Molecules of cell-mediated immunity

Molecules of cell-mediated immunity

A T cell cannot see a whole microbe. Most T cells see a short peptide held out by an MHC molecule on another cell's surface, read by the T-cell receptor, and a naive T cell acts only if a second signal says the danger is real.

How MHC molecules pick up peptides and show them to T cells

6 scenes, 0:55

A film in six scenes on a white page, drawn flat and soft like the MHC and T-cell figures. First, the peach cytosol of an infected cell. A teal viral protein, folded into a tangle of beads, drifts onto the proteasome: a green barrel of four stacked rings of balls under a deeper green cap. The cap unravels it as it pulls it in and down through the barrel, and short teal peptides of different lengths drop out of the bottom and drift towards the lilac ER below. Next, the ER membrane, an amber band, runs across the frame, cytosol above and the lilac lumen below. TAP stands in it, two green halves with balls on top in the cytosol; beside it deep green tapasin reaches from the membrane to a class I molecule hanging upside down in the lumen, a light green ERp57 and calreticulin against them. A peptide comes down through TAP, round underneath and up into class I's groove, and class I lets go and moves off along the membrane; a second peptide comes through and drifts away. Then a peach body cell across the bottom with class I molecules on it, each holding a teal peptide, and a periwinkle T cell coming down from the top: its receptor's two chains land on the middle molecule's peptide, CD8 reaches down to the side of class I, CD3's tails hang inside the T cell, and orange phosphates appear on them one by one. Then the periwinkle surface of a dendritic cell. A khaki rod-shaped bacterium settles on it and sinks into a pocket of the amber membrane, which wraps round it and pinches off as a ring, the phagosome, pale inside. The phagosome moves into the cell and the bacterium breaks into short khaki chains of beads, while a round vesicle buds from the Golgi, a stack of curved sacs at the lower right, carrying two small class II molecules, and fuses with it. Then the inside of that compartment: its membrane across the bottom, the lumen above. Class II, a green and a lime chain, stands on it; a light green strand, the invariant chain, rises from below the membrane, lies in its groove and goes on to a light green knob. A deep green cathepsin eats the strand back from the knob to the groove, and another cuts it beside the groove, leaving three light green beads, CLIP, in the groove; the rest fades. HLA-DM, two deep green chains built like class II, comes alongside it on the side of the green chain; CLIP leaves, and a longer khaki peptide of the bacterium drops from above into the groove, where it is seen end on. Last, the dendritic cell across the bottom with class II holding the khaki peptide, and a periwinkle T cell coming down: its receptor lands on the peptide, CD4 reaches down to class II, CD28 meets B7 at the left and LFA-1 grips ICAM-1 at the right, phosphates appear on CD3's tails, and pink dots of IL-2 leave the T cell.

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The proteasome cuts a viral protein

Scenes

About this film

Class I picks up peptides in the ER, cut in the cytosol by the proteasome, and shows them to CD8 T cells; class II, kept empty by the invariant chain, picks up peptides of what the cell took in, in endosomes, and shows them to CD4 T cells.

Simplified: not to scale: the molecules drawn far larger than the cells and organelles round them, and one of each standing for many; the proteasome drawn side on with one cap, and its protein without the ubiquitin chain that marks it for the cap; the peptides drawn leaving by the uncapped end; each amino acid a bead, the peptide loaded on class I 9 long and the one on class II 15, within their usual 8 to 10 and 13 to 25; the aminopeptidase that trims long peptides in the ER left out; in the groove the peptide is seen end on, as in the figure, so only three beads show; the loading complex drawn with one of each of its parts; calnexin, which holds class I before it joins the complex, left out; loaded class I and class II shown at the surface in the next scene; their way there through the Golgi and in vesicles left out; the bacterium taken in and broken up within seconds, and the phagosome shown joining the endosomes as one compartment; in the cell this takes far longer, class II staying hours in these compartments; the invariant chain, a trimer that holds three class II molecules, drawn as one chain on one class II; in the vesicle only its part in the groove drawn; it is drawn reaching the groove over the top of the molecule, though it runs along the groove, in at one end and out at the other; IL-2 drawn as dots leaving the T cell; the IL-2 receptor, which the T cell makes too, not drawn; each scene draws only the molecules it is about; the others are still there.

