This document provides information on MHC class I and class II molecules, including their structure, function, and role in antigen presentation. It discusses that MHC class I molecules are expressed on all nucleated cells and present intracellular antigens to CD8+ T cells. MHC class II molecules are expressed primarily on antigen presenting cells and present extracellular antigens to CD4+ T cells. The peptide binding grooves of MHC class I and II molecules differ in their structure and the size of peptides they can bind.

1. IMMUNOLOGY

2. MHC CLASS I and CLASS II MOLECULE
VIRUS INFECTED CELL ANTIGEN PRESENTING CELL

3. ABBREVIATIONS
 MHC - Major Histocompatibility Complex
 HLA - Human Leucocyte Antigen
 APC - Antigen Presenting Cell
 NK - Natural Killer Cell
 CD - Cluster Differentiation
 TNF - Tumor Necrosis Factor
 IFN - Interferon
 KIR - Killer cell Immunoglobulin like Receptor
 TAP - Transporter associated with Antigen Processing
 LMP - Latent Membrane Protein
 ERAP - Endoplasmic Reticulum Amino Peptidase
 MIIC - MHC class II containing Compartment
 CLIP - CLass II associated Invariant chain Peptide
 RAGE - Receptor for Advanced Glycation End Products
 NKG2 - Natural Killer Group 2

4. HISTORY
 Genetically determined structures on the cell surface that
regulate immunological response.
• 1980 – Nobel Laureates For Medicine Or Physiology
BARUJ BENACERRAFJEAN DAUSSETGEORGE D. SNELL

5. HISTORY
ROLF M.ZINKERNAGEL PETER C.DOHERTY
1996 – NOBEL LAUREATES FOR MEDICINE OR PHYSIOLOGY
Specificity of the cell mediated immune defense

6. DON WILEY
 Structural studies done by DON
WILEY and OTHERS showed that
different MHC proteins bind and
present different antigen fragments
HISTORY
 IN 1980 K. ZIEGLER AND E.R.UNANUE showed that intra
cellular processing of APC is required to activate T cells

7. Structure and
function of MHC
Molecules

8. CLASSIFICATION
Class I & II MHC Molecules –
 membrane bound glycoproteins
 closely related in both structure and function
Class III MHC Molecule-
 Groups of unrelated proteins
 Do not share any similarity to class I and II
molecules.
 Participates in other aspects of immune response

9. Class I MHC Molecules
All nucleated cells, platelets
Present intracellular antigens to CD8+ T cells
Consists of two polypeptide chains
 α chain – 45 kDa
 β chain – 12 kDa

10. Class I MHC MOLECULE
 α CHAIN
 3 external domains - each approximately 90 amino
acids long.
 A transmembrane domain - 25 hydrophobic amino
acids and a short chain of charged hydrophilic
aminoacids.
 A cytoplasmic anchor segment- 30 amino acid long.

11. CLASS I MHC MOLECULE
 β2 Microglobulin –
 Similar in size and organization to α3 domain
 No transmembrane region
 Bound non covalently to α domain

12. CLASS II MHC MOLECULE
Antigen presenting cells
Present extracellular antigens to CD4+ T cells
Consists of two different polypeptide chains
 α chain – 33 kDa
 β chain – 28 kDa

13. CLASS II MOLECULE
α CHAIN
▪ contains two extra cellular domains – α1
and α2 domain
▪ a transmembrane segment
▪ a cytoplasmic anchor segment
β CHAIN
▪ similar to α chain

14. PEPTIDE BINDING GROOVE
MHC CLASS I MOLECULE –
▪ formed by α1 and α2 domains
▪ socket like opening
▪ bind a peptide of 8 to 10 amino acids
MHC CLASS II MOLECULE –
▪ formed by α1 and β1domains
▪ open-ended groove
▪ bind a peptide of 13 to 18 amino acids

