Complementarity determining region
Encyclopedia
Complementarity determining regions (CDRs) are regions within antibodies (also known as immunoglobulins) or T cell receptor
s where these proteins complement an antigen
's shape. Thus, CDRs determine the protein's affinity and specificity for specific antigens. The CDRs are the most variable part of the molecule, and contribute to the diversity of these molecules, allowing the antibody and the T cell receptor to recognize a vast repertoire of antigens.
and light chain
), there are six CDRs for each antigen receptor that can collectively come into contact with the antigen. A single antibody molecule has two antigen receptors, wherefore it contains twelve CDRs. Sixty CDRs can be found on a pentameric IgM
molecule.
Within the variable domain, CDR1 and CDR2 are found in the variable (V) region of a polypeptide chain, and CDR3 includes some of V, all of diverse (D, heavy chains only) and joint (J), and some of the constant (C) regions. CDR3 is the most variable.
Since most sequence variation associated with immunoglobulins and T cell receptors are found in the CDRs, these regions are sometimes referred to as hypervariable region
s. Among these, CDR3 shows the greatest variability as it is encoded by a recombination of the VJ in the case of a light chain region and VDJ
in the case of heavy chain regions.
The tertiary structure
of an antibody is important to analyze and design new antibodies. Homology modeling
is a computational method to build tertiary structures from amino-acid sequences. The so-called H3-rules are emipirical rules to build models of CDR3.
T cell receptor
The T cell receptor or TCR is a molecule found on the surface of T lymphocytes that is responsible for recognizing antigens bound to major histocompatibility complex molecules...
s where these proteins complement an antigen
Antigen
An antigen is a foreign molecule that, when introduced into the body, triggers the production of an antibody by the immune system. The immune system will then kill or neutralize the antigen that is recognized as a foreign and potentially harmful invader. These invaders can be molecules such as...
's shape. Thus, CDRs determine the protein's affinity and specificity for specific antigens. The CDRs are the most variable part of the molecule, and contribute to the diversity of these molecules, allowing the antibody and the T cell receptor to recognize a vast repertoire of antigens.
Location and structure
In the amino acid sequence of a variable domain of an antigen receptor there are three CDRs (CDR1, CDR2 and CDR3), arranged non-consecutively. Since the antigen receptors are typically composed of two variable domains (on two different polypeptide chains, heavyHeavy chain
]The immunoglobulin heavy chain is the large polypeptide subunit of an antibody .A typical antibody is composed of two immunoglobulin heavy chains and two Ig light chains. Several different types of heavy chain exist that define the class or isotype of an antibody. These heavy chain types vary...
and light chain
Light chain
A light chain is the small polypeptide subunit of a protein complex.More specifically, it can refer to:* Immunoglobulin light chain* Ferritin light chain* Myosin light chain* Kinesin light chain* Dynein light chainLight chain may also refer to:...
), there are six CDRs for each antigen receptor that can collectively come into contact with the antigen. A single antibody molecule has two antigen receptors, wherefore it contains twelve CDRs. Sixty CDRs can be found on a pentameric IgM
IGM
IGM as an acronym or abbreviation can refer to:* Immunoglobulin M , the primary antibody against A and B antigens on red blood cells* International Grandmaster, a chess ranking* intergalactic medium* Intragroup medium - see: Intracluster medium...
molecule.
Within the variable domain, CDR1 and CDR2 are found in the variable (V) region of a polypeptide chain, and CDR3 includes some of V, all of diverse (D, heavy chains only) and joint (J), and some of the constant (C) regions. CDR3 is the most variable.
Since most sequence variation associated with immunoglobulins and T cell receptors are found in the CDRs, these regions are sometimes referred to as hypervariable region
Hypervariable region
A hypervariable region is a location within nuclear DNA or the D-loop of mitochondrial DNA in which base pairs of nucleotides repeat or have substitutions...
s. Among these, CDR3 shows the greatest variability as it is encoded by a recombination of the VJ in the case of a light chain region and VDJ
V(D)J recombination
VJ recombination, also known as somatic recombination, is a mechanism of genetic recombination in the early stages of immunoglobulin and T cell receptors production of the immune system...
in the case of heavy chain regions.
The tertiary structure
Tertiary structure
In biochemistry and molecular biology, the tertiary structure of a protein or any other macromolecule is its three-dimensional structure, as defined by the atomic coordinates.-Relationship to primary structure:...
of an antibody is important to analyze and design new antibodies. Homology modeling
Homology modeling
Homology modeling, also known as comparative modeling of protein refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein...
is a computational method to build tertiary structures from amino-acid sequences. The so-called H3-rules are emipirical rules to build models of CDR3.