SASDBS2: Recombinant Tn antigen-binding lectin from Vatairea macrocarpa

基本情報

• 登録情報: データベース: SASBDB / ID: SASDBS2

試料

Recombinant Tn antigen-binding lectin from Vatairea macrocarpa

• Recombinant Tn antigen-binding lectin (protein), vRML, Vatairea macrocarpa

機能・相同性

分子機能:

carbohydrate binding / metal ion binding

ドメイン・相同性:

Legume lectin / Legume lectin, alpha chain, conserved site / Legume lectins alpha-chain signature. / Legume lectins beta-chain signature. / Legume lectin domain / Legume lectin, beta chain, Mn/Ca-binding site / Legume lectin domain / : / Concanavalin A-like lectin/glucanase domain superfamily

構成要素:

Seed lectin

• 生物種: Vatairea macrocarpa (マメ科)
• 引用: ジャーナル: Int J Biochem Cell Biol / 年: 2016; タイトル: Structural characterization of a Vatairea macrocarpa lectin in complex with a tumor-associated antigen: A new tool for cancer research.; 著者: Bruno L Sousa / José C Silva-Filho / Prashant Kumar / Melissa A Graewert / Ronniery I Pereira / Rodrigo M S Cunha / Kyria S Nascimento / Gustavo A Bezerra / Plínio Delatorre / Kristina Djinovic-Carugo / Celso S Nagano / Karl Gruber / Benildo S Cavada / ; 要旨: Legume lectins are the most thoroughly studied group of lectins and have been widely linked to many pathological processes. Their use as immunohistochemistry markers for cell profiling and cancer diagnosis have made these molecules important tools for immunological studies and have stimulated the prospection and characterization of new lectins. The crystal structures of a recombinant seed lectin from Vatairea macrocarpa (rVML) and its complexes with GalNAcα1-O-Ser, GalNAc and α-lactose, have been determined at 1.90, 1.97, 2.70 and 1.83Å resolution, respectively. Small angle X-ray scattering and calorimetry assays have confirmed the same pH stable oligomerization pattern and binding profiles proposed for its wild-type counterpart. In silico analyzes have explored the potential of this recombinant lectin as new tool for cancer research through a comparative profile with other legume lectins widely used for cancer diagnosis and prognosis. The results suggest the recognition of specific epitopes exhibited on different cancer cells as a process that relies on the disposition of hydrophobic clusters and charged regions around the lectin carbohydrate-binding site, favouring the anchorage of different groups in the antigen boundaries, highlighting the different potential of each analyzed lectin. In conclusion, the experimental results and comparative analysis show that rVML is as a promising tool for cancer research, able to bind with high affinity specific tumor-associated antigens, highly stable and easily produced.

登録者

• Melissa Graewert (EMBL-Hamburg, European Molecular Biology Laboratory (EMBL) - Hamburg outstation, Notkestraße 85, Geb. 25A, 22607 Hamburg, Deutschland, Germany)

モデル

• モデル #416: ; タイプ: atomic / ソフトウェア: CORAL / ダミー原子の半径: 1.90 A / カイ2乗値: 0.920; 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: Recombinant Tn antigen-binding lectin from Vatairea macrocarpa; 試料濃度: 1.00-10.00
• バッファ: 名称: sodium phosphate / 濃度: 100.00 mM / pH: 5 / 組成: 150 mM NaCl, 5% v/v glycerol

要素 #273

名称: vRML / タイプ: protein / 記述: Recombinant Tn antigen-binding lectin / 分子量: 26.213 / 分子数: 4 / 由来: Vatairea macrocarpa / 参照: UniProt: P81371
配列:

SEVVSYSFTK FNPNPKDIIL QGDALVTSKG KLQLTKVKDG KPVDHSLGRA LYAAPIHIWD DSTDRVASFA TSFSFVVEAP DESKTADGIA FFLAPPDTQP QKDGGFLGLF NDSNKSIQTV AVEFDTFSNT WDPSARHIGI NVNSIESMKY VKWGWENGKV ANVYISYEAS TKTLTASLTY PSNATSYIVS ANVDLKSALP EWVRVGFSAT SGLSRDHVET HDVLDWSFTS TLQAPSDDSN

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

タイトル: Tn antigen-binding lectin from V. macrocarpa. / 測定日: 2014年1月11日 / 保管温度: 10 °C / 照射時間: 0.05 sec. / フレーム数: 20 / 単位: 1/nm /

	Min	Max
Q	0.0199	4.4962

距離分布関数 P(R)

ソフトウェア P(R): GNOM 5.0 / ポイント数: 978 /

	Min	Max
Q	0.0778983	2.65196
P(R) point	1	978
R	0	9.5

結果

カーブのタイプ: single_conc
コメント: Note: Carries a tyrosine mutation, instead of phenylalanine, at position 6 (F6Y - cf UniProt P81371).

	実験値	Standard	Porod
分子量	100 kDa	70 kDa	100 kDa
体積	-	-	168 nm3

	P(R)	P(R) error	Guinier	Guinier error
前方散乱 I0	1787	1.8	1813.1	2.8
慣性半径, Rg	3.13 nm	0.02	3.17 nm	0.4

	Min	Max
D	-	9.5
Guinier point	23	148