16. MHC CLASS I MOLECULE MHC CLASS I PEPTIDE BINDING
GROOVE

17. MHC CLASS II MOLECULE MHC CLASS II PEPTIDE BINDING
GROOVE

18. GENERAL
ORGANIZATION AND
INHERITANCE OF MHC

19. MAJOR HISTOCOMPATIBILITY
COMPLEX
MHC is a collection of genes arrayed within a
long continuous stretch of DNA on
▪ chromosome 6 – humans
▪ chromosome 17 – mice
MHC is referred to as
▪ HLA complex – humans
▪ H-2 complex – mice

20. ORGANIZATION OF MHC COMPLEX
in human chromosome 6

21.  MHC CLASS I MOLECULE
▪ classical class I loci (A, B, C) - α chain
▪ non classical class I loci - HLA-E, F, G molecule
▪ β2 microglobulin - chromosome 15
 MHC CLASS II MOLECULE
▪ classical class II loci (DP, DQ, DR) – both α and β chain
▪ non classical class II loci (DM, DO) – HLA-DM, HLA-DO

22. HUMAN MHC LOCI – CHROMOSOME 6

23. CLASS I MHC MOLECULE CLASS II MHC MOLECULE

24. POLYMORPHISM - many alternative forms of each
gene or allele exists with in the population
• Many alternative forms of each allele exits in
the population.

25. POLYGENIC
Multiple genes with same function but with
different structure

26. LINKAGE DISEQUILIBRIUM
Non random association of alleles of two or more
different genes, at two different loci with a
frequency greater than would be expected by
chance.
Usually these alleles are located close to one
another in the same chromosome
Depends on,
▪ natural selection
▪ population size
▪ mutation rate

27. GENETIC RECOMBINATION

28. MHC Molecule expressed on the APC
of a heterozygote offspring
centromere
centromere
Class II LOCI
CLASS I LOCI

29. Mating of two inbred mice with
different MHC haplotypes

30. SKIN TRANSPLANTATION

31. The MHC molecules expressed by an individual are fixed.
However the promiscuity of antigen binding ensures the
enormous flexibility of MHC molecules to bind to various
peptides.
It is rare for any two unrelated individuals to have identical
sets of HLA genes.
Not all alleles encode proteins.
Human class II genes are highly polymorphic and in some
cases an individual can inherit different number of genes.
The theoretical number of combinations possible are 1.7
billion class I haplotypes, 1015 class II haplotypes. Thus
bringing a total of more than 1.7 x1027 combinations.
High level of MHC polymorphism provide better survival
advantage.

32. FUNCTIONAL RELEVANCE FOR MHC
POLYMORPHISM
• Polymorphism in the MHC is clustered largely
with in the membrane distal α1 and α2
domains of class I, α1 and β1 domains of class
II molecules.
• Allelic differences contribute to the observed
differences in the ability of MHC molecules to
interact with a given peptide ligand

33. Genetic diversity of MHC loci in human
population
(2013)
(2605)
(1551)
(1200)
(7)

35. MHC CLASS I EXPRESSION
Nucleated cells and platelets
Level of expression differs among different cell
types
Highest – lymphocytes (5x105 molecules /cell)
Low – fibroblasts, myocytes, hepatocytes,
neural cells.
Different individual with in a species present
different viral peptides.

36. MHC CLASS II MOLECULE
Antigen presenting cells
Level of expression significantly increases after
activation.
pAPCs differ by
▪ mechanism of antigen uptake
▪ constitutive expression of class II MHC
molecule.
▪ inherent co-stimulatory activity.

37.  PROFESSIONAL APC
 DENDRITIC CELLS –
▪ most effective
▪ constitutively express high levels of MHC class II molecule
▪ inherent co-stimulatory activity
▪ activate naïve TH cells.
 MACROPHAGES –
to be activated before they express sufficient level of MHC
class II molecule and co-stimulatory activity
 B CELLS –
▪ constitutively express MHC class II molecule
▪ to be activated for co-stimulatory activity.
 NON PROFESSIONAL APC
1.Fibroblasts
2.Glial cells
3.Pancreatic β cells
4.Thymic epithelial cells
5.Thyroid epithelial cells
6.vascular endothelial cells

