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Structural View of Biology


The major molecules of protein synthesis, from DNA to RNA to ribosomes to folded proteins, are available in the PDB archive. Proteins are built in several steps in all living organisms. The blueprint for each protein is stored in the genome, encoded in strands of DNA. This information is transcribed into an RNA copy, which is then used to construct the protein chain. After the chain is synthesized, it may be modified with special chemical groups, chaperoned into its proper folded shape, and ultimately destroyed when it is not needed any longer.

The genetic information in DNA is used to build RNA strands. The enzyme RNA polymerase separates the DNA double helix and builds an RNA strand with a complementary sequence of nucleotides. This process is highly regulated to ensure that RNA is made at the proper time.

Scroll to a Molecule of the Month Feature in this subcategory:

  • Aconitase and Iron Regulatory Protein 1

    Aconitase and Iron Regulatory Protein 1

    Aconitase is an essential enzyme in the tricarboxylic acid cycle and iron regulatory protein 1 interacts with messenger RNA to control the levels of iron inside cells. You might ask: what do these two proteins have in common? They were discovered and studied by different researchers, who gave them names that described their two very different functions. But surprisingly, when they looked at the amino acid sequence of these proteins, they turned out to be identical. The same protein is performing two very different jobs.

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    Discussed Structures
    aconitase
    aconitase
    aconitase
    aconitase
    iron regulatory protein (aconitase)
    iron regulatory protein (aconitase)
  • Catabolite Activator Protein

    Catabolite Activator Protein

    Bacteria love sugar. In particular, bacteria love glucose, which is easily digestible and quickly converted to chemical energy. When glucose is plentiful, bacteria ignore other nutrients in their environment, feasting on their favored source. But, when glucose is rare, they shift gears and mobilize the machinery needed to use other sources of energy.

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    Discussed Structures
    catabolite activator protein (CAP)
    catabolite activator protein (CAP)
    catabolite activator protein and RNA polymerase
    catabolite activator protein and RNA polymerase
  • Enhanceosome

    Enhanceosome

    Take a moment to ponder the form of your body: the shape of your face, the color of your eyes, the length of your fingers, the perfect articulation of your bones and muscles, the way your hair grows curly or straight. Now let your imagination travel inward, and think of the complex shapes and functions of your different cells, and the teeming molecular world inside each one. Remarkably, this amazing structure and form and function is specified by information in the genome, which encodes a mere 20,000-25,000 protein-coding genes. One of the great puzzles being pieced together by scientists is the mechanism by which these genes, and the methods used to control their expression, specify all of these different aspects of life.

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    Discussed Structures
    interferon-beta enhancer
    interferon-beta enhancer
    interferon-beta enhancer
    interferon-beta enhancer
    interferon-beta enhancer
    interferon-beta enhancer
    interferon-beta enhancer
    interferon-beta enhancer
  • Estrogen Receptor

    Estrogen Receptor

    Estrogens are small, carbon-rich molecules built from cholesterol. This is quite different than larger hormones, such as insulin and growth hormone, which are sensed by receptors on the cell surface. Estrogens pass directly into cells throughout the body, so the cell can use receptors that are in the nucleus, right at the site of action on the DNA. When estrogen enters the nucleus, it binds to the estrogen receptor, causing it to pair up and form a dimer. This dimer then binds to several dozen specific sites in the DNA, strategically placed next to the genes that need to be activated. Then, the DNA-bound receptor activates the DNA-reading machinery and starts the production of messenger RNA.

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    Discussed Structures
    estrogen receptor hormone-binding domain
    estrogen receptor hormone-binding domain
    estrogen receptor DNA-binding domain
    estrogen receptor DNA-binding domain
    estrogen receptor and tamoxifen
    estrogen receptor and tamoxifen
  • Exosomes

    Exosomes

    Our genetic information is stored safely inside the nucleus of each cell. However, most of the action in a typical cell occurs outside the nucleus: proteins are built in the cytoplasm, energy is produced in the mitochondria, and interactions with the environment occur at the cell surface. So, the nucleus needs a way to communicate with the rest of the cell. RNA molecules perform this job. They are the messengers that deliver genetic information from the nucleus to places where it is needed for synthesis and control.