8 sources
  1. Janeway CA Jr, Travers P, Walport M, Shlomchik MJ. Immunobiology, 5th edition. Garland Science, 2001. Sections 3-12, 3-13, 3-18, 5-2 to 5-7, 8-4, 8-5, 8-9, 8-10 and 8-12.
  2. Rock KL, Reits E, Neefjes J. Present yourself! By MHC class I and MHC class II molecules. Trends Immunol. 2016;37(11):724–737.
  3. Lander GC, Martin A, Nogales E. The proteasome under the microscope: the regulatory particle in focus. Curr Opin Struct Biol. 2013;23(2):243–251.
  4. Wieczorek M, Abualrous ET, Sticht J, et al. Major histocompatibility complex (MHC) class I and MHC class II proteins: conformational plasticity in antigen presentation. Front Immunol. 2017;8:292.
  5. Cloutier M, Fortin JS, Thibodeau J. The transmembrane domain and luminal C-terminal region independently support invariant chain trimerization and assembly with MHCII into nonamers. BMC Immunol. 2021;22:56.
  6. Mariuzza RA, Agnihotri P, Orban J. The structural basis of T-cell receptor (TCR) activation: an enduring enigma. J Biol Chem. 2020;295(4):914–925.
  7. Kumar and Clark's Clinical Medicine, 10th edition. Elsevier, 2021. Chapter 3, Immunity: phagocytosis (Fig. 3.3).
  8. Chen L, Flies DB. Molecular mechanisms of T cell co-stimulation and co-inhibition. Nat Rev Immunol. 2013;13(4):227–242.
Contents10 sections

At a glance

  1. αβ T cells, most T cells, recognise antigen only as a short peptide bound to an MHC molecule (in humans HLA) on another cell's surface, each only on one particular self MHC molecule. This is MHC restriction.
  2. MHC class I (HLA-A, -B and -C) is a heavy chain with β2-microglobulin, on almost every nucleated cell. It shows peptides of 8 to 10 amino acids from proteins made in the cell to CD8 T cells.
  3. MHC class II (HLA-DR, -DQ and -DP) is an α and a β chain, mainly on dendritic cells, macrophages and B cells. It shows longer peptides from what the cell has taken in to CD4 T cells.
  4. Class I loads in the ER: the proteasome cuts cytosolic proteins, TAP carries the peptides in, and tapasin helps fit them. Class II leaves the ER with the invariant chain, and in endosomes HLA-DM swaps its last fragment, CLIP, for an antigen peptide.
  5. The T-cell receptor is an α and a β chain, each with a variable and a constant domain. It cannot signal on its own: CD3 signals for it, and CD4 or CD8 binds the MHC molecule beside it and brings the kinase Lck.
  6. A naive T cell needs a second signal, CD28 meeting CD80 or CD86 on an activated antigen-presenting cell. CTLA-4 and PD-1 are brakes; drugs that block them treat cancer, and abatacept, which blocks CD80 and CD86, treats arthritis.

What a T cell sees

An antibody binds its antigen as it is, a folded protein or a sugar on a microbe's surface, wherever it finds it. A T lymphocyte cannot. Its T-cell receptor (TCR) recognises a short peptide, cut from a protein inside a cell and held out on that cell's surface by a major histocompatibility complex (MHC) molecule. The receptor touches the peptide and the MHC molecule together, so a T cell responds to its peptide only when it is held by one particular MHC molecule of its own body: MHC restriction.

This is what makes cell-mediated immunity work. A virus inside a cell is out of antibody's reach, but the cell shows pieces of the viral proteins it is making, and a T cell can find it and kill it. A macrophage that has swallowed a bacterium shows pieces of it, and a T cell can tell it to kill harder.

The molecules of cell-mediated immunity are those of this meeting. On the presenting cell, the MHC molecules and the machinery that loads them. On the T cell, the TCR, the CD3 complex that signals for it, and the co-receptors CD4 and CD8. Between the two, the co-stimulatory and inhibitory molecules that decide whether the T cell acts, the adhesion molecules that hold the cells together, and the cytokines that carry the message on.

