loop binding protein (SLBP) and 3

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Area of Science:

Molecular Biology
Structural Biology
Biochemistry

Background:

Replication-dependent histone mRNAs possess a conserved 3'-end stem-loop (SL) structure.
Stem-loop binding protein (SLBP) regulates histone mRNA metabolism by binding the SL.
3'-5' exonuclease (3'hExo) trims the 3'-end of histone mRNA post-processing.

Purpose of the Study:

To determine the structural basis of the interaction between SLBP, 3'hExo, and the SL RNA.
To elucidate the mechanism of histone mRNA 3'-end processing and regulation.

Main Methods:

X-ray crystallography of a ternary complex.
Biochemical assays to assess protein-RNA interactions and enzymatic activity.

Main Results:

The crystal structure reveals a ternary complex of human SLBP RNA binding domain, human 3'hExo, and a 26-nucleotide SL RNA.
SLBP specifically recognizes a single base in the SL RNA, while both proteins primarily recognize the RNA's overall shape.
SLBP and 3'hExo do not directly contact each other; their cooperative binding is mediated by induced structural changes in the SL RNA loop.
The 3' flanking sequence is positioned in the 3'hExo active site, but complex formation restricts trimming.

Conclusions:

The structure provides insights into the coordinated regulation of histone mRNA processing by SLBP and 3'hExo.
The findings highlight the importance of RNA shape complementarity in protein recognition and complex formation.
The ternary complex structure explains how 3'hExo activity is modulated during histone mRNA metabolism.