SASDAT6: Integrin beta4, fragment of the cytoplasmic region encompassing t...

基本情報

• 登録情報: データベース: SASBDB / ID: SASDAT6

試料

Integrin beta4, fragment of the cytoplasmic region encompassing the third and fourth FnIII domains

• Integrin beta-4 (protein), Homo sapiens

機能・相同性

分子機能:

trophoblast cell migration / Type I hemidesmosome assembly / hemidesmosome assembly / nail development / hemidesmosome / peripheral nervous system myelin formation / Laminin interactions / skin morphogenesis / filopodium assembly / mesodermal cell differentiation / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / integrin complex / Assembly of collagen fibrils and other multimeric structures / Syndecan interactions / cell leading edge / basement membrane / cell-matrix adhesion / basal plasma membrane / integrin-mediated signaling pathway / G protein-coupled receptor binding / cell motility / cell-cell adhesion / response to wounding / autophagy / integrin binding / cell junction / nuclear membrane / receptor complex / cell adhesion / focal adhesion / nucleolus / cell surface / extracellular exosome / metal ion binding / plasma membrane

ドメイン・相同性:

Integrin beta-4 subunit / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / Domains in Na-Ca exchangers and integrin-beta4 / CalX-like domain superfamily / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / EGF-like domain, extracellular / EGF-like domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / EGF-like domain signature 1. / Fibronectin type III domain / EGF-like domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold

構成要素:

Integrin beta-4

• 生物種: Homo sapiens (ヒト)
• 引用: ジャーナル: Acta Crystallogr D Biol Crystallogr / 年: 2015; タイトル: Combination of X-ray crystallography, SAXS and DEER to obtain the structure of the FnIII-3,4 domains of integrin α6β4.; 著者: Noelia Alonso-García / Inés García-Rubio / José A Manso / Rubén M Buey / Hector Urien / Arnoud Sonnenberg / Gunnar Jeschke / José M de Pereda / ; 要旨: Integrin α6β4 is a major component of hemidesmosomes that mediate the stable anchorage of epithelial cells to the underlying basement membrane. Integrin α6β4 has also been implicated in cell proliferation and migration and in carcinoma progression. The third and fourth fibronectin type III domains (FnIII-3,4) of integrin β4 mediate binding to the hemidesmosomal proteins BPAG1e and BPAG2, and participate in signalling. Here, it is demonstrated that X-ray crystallography, small-angle X-ray scattering and double electron-electron resonance (DEER) complement each other to solve the structure of the FnIII-3,4 region. The crystal structures of the individual FnIII-3 and FnIII-4 domains were solved and the relative arrangement of the FnIII domains was elucidated by combining DEER with site-directed spin labelling. Multiple structures of the interdomain linker were modelled by Monte Carlo methods complying with DEER constraints, and the final structures were selected against experimental scattering data. FnIII-3,4 has a compact and cambered flat structure with an evolutionary conserved surface that is likely to correspond to a protein-interaction site. Finally, this hybrid method is of general application for the study of other macromolecules and complexes.

登録者

• Jose M de Pereda (USAL, La Universidad de Salamanca, Salamanca, Spain)

モデル

• モデル #219: ; タイプ: dummy / ソフトウェア: DAMMIF / ダミー原子の半径: 1.50 A / カイ2乗値: 1.976836; 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 #220: ; タイプ: atomic / ソフトウェア: CRYSOL / カイ2乗値: 1.297321; 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: Integrin beta4, fragment of the cytoplasmic region encompassing the third and fourth FnIII domains; 試料濃度: 1.50-48.60
• バッファ: 名称: Sodium Phosphate / 濃度: 20.00 mM / pH: 7.5 / 組成: 150 mM NaCl, 5% glycerol, 3 mM DTT

要素 #133

タイプ: protein / 記述: Integrin beta-4 / 分子量: 23.359 / 分子数: 1 / 由来: Homo sapiens / 参照: UniProt: P16144
配列:

GSHMVPDTPT RLVFSALGPT SLRVSWQEPR CERPLQGYSV EYQLLNGGEL HRLNIPNPAQ TSVVVEDLLP NHSYVFRVRA QSQEGWGRER EGVITIESQV HPQSPLCPLP GSAFTLSTPS APGPLVFTAL SPDSLQLSWE RPRRPNGDIV GYLVTCEMAQ GGGPATAFRV DGDSPESRLT VPGLSENVPY KFKVQARTTE GFGPEREGII TIES

実験情報

• ビーム: 設備名称: PETRA III P12 / 地域: Hamburg / 国: Germany / 線源: X-ray synchrotron / 波長: 0.12 Å / スペクトロメータ・検出器間距離: 3.1 mm
• 検出器: 名称: Pilatus 2M

スキャン

測定日: 2013年8月6日 / 保管温度: 10 °C / セル温度: 10 °C / 照射時間: 0.05 sec. / フレーム数: 20 / 単位: 1/nm /

	Min	Max
Q	0.0576	3.4909

距離分布関数 P(R)

ソフトウェア P(R): GNOM 4.6 / ポイント数: 494 /

	Min	Max
Q	0.05955	3.013
P(R) point	1	494
R	0	7

結果

D max: 7 / カーブのタイプ: extrapolated
コメント: Combined use of SAXS, crystal structures, site directed spin labeling, double electron-electron resonance (DEER), and molecular modeling to analyze the structure of FnIII-3,4.

	実験値	Standard	Porod
分子量	19.2 kDa	19.2 kDa	20 kDa
体積	-	-	32 nm3

	P(R)	Guinier
前方散乱 I0	586	590
慣性半径, Rg	2.2 nm	2.2 nm