MHC class I and class II
Three views on a pale plate. In the first a peach body cell fills the bottom, a band of amber membrane along its top. On it stands MHC class I, seen side on with its groove running into the page: two broad green domains side by side at the top, each with a round helix end at its inner shoulder, and between them, in the notch, a short teal-green peptide seen end on. Below the right one a smaller green domain, α3, runs on as a strand down through the membrane into the cell; below the left one a pale lime domain, β2-microglobulin, rests beside it without reaching the membrane. In the second a pale blue dendritic cell takes the bottom, and on it MHC class II: a green chain on the left and a lime chain on the right, each with a top domain and one below it, both running down through the membrane, a khaki peptide in the notch between the top domains. In the third both grooves are seen from above, class I at the top and class II below. Each is a rounded floor with a coiled helix along either side. Class I's floor and both its helices are green, its helices drawn in towards each other at the ends, where two green knobs close the groove round a row of nine teal-green residues. Class II's floor is half green and half lime, a green helix along its far side and a lime one along its near side, and its row of fifteen khaki residues runs out past both ends. Step 1 of 3: MHC class I. A heavy chain of three domains, α1, α2 and α3, crosses the membrane, β2-microglobulin bound beside α3, and the peptide sits between α1 and α2.

Step 1 of 3MHC class I. A heavy chain of three domains, α1, α2 and α3, crosses the membrane, β2-microglobulin bound beside α3, and the peptide sits between α1 and α2.

Point at a name or a part to light it.

Both classes hold a peptide between two helices on a floor of β-sheet. Class I's groove is closed, so it takes peptides of 8 to 10 amino acids, from proteins made in the cell; class II's is open, so longer peptides, from what the cell has taken in, hang out of its ends.

Simplified: not to scale: the molecules drawn larger than the cell they stand on, the grooves larger again; in the side views the groove runs into the page, so the peptide is seen end on; the view from above shows its length; each groove's floor, a sheet of eight β-strands, drawn plain; class II's split at its middle to show that each chain gives half; each amino acid a bead, without its side chain; the pockets for the anchor residues not drawn, and the knobs at class I's ends standing for the conserved residues that close it; the sugars on the MHC molecules left out; the tails inside the cell drawn short.

4 sources
  1. Janeway CA Jr, Travers P, Walport M, Shlomchik MJ. Immunobiology, 5th edition. Garland Science, 2001. Sections 3-13 and 3-14.
  2. Wieczorek M, Abualrous ET, Sticht J, et al. Major histocompatibility complex (MHC) class I and MHC class II proteins: conformational plasticity in antigen presentation. Front Immunol. 2017;8:292.
  3. Rock KL, Reits E, Neefjes J. Present yourself! By MHC class I and MHC class II molecules. Trends Immunol. 2016;37(11):724–737.
  4. Kumar and Clark's Clinical Medicine, 10th edition. Elsevier, 2021. Chapter 3, Immunity: the major histocompatibility complex.

The MHC and its genes

In humans the MHC is called HLA, human leucocyte antigen, a group of genes on the short arm of chromosome 6. It has three classes:

  • Class I: the classical genes HLA-A, HLA-B and HLA-C. Each encodes a heavy chain, which pairs with β2-microglobulin, made by a gene elsewhere.
  • Class II: the regions HLA-DR, HLA-DQ and HLA-DP, each with genes for an α and a β chain. The region also holds genes for antigen processing, among them TAP, HLA-DM and proteasome subunits.
  • Class III: genes for other proteins of immunity, such as tumour necrosis factor and the complement components C2 and C4. They do not present peptides.

Three features make HLA unlike most genes.

  • Polymorphism. The classical HLA genes are the most variable in the genome: over 11,000 alleles of HLA-B and over 9,000 each of HLA-A and HLA-C are known, many of them coding for the same protein. The differences between the proteins lie mostly in the peptide-binding groove, so different HLA molecules bind different peptides.
  • Codominance. Both the maternal and the paternal alleles are expressed. A person has up to six classical class I molecules, two each of A, B and C, and more of class II, each binding its own range of peptides.
  • Inheritance as a block. The genes lie close together and pass to a child as a set from each parent, a haplotype. So a child has half its HLA from each parent, and each brother or sister with the same parents has a one in four chance of being a full HLA match.

