SASDFS4: HP0242 from Helicobacter pylori, N-terminal domain of syntaxin-1A...

基本情報

• 登録情報: データベース: SASBDB / ID: SASDFS4

試料

HP0242 from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain (Domain A (PDB:3MLI)-Linker (PDB:1BR0)-Domain B (PDB:4DZL))

• HP0242 from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain (protein), Fusion protein2, Helicobacter pylori, Rattus norvegicus, de novo design

• 生物種: Helicobacter pylori (ピロリ菌); Rattus norvegicus (ドブネズミ); de novo design (unknown)
• 引用: ジャーナル: ACS Synth Biol / 年: 2019; タイトル: Construction of a Quadrangular Tetramer and a Cage-Like Hexamer from Three-Helix Bundle-Linked Fusion Proteins.; 著者: Takaaki Miyamoto / Yugo Hayashi / Keito Yoshida / Hiroki Watanabe / Takayuki Uchihashi / Kento Yonezawa / Nobutaka Shimizu / Hironari Kamikubo / Shun Hirota / ; 要旨: Self-assembled protein nanostructures have gained interest, owing to their potential applications in biomaterials; however, successful design and construction of protein nanostructures are limited. Herein, we constructed fusion protein 1 by linking the C-terminus of a dimerization domain and the N-terminus of another dimerization domain with a three-helix bundle protein, where it self-assembled mainly into tetramers. By replacing the C-terminal dimerization domain of 1 with a trimerization domain (fusion protein 2), hexamers were mainly obtained. According to ab initio structural models reconstructed from the small-angle X-ray scattering data, the tetramer of 1 and hexamer of 2 adopted quadrangle and cage-like structures, respectively, although they were combinations of different conformations. High-speed atomic force microscopy observations indicated that the tetramer and hexamer exhibit conformational dynamics. These results show that the present method utilizing three-helix bundle-linked fusion proteins is useful in the construction of protein nanostructures.

登録者

• Hironari Kamikubo (Nara Institute of Science and Technology)

モデル

• モデル #2930: ; タイプ: mix / ダミー原子の半径: 1.90 A / カイ2乗値: 0.10 / P-value: 0.000088; Omokage検索でこの集合体の類似形状データを探す (詳細)

試料

• 試料: 名称: HP0242 from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain (Domain A (PDB:3MLI)-Linker (PDB:1BR0)-Domain B (PDB:4DZL)); 試料濃度: 1.90-6.80
• バッファ: 名称: 20 mM Tris-HCl 150 mM NaCl / pH: 8

要素 #1583

名称: Fusion protein2 / タイプ: protein
記述: HP0242 from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain
分子量: 29.855 / 分子数: 6
由来: Helicobacter pylori, Rattus norvegicus, de novo design
配列:

MGSSHHHHHH SSGLVPRGSH MRDYSELEIF EGNPLDKWND IIFHASKKAS KKELERLLEL LALCETFIEK EDLEEKFESF AKALRIDEEL QQKIESRKTD IVIQSMANIL SALFMDEFFE QVEEIRGFID KIAENVEEVK RKHSAILASP NPDEKTKEEL EELMSDIKKT ANKVRSKLKS IEQSIEQEEG LNRSSADLRI RKTQHSTLSR KFVEVMSEYN ATQSDYGSGG EIAAIKQEIA AIKKEIAAIK WEIAAIKQGY G

実験情報

• ビーム: 設備名称: Nara Institute of Science and Technology Rigaku Nano-Viewer; 地域: Ikoma / 国: Japan / 線源: X-ray in house / 波長: 0.15418 Å / スペクトロメータ・検出器間距離: 0.75 mm
• 検出器: 名称: Pilatus 200K / タイプ: Pilatus / Pixsize x: 172 mm

スキャン

タイトル: HP0242 from Helicobacter pylori, N-terminal domain of syntaxin-1A from Rattus norvegicus, de novo designed coiled-coil trimer domain (Domain A (PDB:3MLI)-Linker (PDB:1BR0)-Domain B (PDB:4DZL))
測定日: 2017年3月29日 / 保管温度: 4 °C / セル温度: 20 °C / 照射時間: 60 sec. / フレーム数: 25 / 単位: 1/A /

	Min	Max
Q	0.0138	0.3003

距離分布関数 P(R)

ソフトウェア P(R): GNOM 5.0 / ポイント数: 218 /

	Min	Max
Q	0.015662	0.215586
P(R) point	1	218
R	0	240

結果

カーブのタイプ: extrapolated

	実験値	Standard	Standard error	Porod
分子量	187 kDa	187 kDa	10	401 kDa
体積	-	-	-	642 nm3

	P(R)	P(R) error	Guinier	Guinier error
前方散乱 I0	40.9	2.2	40.11	3.11
慣性半径, Rg	7 nm	0.3	6.53 nm	0.6

	Min	Max
D	-	24
Guinier point	1	8