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    Discussed Structures
    exosome
    exosome
    exosome
    exosome
    poly(A)-specific ribonuclease
    poly(A)-specific ribonuclease
    scavenger mRNA decapping enzyme
    scavenger mRNA decapping enzyme
  • Messenger RNA Capping

    Messenger RNA Capping

    In our cells, transcription is not just a simple process of reading DNA and building a complimentary RNA strand. Almost immediately after RNA polymerase begins, the cell is making changes. When the mRNA is only about 30 nucleotides long, the cell makes its first change: it connects a guanosine nucleotide to the end.

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    Discussed Structures
    mRNA Capping Enzymes
    mRNA Capping Enzymes
    mRNA Capping Enzymes
    mRNA Capping Enzymes
    mRNA Capping Enzymes
    mRNA Capping Enzymes
  • Oct and Sox Transcription Factors

    Oct and Sox Transcription Factors

    The development of a complete human being from a single cell is one of the great miracles of life. A human egg cell contains about 30,000 genes that encode proteins, and of these, about 3,000 of these genes encode transcription factors. Transcription factors determine when genes will be turned on and turned off, orchestrating the many processes involved in the development of an embryo and the many tasks performed by each cell after a child is born. Amazingly, there is only about 1 transcription factor for every 10 genes, posing a puzzle: how does this limited set of proteins control the many genes and processes that must be regulated?

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    Discussed Structures
    Oct1 and Sox2
    Oct1 and Sox2
  • Poly(A) Polymerase

    Poly(A) Polymerase

    Most of the RNA found in our cells is built using our DNA genome as a template. In special cases, however, our cells also build RNA strands without a template. For instance, the end of (almost) every messenger RNA strand is composed of a long string of repeated adenosine nucleotides. These long poly(A) tails are not encoded in the genome. Instead, they are added after RNA polymerase finishes its normal process of transcription. After RNA polymerase releases the RNA strand, other enzymes add the finishing touches, editing out introns, adding a cap to the front end, and building the long poly(A) tail at the other end.

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    Discussed Structures
    poly(A) polymerase
    poly(A) polymerase
    poly(A) polymerase and RNA
    poly(A) polymerase and RNA
    poly(A)-binding protein and RNA
    poly(A)-binding protein and RNA
  • RNA Polymerase

    RNA Polymerase

    RNA is a versatile molecule. In its most familiar role, RNA acts as an intermediary, carrying genetic information from the DNA to the machinery of protein synthesis. RNA also plays more active roles, performing many of the catalytic and recognition functions normally reserved for proteins. In fact, most of the RNA in cells is found in ribosomes--our protein-synthesizing machines--and the transfer RNA molecules used to add each new amino acid to growing proteins. In addition, countless small RNA molecules are involved in regulating, processing and disposing of the constant traffic of messenger RNA. The enzyme RNA polymerase carries the weighty responsibility of creating all of these different RNA molecules.

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    Discussed Structures
    RNA polymerase
    RNA polymerase
    bacteriophage RNA polymerase
    bacteriophage RNA polymerase
  • Reverse Transcriptase

    Reverse Transcriptase

    Viruses are tricky. They use all sorts of unusual mechanisms during their attacks on cells. HIV is no exception. It is a retrovirus, which means that it has the ability to insert its genetic material into the genome of the cells that it infects. But, infectious HIV particles carry their genome in RNA strands. Somehow, during infection, the virus needs to make a DNA copy of its RNA genome. This is very unusual, because all of the normal cellular machinery is designed to make RNA copies from DNA, but not the reverse. DNA is normally only created using other DNA strands as a template. This tricky reversal of synthesis is performed by the enzyme reverse transcriptase, shown here from PDB entry 3hvt. Inside its large, claw-shaped active site, it copies the HIV RNA and creates a double-stranded DNA version of the viral genome. This then integrates into the cell's DNA, and later instructs the cell to make additional copies of the virus.