So each person presents a slightly different set of peptides, and a population as a whole is unlikely to meet a microbe none of its members can present. The price is in transplantation: a graft from a donor with other HLA molecules is seen as foreign and rejected, which is how the MHC got its name, from histocompatibility.

MHC class I

A class I molecule is a heavy chain with three domains, α1, α2 and α3, crossing the membrane, and a small protein bound to it, β2-microglobulin. The α3 domain and β2-microglobulin are immunoglobulin-like domains near the membrane. The α1 and α2 domains form the top: a floor of β-sheet with two α-helices lying on it, the walls of a groove.

The groove of class I is closed at both ends, so its peptide must fit inside: usually 8 to 10 amino acids. A few of the peptide's side chains, its anchor residues, sit in pockets of the groove, and which anchors fit depends on the allele.

Class I is made by almost every nucleated cell, because a virus can infect almost any of them. Red cells, which have no nucleus, carry little or none. Its peptides come from inside the cell, and it shows them to CD8 T cells, most of which kill.

MHC class II

A class II molecule has two chains, α and β, each with two domains, both crossing the membrane. The α1 and β1 domains form the groove, the α2 and β2 domains sit near the membrane. Its groove is open at both ends, so it holds longer peptides, usually 13 to 25 amino acids, whose ends hang out.

Class II is made mainly by the antigen-presenting cells: dendritic cells, macrophages and B cells. Interferon-γ raises it on these and can induce it on cells that normally lack it, such as some epithelial cells in inflammation. Its peptides come from what the cell has taken in, and it shows them to CD4 T cells, the helpers.

Loading the groove

Neither class goes to the surface empty. Each is loaded in its own compartment, and the compartment decides which proteins its peptides come from.

  1. 1

    Class I: cut in the cytosol

    The proteasome breaks down proteins of the cytosol, old or misfolded self proteins and, in an infected cell, viral ones. Interferons make it switch in subunits that give more peptides of the right kind, the immunoproteasome.

  2. 2

    Class I: into the ER

    TAP, the transporter associated with antigen processing, pumps peptides into the endoplasmic reticulum. An aminopeptidase there trims those that are too long.

  3. 3

    Class I: loaded and sent out

    The new heavy chain and β2-microglobulin wait in the peptide-loading complex, where tapasin, with the chaperones calreticulin and ERp57, helps them take a peptide that fits well. Loaded, the molecule is stable and goes through the Golgi to the surface.

Very few peptides make it: of all the proteasome makes, about 0.02% end up presented. Most are broken down further in the cytosol.

  1. 1

    Class II: kept empty in the ER

    New class II binds the invariant chain, which fills its groove so that it takes none of the ER's peptides, and steers it out of the Golgi to the endosomes.

  2. 2

    Class II: cut in the endosome

    Meanwhile the cell has taken in a microbe or a protein. In acid endosomes proteases, cathepsins, cut it into peptides, and cut the invariant chain too, leaving only its piece in the groove, CLIP.

  3. 3

    Class II: CLIP swapped for a peptide

    HLA-DM, a class II-like molecule that binds no peptide itself, binds class II, speeds the release of CLIP and holds the empty groove open until a peptide that binds better takes its place. Loaded, class II goes to the surface.

Dendritic cells have one more route, cross-presentation. They can put peptides from something they have engulfed, such as a virus-infected cell, onto class I as well. This is how a dendritic cell that is not itself infected can start a CD8 T-cell response against a virus.

The T-cell receptor and CD3

The T-cell receptor is a heterodimer, on most T cells an α and a β chain. Each chain has a variable and a constant domain, folded like an antibody's, and crosses the membrane. Six loops at the tips of the variable domains, three from each chain, touch the peptide and the helices of the MHC molecule. A T cell carries many copies of one receptor, made by gene rearrangement as a B cell makes its antibody. Unlike an antibody, the TCR is never secreted and its genes do not mutate further once the cell has matured.

