AMPA Receptor

Receptors for the neurotransmitter glutamate in our brain come in several shapes and sizes.

AMPA receptor, with an inhibitor (red) bound to the glutamate-binding domains. The location of the cell membrane is shown schematically in gray.
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Nerve cells in our brain communicate with one another using small neurotransmitter molecules. These come in many shapes and sizes, such as acetylcholine, serotonin and endorphins, allowing the nervous system to shape the way neurons talk to one another. The amino acid glutamate is one of the most common neurotransmitters used to carry excitatory signals. It is released by neurons into synapses, where they stimulate neighboring neurons by binding to glutamate-specific receptors (an illustration of an excitatory synapse is included at PDB-101 in the gallery of Molecular Landscapes).

AMPA Action

AMPA receptors (shown here from PDB entry 3kg2) are the most common excitatory glutamate receptors in the brain. They have modular structures, and each part has a specific task. The portion at the top recognizes and binds to glutamate (and similar neurotransmitters), and the portion at the bottom forms an ion channel through the membrane. When glutamate binds, it causes a change in shape that tugs on the channel, causing it to open and allow ions to flood through the membrane. There is also an additional tail at the bottom of the receptor, which is not seen in this structure because it is so flexible. It interacts with scaffolding proteins that organize the structure of the neuronal synapse.

Learning and Memory

Communication between neurons is highly complex, to capture the many subtle shades of thought and memory. At the simplest level, AMPA receptors each have four chains, each with a separate binding site for glutamate, so the response isn't simply on or off. Also, AMPA receptors close very quickly after receiving a message, becoming desensitized for a time against additional messages. Layers of complexity are added to these simple actions to store memories, by adding more receptors to a synapse or taking them away, or by modifying amino acids in individual receptors to tune their action.

Three types of ionotropic glutamate receptors. An accessory protein is shown in green bound to the ion channel portion of the AMPA receptor.
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Layers of Complexity

To make things even more complex, our brains have additional options for tailoring glutamate signaling. Several accessory proteins bind to AMPA receptors, such as the TARP protein shown here from PDB entry 5weo. Each receptor can also be composed of different combinations of several similar forms of the protein. Additionally, there are two other classes of glutamate receptors with slightly different actions, known as NMDA receptors (shown here from PDB entry 4pe5) and kainate receptors (PDB entry 5kuf), both named after inhibitor molecules that were crucial for their discovery. Together, they help build up the rich environment of signaling that controls our inner world of thought.

Exploring the Structure

AMPA Receptor

This structure (PDB entry 4u5c) shows how things can go wrong. Some cone snails make a small protein toxin that they use to paralyze their prey. It binds in the middle of the glutamate-binding portion of the receptor, corrupting its action. To explore this structure in more detail, click on the image for an interactive JSmol. As you look at this structure, notice that there is a mismatch of symmetry between the different parts: the ion channel forms a typical four-fold structure, but the glutamate-binding portions are two side-by-side dimers.

Topics for Further Discussion

  1. Ionotropic glutamate receptors are quite flexible--as you look at these structures, notice the many different arrangements of the transmembrane domains relative to the glutamate-binding domains.
  2. These structures are all missing portions of the receptors, which are not observed because they are so flexible. You can use the Protein Feature View to determine which portions of the protein chain are included in the structure entries.

References

  1. Chen, S., Gouaux, E. (2019) Structure and mechanism of AMPA receptor -- auxiliary protein complexes. Current Opinion in Structural Biology 54: 104-111.
  2. Zhu, S., Gouaux, E. (2017) Structure and symmetry inform gating principles of ionotropic glutamate receptors. Neuropharmacology 112: 11-15.
  3. 5weo: Twomey, E.C., Yelshanskaya, M.V., Grassucci, R.A., Frank, J., Sobolevsky, A.I. (2017) Channel opening and gating mechanism in AMPA-subtype glutamate receptors. Nature 549: 60-65.
  4. 5kuf: Meyerson, J.R., Chittori, S., Merk, A., Rao, P., Han, T.H., Serpe, M., Mayer, M.L., Subramaniam, S. (2016) Structural basis of kainate subtype glutamate receptor desensitization. Nature 537: 567-571.
  5. 4u5c: Chen, L., Durr, K.L., Gouaux, E. (2014) X-ray structures of AMPA receptor-cone snail toxin complexes illuminate activation mechanism. Science 345: 1021-1026.
  6. 4pe5: Karakas, E., Furukawa, H. (2014) Crystal structure of a heterotetrameric NMDA receptor ion channel. Science 344: 992-997.
  7. Yokoi, N., Fukata, M., Fukata, Y. (2012) Synaptic plasticity regulated by protein-protein interactions and posttranslational modifications. International Review of Cell and Molecular Biology 297:1-43.
  8. 3kg2: Sobolevsky, A.I., Rosconi, M.P., Gouaux, E. (2009) X-ray structure, symmetry and mechanism of an AMPA-subtype glutamate receptor. Nature 462: 745-756.

July 2019, David Goodsell

doi:10.2210/rcsb_pdb/mom_2019_7
About Molecule of the Month
The RCSB PDB Molecule of the Month by David S. Goodsell (The Scripps Research Institute and the RCSB PDB) presents short accounts on selected molecules from the Protein Data Bank. Each installment includes an introduction to the structure and function of the molecule, a discussion of the relevance of the molecule to human health and welfare, and suggestions for how visitors might view these structures and access further details. More
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