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    Discussed Structures
    reverse transcriptase with DNA
    reverse transcriptase with DNA
    reverse transcriptase with nevirapine
    reverse transcriptase with nevirapine
  • Self-splicing RNA

    Self-splicing RNA

    Nature is full of surprises, and you can be sure that once you think you understand something, Nature will come up with an exception. Twenty years ago, this was the case with enzymes. After decades of work, biochemists thought that proteins were the only molecules that catalyzed chemical reactions in the cell, so it came as a surprise when Thomas Cech and his coworkers discovered a natural RNA splicing reaction that occurs even when all of the proteins are removed. Since then, researchers have discovered many additional examples of ribozymes--RNA molecules that perform chemical tasks.

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    Discussed Structures
    self-splicing intron
    self-splicing intron
    hammerhead ribozyme
    hammerhead ribozyme
  • TATA-Binding Protein

    TATA-Binding Protein

    The enzyme RNA polymerase performs the delicate task of unwinding the two strands of DNA and transcribing the genetic information into a strand of RNA. But how does it know where to start? Our cells contain 30,000 genes encoded in billions of nucleotides. For each gene, the cell must be able to start transcription at the right place and at the right time.

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    Discussed Structures
    TATA-binding protein and DNA
    TATA-binding protein and DNA
    TATA-binding protein and TFIIB
    TATA-binding protein and TFIIB
    TATA-binding protein and TFIID
    TATA-binding protein and TFIID
  • Zinc Fingers

    Zinc Fingers

    As you are browsing through the proteins in the PDB, you may notice something: most proteins are big. They contain hundreds of amino acids, even though most of the work is often done by a few amino acids on one side. Why are proteins so big? One reason that proteins are so large is that they must self-assemble inside cells. Proteins are built as floppy chains that fold all by themselves (or with a little help from chaperones) into stable, compact structures. These folded structures are stabilized by hydrogen bonds, charge-charge interactions and hydrophobic forces between the different amino acids, which all line up like pieces in a jigsaw puzzle when the protein folds. A single hydrogen bond or a few charge pairs would not be enough, but a chain of hundreds of amino acids has hundreds of interactions that together glue the protein into a stable structure.

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    Discussed Structures
    zinc fingers bound to DNA
    zinc fingers bound to DNA
    zinc fingers bound to RNA
    zinc fingers bound to RNA
  • lac Repressor

    lac Repressor

    DNA is filled with information. Our own DNA contains the instructions for building tens of thousands of different proteins and RNA, which perform all the different functions that keep us alive. As discovered by Watson and Crick fifty years ago, this genetic information is stored in the sequence of adenine, thymine, cytosine and guanine bases in the DNA. Their model of the DNA double helix showed how the information is read by separating the two strands of DNA and then pairing the exposed surfaces of the bases with appropriate partners, such that adenine always pairs with thymine and cytosine pairs with guanine.

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    Discussed Structures
    lac repressor tetramerization and core domains
    lac repressor tetramerization and core domains
    lac repressor core and DNA-binding domains
    lac repressor core and DNA-binding domains
    beta-galactosidase
    beta-galactosidase
    galactoside acetyltransferase
    galactoside acetyltransferase
    lactose permease
    lactose permease
  • p53 Tumor Suppressor

    p53 Tumor Suppressor

    Our cells face many dangers, including chemicals, viruses, and ionizing radiation. If cells are damaged in sensitive places by these attackers, the effects can be disastrous. For instance, if key regulatory elements are damaged, the normal controls on cell growth may be blocked and the cell will rapidly multiply and grow into a tumor. p53 tumor suppressor is one of our defenses against this type of damage. p53 tumor suppressor is normally found at low levels, but when DNA damage is sensed, p53 levels rise and initiate protective measures. p53 binds to many regulatory sites in the genome and begins production of proteins that halt cell division until the damage is repaired. Or, if the damage is too severe, p53 initiates the process of programmed cell death, or apoptosis, which directs the cell to commit suicide, permanently removing the damage.

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    Discussed Structures
    p53 tumor suppressor tetramerization domain
    p53 tumor suppressor tetramerization domain
    p53 tumor suppressor DNA-binding domain
    p53 tumor suppressor DNA-binding domain

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