A minority of T cells carry a γ and a δ chain instead. These γδ T cells are found mainly within epithelia, where they take part in their defence.

The α and β chains have only short tails inside the cell and no signalling motifs. The signal comes from the CD3 complex bound to them: three pairs of chains, CD3εγ, CD3εδ and ζζ. Their tails carry ITAMs, immunoreceptor tyrosine-based activation motifs, one on each ε, γ and δ chain and three on each ζ chain. When the receptor binds its peptide, the kinase Lck phosphorylates these tyrosines, and the signal spreads into the cell.

How a T cell reads a peptide
Four scenes on a pale plate, one in each step, each with a pale blue T cell across the top and another cell across the bottom, their amber membranes facing across a gap. In the middle the T-cell receptor hangs from the T cell, two chains of two rounded domains each, the left one a brighter deep green, the right one forest green, small beads at their tips resting on an MHC molecule standing on the lower cell with a peptide in the notch at its top. Beside the receptor four small light green CD3 domains stand on the T cell's membrane, and light green tails run up from them and from under the receptor into the T cell, each with dark marks and small orange phosphate beads. In the first the lower cell is a pale blue dendritic cell and the MHC molecule is class II, with a khaki peptide; to the right a row of four forest green CD4 domains slants down from the T cell to touch its lower right domain, and its tail inside the T cell holds a green two-lobed Lck beside the CD3 tails. In the second the lower cell is a peach body cell and the MHC molecule is class I, with a teal-green peptide, and two forest green CD8 heads on long stalks touch its lower right domain, Lck on one tail. In the third, at the left, a lime CD28 head on a stalk from the T cell meets a green CD80 or CD86 of two domains on the dendritic cell, and at the right a light green LFA-1, two long legs and an open head, meets a forest green ICAM-1, a row of five small domains. In the fourth a deeper green CTLA-4 holds that CD80 or CD86 instead, CD28 hangs free beside it with nothing to bind, and at the right a forest green PD-1 meets a lime PD-L1. Step 1 of 4: A CD4 T cell reads class II. The receptor's loops touch the peptide and the helices, CD4 binds the β2 domain, and its Lck phosphorylates the ITAMs on the CD3 tails.

Step 1 of 4A CD4 T cell reads class II. The receptor's loops touch the peptide and the helices, CD4 binds the β2 domain, and its Lck phosphorylates the ITAMs on the CD3 tails.

Point at a name or a part to light it.

Signal one is the receptor reading its peptide on MHC, with CD3 and the co-receptor's Lck passing the signal in. A naive T cell also needs signal two, CD28 on CD80 or CD86; once active it makes CTLA-4 and PD-1, the brakes.

Simplified: not to scale: the molecules drawn far larger than the cells; one receptor complex drawn; a T cell meets its peptide with many at once; each ITAM, a pair of tyrosines, drawn as one mark with one phosphate; CD28, CTLA-4, CD80 and others pair up on the membrane; each drawn as a single chain; CD8 drawn as two heads on long stalks; how they sit on α3 simplified; LFA-1, an α and a β chain, drawn as two legs and a head; each step draws only the molecules it is about; the others are still there.

4 sources
  1. Mariuzza RA, Agnihotri P, Orban J. The structural basis of T-cell receptor (TCR) activation: an enduring enigma. J Biol Chem. 2020;295(4):914–925.
  2. Janeway CA Jr, Travers P, Walport M, Shlomchik MJ. Immunobiology, 5th edition. Garland Science, 2001. Sections 3-12, 3-13, 3-18, 6-8, 8-4 and 8-5.
  3. Chen L, Flies DB. Molecular mechanisms of T cell co-stimulation and co-inhibition. Nat Rev Immunol. 2013;13(4):227–242.
  4. Kumar and Clark's Clinical Medicine, 10th edition. Elsevier, 2021. Chapter 3, Immunity: T-cell activation and immune checkpoints.

The co-receptors CD4 and CD8

Every mature αβ T cell carries one of two co-receptors, and which one decides which MHC class it can read.

