SASDBP2: Human linear triubiquitin (Human linear tri-ubiquitin, Triubiquitin)

基本情報

• 登録情報: データベース: SASBDB / ID: SASDBP2

試料

Human linear triubiquitin

• Human linear tri-ubiquitin (protein), Triubiquitin, Homo sapiens

機能・相同性

分子機能:

hypothalamus gonadotrophin-releasing hormone neuron development / female meiosis I / fat pad development / female gonad development / seminiferous tubule development / male meiosis I / energy homeostasis / modification-dependent protein catabolic process / protein tag activity / protein ubiquitination / ubiquitin protein ligase binding / RNA binding / nucleus / cytosol

ドメイン・相同性:

Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily

構成要素:

Epididymis secretory protein Li 50

• 生物種: Homo sapiens (ヒト)
• 引用: ジャーナル: Acta Crystallogr D Struct Biol / 年: 2016; タイトル: New conformations of linear polyubiquitin chains from crystallographic and solution-scattering studies expand the conformational space of polyubiquitin.; 著者: Trung Thanh Thach / Donghyuk Shin / Seungsu Han / Sangho Lee / ; 要旨: The conformational flexibility of linkage-specific polyubiquitin chains enables ubiquitylated proteins and their receptors to be involved in a variety of cellular processes. Linear or Met1-linked polyubiquitin chains, associated with nondegradational cellular signalling pathways, have been known to adopt multiple conformations from compact to extended conformations. However, the extent of such conformational flexibility remains open. Here, the crystal structure of linear Ub2 was determined in a more compact conformation than that of the previously known structure (PDB entry 3axc). The two structures differ significantly from each other, as shown by an r.m.s.d. between C(α) atoms of 3.1 Å. The compactness of the linear Ub2 structure in comparison with PDB entry 3axc is supported by smaller values of the radius of gyration (Rg; 18 versus 18.9 Å) and the maximum interatomic distance (Dmax; 55.5 versus 57.8 Å). Extra intramolecular hydrogen bonds formed among polar residues between the distal and proximal ubiquitin moieties seem to contribute to stabilization of the compact conformation of linear Ub2. An ensemble of three semi-extended and extended conformations of linear Ub2 was also observed by small-angle X-ray scattering (SAXS) analysis in solution. In addition, the conformational heterogeneity in linear polyubiquitin chains is clearly manifested by SAXS analyses of linear Ub3 and Ub4: at least three distinct solution conformations are observed in each chain, with the linear Ub3 conformations being compact. The results expand the extent of conformational space of linear polyubiquitin chains and suggest that changes in the conformational ensemble may be pivotal in mediating multiple signalling pathways.

登録者

• Trung Thanh Thach
• Donghyuk Shin

モデル

• モデル #407: ; タイプ: mix / ソフトウェア: EOM / ダミー原子の半径: 1.90 A / カイ2乗値: 0.527687469241; Omokage検索でこの集合体の類似形状データを探す (詳細)
• モデル #408: ; タイプ: mix / ソフトウェア: EOM / ダミー原子の半径: 1.90 A / カイ2乗値: 0.527687469241; 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: Human linear triubiquitin / 試料濃度: 1.05-4.20
• バッファ: 名称: Tris / 濃度: 50.00 mM / pH: 7.5 / 組成: 150mM NaCl, 0.5 mM EDTA

要素 #269

名称: Triubiquitin / タイプ: protein / 記述: Human linear tri-ubiquitin / 分子量: 25.658 / 分子数: 1 / 由来: Homo sapiens / 参照: UniProt: Q5U5U6
配列:

MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGGMQIF VKTLTGKTIT LEVEPSDTIE NVKAKIQDKE GIPPDQQRLI FAGKQLEDGR TLSDYNIQKE STLHLVLRLR GGMQIFVKTL TGKTITLEVE PSDTIENVKA KIQDKEGIPP DQQRLIFAGK QLEDGRTLSD YNIQKESTLH LVLRLRGG

実験情報

• ビーム: 設備名称: Pohang Accelerator Laboratory 5C / 地域: Pohang / 国: South Korea / 線源: X-ray synchrotron / 波長: 1.907 Å / スペクトロメータ・検出器間距離: 1.4 mm
• 検出器: 名称: ADSC Quantum 315 / タイプ: CCD

スキャン

タイトル: Human linear tri-ubiquitin / 測定日: 2014年11月3日 / 保管温度: 22 °C / 照射時間: 60 sec. / フレーム数: 5 / 単位: 1/nm /

	Min	Max
Q	0.2287	2.2399

距離分布関数 P(R)

ソフトウェア P(R): GNOM 4.5a / ポイント数: 219 /

	Min	Max
Q	0.0247	0.224
P(R) point	5	223
R	0	86.32

結果

カーブのタイプ: single_conc
コメント: Note: The displayed results show a merged data set derived from a concentration series. Data were normalised to protein concentration and the high angle data from highest concentration and low angle data from lowest concentration were merged to generate final SAXS profile. Because of the flexibility of linear-triubiquitin molecule, ensemble optimisation method, EOM, was performed. The models shown above are two triubiquitin examples from the final EOM output. All EOM models, the radius of gyration distribution and maximum particle dimension distribution can be found in the full entry zip archive.

	実験値	Porod
分子量	27.05 kDa	-
体積	-	35.9 nm3

	P(R)	P(R) error	Guinier	Guinier error
前方散乱 I0	409.5	5.6	402.7	1.8
慣性半径, Rg	2.6 nm	0.05	2.45 nm	0.04

	Min	Max
D	-	8.63
Guinier point	3	34