5JIU

The crystal structure of RanBPM/9 IUS-SPRY domain in complex with DDX-4 peptide

5JIU の概要

• エントリーDOI: 10.2210/pdb5jiu/pdb
• 関連するPDBエントリー: 5JI7 5JI9 5JIA
• 分子名称: Ran-binding protein 9, Probable ATP-dependent RNA helicase DDX4, CHLORIDE ION, ... (4 entities in total)
• 機能のキーワード: beta sandwich, ran binding protein, transport protein, ran binding protein-peptide complex, ran binding protein/peptide
• 由来する生物種: Homo sapiens (Human); 詳細
• 細胞内の位置: Cytoplasm : Q96S59 Q61496
• タンパク質・核酸の鎖数: 4
• 化学式量合計: 56962.24

構造登録者

Hong, S.K.,Kim, K.-H.,Kim, E.E. (登録日: 2016-04-22, 公開日: 2016-11-09, 最終更新日: 2023-11-08)

主引用文献

Hong, S.K.,Kim, K.H.,Song, E.J.,Kim, E.E.
Structural Basis for the Interaction between the IUS-SPRY Domain of RanBPM and DDX-4 in Germ Cell Development.
J.Mol.Biol., 428:4330-4344, 2016

PubMed Abstract: RanBPM and RanBP10 are non-canonical members of the Ran binding protein family that lack the Ran binding domain and do not associate with Ran GTPase in vivo. Rather, they have been shown to be scaffolding proteins that are important for a variety of cellular processes, and both of these proteins contain a SPRY domain, which has been implicated in mediating protein-protein interactions with a variety of targets including the DEAD-box containing ATP-dependent RNA helicase (DDX-4). In this study, we have determined the crystal structures of the SPIa and the ryanodine receptor domain and of approximately 70 upstream residues (immediate upstream to SPRY motif) of both RanBPM and RanBP10. They are almost identical, composed of a β-sandwich fold with a set of two helices on each side located at the edge of the sheets. A unique shallow binding surface is formed by highly conserved loops on the surface of the β-sheet with two aspartates on one end, a positive patch on the opposite end, and a tryptophan lining at the bottom of the surface. The 20-mer peptide (residues 228-247) of human DDX-4, an ATP-dependent RNA helicase known to regulate germ cell development, binds to this surface with a K of ~13μM. The crystal structure of the peptide complex and the mutagenesis studies elucidate how RanBPM can recognize its interaction partners to function in gametogenesis.

PubMed: 27622290
DOI: 10.1016/j.jmb.2016.09.004

実験手法

X-RAY DIFFRACTION (2.054 Å)