  • CD4, a single chain of four immunoglobulin-like domains, binds the β2 domain of class II. CD4 T cells, the helpers, see peptides from what antigen-presenting cells have taken in.
  • CD8, usually an α and a β chain, binds the α3 domain of class I. CD8 T cells, mostly cytotoxic, see peptides from inside any cell.

Both bind a part of the MHC molecule that is the same in every allele, away from the peptide. Both carry Lck on their tails, so binding brings the kinase to the CD3 complex. With its co-receptor a T cell responds to about 100 complexes of its peptide on a cell; without it, it needs about 10,000. CD4 is also what HIV binds, with a chemokine co-receptor such as CCR5, to enter cells, which is why HIV destroys the helpers.

The second signal, and the brakes

Recognising its peptide is signal one. A naive T cell that gets signal one alone does not divide; it is switched off and can stay unresponsive. It needs signal two, co-stimulation, from the same antigen-presenting cell.

CD28 on the T cell binds CD80 and CD86 (B7-1 and B7-2) on the antigen-presenting cell. Dendritic cells make CD80 and CD86 when their pattern-recognition receptors have sensed a microbe. So a T cell is started only where innate immunity has found danger, and a self peptide shown by a resting cell switches the T cell off rather than on.

Once activated, a CD4 T cell signals back. CD40 ligand on it binds CD40 on dendritic cells, macrophages and B cells, and switches them on in turn: dendritic cells to start CD8 responses, B cells to switch class.

The activated T cell also puts out brakes, the immune checkpoints.

  • CTLA-4, made after activation, binds CD80 and CD86 more tightly than CD28 does. It takes them away from CD28 and sends a signal that holds the cell back.
  • PD-1, also made after activation, binds PD-L1 and PD-L2. PD-L1 is made by many cells, dendritic cells and many outside the immune system, and most notably by tumour cells, which use it to switch off the T cells that come to kill them.

Holding on, and passing it on

T-cell receptors bind their peptide–MHC weakly, so the two cells need more to hold them together. LFA-1, an integrin on the T cell, binds ICAM-1 on the other cell. When the receptor signals, LFA-1 changes shape and grips much harder, holding the two cells together while the T cell responds.

What the T cell then does it does through more molecules. An activated T cell makes interleukin-2 and the α chain of its receptor, CD25, which makes the receptor high-affinity, and so drives its own division. CD4 T cells make cytokines such as interferon-γ, which arms macrophages, and CD8 T cells kill with perforin, granzymes and Fas ligand. The kinds of T cell and their work are the next topic.

in a peptide on MHC class I, in a groove closed at both ends
8–10amino acids
in a peptide on MHC class II, in a groove open at both ends
13–25amino acids
of the peptides the proteasome makes that end up presented
0.02%

Class I and class II side by side

MHC class IMHC class II
GenesHLA-A, -B, -CHLA-DR, -DQ, -DP
Chainsheavy chain (α1, α2, α3) and β2-microglobulinα (α1, α2) and β (β1, β2)
Grooveα1 and α2; closed endsα1 and β1; open ends
Peptide8 to 10 amino acids13 to 25 amino acids
Made byalmost every nucleated celldendritic cells, macrophages, B cells; others when induced
Peptides fromproteins in the cytosol: self, viral, tumourwhat the cell has taken in
Loaded inendoplasmic reticulumendosomes
Helpersproteasome, TAP, tapasininvariant chain, cathepsins, HLA-DM
Read byCD8 T cells, binding α3CD4 T cells, binding β2

Check yourselfAnswer, then say how sure you were: a lucky guess still counts as a weak point.

1A virus can infect almost any cell of the body. Which molecule lets a CD8 T cell find an infected cell, whatever its kind?

2Why does MHC class I hold peptides of about 8 to 10 amino acids, while class II holds longer ones?

3In a rare deficiency of TAP, the transporter in the ER membrane, which molecule is scarce on the cell surface?

4What is CLIP, and what removes it?

5Where on the MHC molecule do the co-receptors bind?

6Abatacept is CTLA-4 joined to an antibody's Fc. How does it calm rheumatoid arthritis?