38. VARIOUS REGULATORS
 GENETIC REGULATORY COMPONENTS –
CIITA, RFX – class II MHC transactivators. If defective causes
bare lymphocyte syndrome.
 VIRAL INTERFERENCE –
Viral infection interfere with MHC class I expression by,
▪ decreased level of components needed for peptide
transport,
▪ or MHC class I assembly
▪ decreased transcription
 CYTOKINE MEDIATED SIGNALLING –
▪ early stages of infection – IFN α and TNF α
▪ later stages of infection – IFN γ

39.  The alleles in MHC haplotype
determine which fragment of
peptide to be presented
 This variability in immune response
to an antigen among different
individuals is explained by two
models viz.,
▪ determinant-selection model
▪ holes-in-the-repertoire model

40.  Determinant-selection model –
 Different class II MHC molecules differ in their
ability to bind particular processed antigens.
 And some peptides may be more crucial to
eliminate the pathogen than others.
 Holes-in-the-repertoire model –
T cells bearing receptors that recognize certain
foreign antigens which happen to closely
resemble self antigens may be eliminated during
T cell development, leaving the organism without
the cells/receptors for future responses to foreign
molecules.

41. PEPTIDE BINDING
Each individual has 6 different class I molecule
and 12 or more different class II molecule.
Peptide binding by class I and II molecules
does not exhibit fine specificity.
A given MHC molecule can bind to several
different peptides and some peptides can bind
to several different MHC molecules.
So the binding between peptide and MHC is
often referred to as promiscuous.

42.  In both types of MHC molecules peptide ligands are held in
largely extended conformation that runs along the length of
the groove.

43. MHC CLASS I and CLASS II MOLECULE
with BOUND PEPTIDES

44. PEPTIDE BINDING GROOVE OF MHC
CLASS I MOLECULE

45. PEPTIDE BINDING GROOVE OF MHC
CLASS II MOLECULE

46.  ANCHOR RESIDUES – The amino acid residues of the peptide
that anchor the peptide to MHC class I binding groove.
▪ There is a carboxy terminal anchor usually formed by a
hydrophobic amino acid and amino terminal anchor either in 2nd
or 2nd and 3rd position also formed by hydrophobic amino acid.
 The amino acid residues lining the binding site vary among
different class I allelic molecule which determines the
classical identity of anchor residues.

48. PROCESSING OF ANTIGEN
K. ZIEGLER , E.R. UNANUE
1980

50. ENDOGENOUS PATHWAY
 STANDARD PROTEASOME – 14 subunits.
 IMMUNOPROTEASOME –
▪ present in pAPCs and infected cells
▪ in response to the cytokines IFN γ and TNFα the
genes LMP2 and LMP7 encode replacement catalytic
protein subunits that convert standard proteasomes to
immunoproteasomes.
▪ increased level of protein degradation and turn
over more rapidly.
 The proteasome complex cleaves peptide bonds in an
ATP-dependent manner.

51. ENDOGENOUS PATHWAY
CYTOSOLIC PROTEOLYTIC SYSTEM

52. TAP PROTEIN
 Membrane spanning heterodimer.
 Consists of two proteins : TAP1 and TAP2
 Has multiple transmembrane segments, a domain
projecting into the lumen of RER and an ATP-binding
domain that projects into the cytosol.
 Encoded by TAP1 and TAP2 genes within class II MHC region
and different allelic forms of these regions exists.
 Both TAP1 and TAP2 belong to the family of ATP-binding
cassette proteins.
 These proteins mediate ATP dependent transport of
aminoacids, sugars, ions, and peptides.
 TAP has affinity for peptides containing 8 to16 aminoacids.

53. ENTRY INTO ENDOPLASMIC RETICULUM

54. ASSEMBLY AND STABILIZATION OF
CLASS I MOLECULE

55. EXOGENOUS PATHWAY

56. INVARIANT CHAIN
CD 74
Non MHC encoded protein
Interacts with class II molecule preventing any
endogenously derived peptide from binding
Also involved in the folding of class II α andβ
chains, their exit from RER, and subsequent
routing.

