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Canonical structures of short CDR-L3 in antibodies.

Teplyakov A, Gilliland GL - Proteins (2014)

Bottom Line: Their correct identification is essential for successful prediction of antibody structure.This in turn requires regular updates of the classification of canonical structures to match the expanding experimental database.We have analyzed all crystal structures of Fab and Fv with the eight-residue CDR-L3 and identified three major canonical structures covering 82% of a nonredundant set.

View Article: PubMed Central - PubMed

Affiliation: Biotechnology Center of Excellence, Janssen Research and Development, LLC, Spring House, Pennsylvania, 19477.

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Canonical structures for CDR-L3. A: The most typical nine-residue canonical structure L3–9-cis7 (yellow) superimposed on L3-8-NP (blue). B: L3-8-NP (blue) and L3-8-P7 (orange). C: L3-8-NP (blue) and L3-8-P6 (green). D: L3-8-NP (blue) and L3-8-NP-sub (pink). For non-Pro residues only backbone atoms are shown. Pro95 in L3–9-cis7 and Pro94 in L3-8-P6 are cis, Pro96 in L3-8-P7 is trans. Main-chain hydrogen bonds are shown by dashed lines.
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fig01: Canonical structures for CDR-L3. A: The most typical nine-residue canonical structure L3–9-cis7 (yellow) superimposed on L3-8-NP (blue). B: L3-8-NP (blue) and L3-8-P7 (orange). C: L3-8-NP (blue) and L3-8-P6 (green). D: L3-8-NP (blue) and L3-8-NP-sub (pink). For non-Pro residues only backbone atoms are shown. Pro95 in L3–9-cis7 and Pro94 in L3-8-P6 are cis, Pro96 in L3-8-P7 is trans. Main-chain hydrogen bonds are shown by dashed lines.

Mentions: CDR-L3 connects two C-terminal β-strands of the VL domain and forms a wide loop anchored at positions 90 and 97, which are part of the β-scaffold [Fig. 1(A)]. CDR-L3 typically contains nine residues between the invariant residues Cys88 and Phe98 with a cis-proline occupying position 95. Due to junctional diversity in V-J recombination, a significant fraction of antibodies contains only eight residues in CDR-L3. Structurally, the deletion occurs at position 95 resulting in the sequences either without Pro, or with a Pro at positions 94 or 96.


Canonical structures of short CDR-L3 in antibodies.

Teplyakov A, Gilliland GL - Proteins (2014)

Canonical structures for CDR-L3. A: The most typical nine-residue canonical structure L3–9-cis7 (yellow) superimposed on L3-8-NP (blue). B: L3-8-NP (blue) and L3-8-P7 (orange). C: L3-8-NP (blue) and L3-8-P6 (green). D: L3-8-NP (blue) and L3-8-NP-sub (pink). For non-Pro residues only backbone atoms are shown. Pro95 in L3–9-cis7 and Pro94 in L3-8-P6 are cis, Pro96 in L3-8-P7 is trans. Main-chain hydrogen bonds are shown by dashed lines.
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4260120&req=5

fig01: Canonical structures for CDR-L3. A: The most typical nine-residue canonical structure L3–9-cis7 (yellow) superimposed on L3-8-NP (blue). B: L3-8-NP (blue) and L3-8-P7 (orange). C: L3-8-NP (blue) and L3-8-P6 (green). D: L3-8-NP (blue) and L3-8-NP-sub (pink). For non-Pro residues only backbone atoms are shown. Pro95 in L3–9-cis7 and Pro94 in L3-8-P6 are cis, Pro96 in L3-8-P7 is trans. Main-chain hydrogen bonds are shown by dashed lines.
Mentions: CDR-L3 connects two C-terminal β-strands of the VL domain and forms a wide loop anchored at positions 90 and 97, which are part of the β-scaffold [Fig. 1(A)]. CDR-L3 typically contains nine residues between the invariant residues Cys88 and Phe98 with a cis-proline occupying position 95. Due to junctional diversity in V-J recombination, a significant fraction of antibodies contains only eight residues in CDR-L3. Structurally, the deletion occurs at position 95 resulting in the sequences either without Pro, or with a Pro at positions 94 or 96.

Bottom Line: Their correct identification is essential for successful prediction of antibody structure.This in turn requires regular updates of the classification of canonical structures to match the expanding experimental database.We have analyzed all crystal structures of Fab and Fv with the eight-residue CDR-L3 and identified three major canonical structures covering 82% of a nonredundant set.

View Article: PubMed Central - PubMed

Affiliation: Biotechnology Center of Excellence, Janssen Research and Development, LLC, Spring House, Pennsylvania, 19477.

Show MeSH
Related in: MedlinePlus