4NIK

Structure of human Gankyrin in complex to the single chain antibody F5

4NIK の概要

• エントリーDOI: 10.2210/pdb4nik/pdb
• 関連するPDBエントリー: 1QYM 1UOH
• 分子名称: 26S proteasome non-ATPase regulatory subunit 10, Single-chain Fv fragment antibody (3 entities in total)
• 機能のキーワード: beta-hairpin-alpha-hairpin repeat, oncoprotein, 26s proteasome, oncoprotein-immune system complex, oncoprotein/immune system
• 由来する生物種: Homo sapiens (human); 詳細
• 細胞内の位置: Cytoplasm : O75832
• タンパク質・核酸の鎖数: 2
• 化学式量合計: 51738.00

構造登録者

Sato, Y.,Weiss, E.,Rochel, N. (登録日: 2013-11-06, 公開日: 2014-09-10, 最終更新日: 2024-10-16)

主引用文献

Robin, G.,Sato, Y.,Desplancq, D.,Rochel, N.,Weiss, E.,Martineau, P.
Restricted diversity of antigen binding residues of antibodies revealed by computational alanine scanning of 227 antibody-antigen complexes
J.Mol.Biol., 426:3729-3743, 2014

PubMed Abstract: Antibody molecules are able to recognize any antigen with high affinity and specificity. To get insight into the molecular diversity at the source of this functional diversity, we compiled and analyzed a non-redundant aligned collection of 227 structures of antibody-antigen complexes. Free energy of binding of all the residue side chains was quantified by computational alanine scanning, allowing the first large-scale quantitative description of antibody paratopes. This demonstrated that as few as 8 residues among 30 key positions are sufficient to explain 80% of the binding free energy in most complexes. At these positions, the residue distribution is not only different from that of other surface residues but also dependent on the role played by the side chain in the interaction, residues participating in the binding energy being mainly aromatic residues, and Gly or Ser otherwise. To question the generality of these binding characteristics, we isolated an antibody fragment by phage display using a biased synthetic repertoire with only two diversified complementarity-determining regions and solved its structure in complex with its antigen. Despite this restricted diversity, the structure demonstrated that all complementarity-determining regions were involved in the interaction with the antigen and that the rules derived from the natural antibody repertoire apply to this synthetic binder, thus demonstrating the robustness and universality of our results.

PubMed: 25174334
DOI: 10.1016/j.jmb.2014.08.013

実験手法

X-RAY DIFFRACTION (2.5 Å)