57. ASSEMBLY OF CLASS II MHC
MOLECULE

60. CROSS PRESENTATION
First reported by Michael Bevan and later
described in detail by Peter Cresswell and
colleagues.
Internalized antigens that would normally be
handled by the exogenous pathway leading to
class II MHC presentation is redirected to class I
peptide loading pathway.
When this form of antigen presentation leads to
the activation of CTL responses, it is referred to as
cross-priming.
Dendritic cells are most efficient cross-presenters.

61. MECHANISM
Two hypothesis
1. Cross presenting cells possess special-processing
machinery that allows loading of exogenously
derived peptides onto class I MHC molecules.
2. Specialized endocytosis machinery that can send
internalized antigen directly to an organelle
where the peptides are loaded to class I MHC
molecule
 Though it has not been resolved cross presented
antigens has been found to enter the cytoplasm.

62. LICENSED DENDRITIC CELLS
Dendritic cells first present the antigen by
classical exogenous pathway to CD4+ T cells.
These activated helper cells might then return the
favour by inducing costimulatory molecules in DC
and by cytokine secretion, supplying a “second
opinion” that it licenses the DC to cross present
the antigen to CD8+ T cells.
This helps to avoid accidental induction of CTLs to
self-proteins.

63. CROSS PRESENTING DENDRITIC CELL

65. CD1
The nonpeptide antigens are presented by
members of CD1 family of nonclassical class I
molecules.
Structurally similar to classical MHC class I but
overlap functionally with MHC class II.
Five human CD1 genes are known in
chromosome 1.
Very little polymorphism
Expressed by thymocytes, B cells, DCs,
hepatocytes and epithelial cels.

66. The peptide binding groove as both deeper and narrower than
classical MHC molecules
 Short chain self lipids with relatively low affinity are
loadedonto CD1 molecules in ER and allow CD1 folding.
When they encounter long chain, high affinity lipid antigens
self lipids are exchanged.
These newly loaded CD1 molecules return to the surface for
recognition by CD1-restricted T cells.

67. NON CLASSICAL MHC CLASS I
MOLECULES
HLA-E –
 They are transported to cell surface only when they
are bound to the peptide derived from HLA-A, HLA-B,
or HLA-C.
 The amount of HLA-E on the surface is an indicator of
the overall level of class I MHC biosynthesis in the
cell.
 They are recognized by CD94-NKG2A receptor of
natural killer cell

68. HLA-F
Present in cells of thymus. Spleen and tonsil.
Comes to the surface only when the lymphocytes are activated.
HLA-G
Present in fetal cells at maternal – fetal interface.
They are credited with inhibiting the rejection by
maternal CD8+ T cells by protecting the fetus from
identification as foreign, which may occur when
paternally derived antigens begin to appear on
developing fetus.

69. HLA DM
Non classical MHC class II molecule
Catalyze the exchange of CLIP with antigenic
peptides.
It is a heterodimer and relatively non
polymorphic
Found predominantly in the endosomal
compartment

70. HLA DO
Observed in B cells, dendritic cells
Relatively non polymorphic class II molecule
Expression is not induced by IFNγ.
Negative regulator of antigen binding by
modulating the function of HLA-DM.
Following cell activation DO expression is
down regulated.

71. CLASS III MHC MOLECULE
 Extremely gene dense
 Contain about 62 genes
 The genes C4A and C4B are highly polymorphic.
 Some important products include
I. C4, C2 and factor B
II. TNF α and β
III. NOTCH-4
IV. PBX2 gene product – regulating the expansion of
hematopoietic precursor
V. RAGE – upregulated in vasculopathies, atherosclerosis,
and vasculitis.

72. NK CELLS

73. INHIBING RECEPTORS -
KIR receptors recognize HLA-B or HLA-C
CD94-NKG2A receptors recognize HLA-E
ACTIVATING RECEPTORS –
NKG2D – ligands are nonpolymorphic MHC class I like
molecules that do not associate with β2 microglobulin.
They are found in cells undergoing stress either due to
DNA damage or VIRAL infection.