SASDEJ8: Human Guanylate Binding Protein 1 (hGBP1), dimer from SEC-SAXS

基本情報

• 登録情報: データベース: SASBDB / ID: SASDEJ8

試料

Human Guanylate Binding Protein 1 (hGBP1), dimer from SEC-SAXS

• human Guanylate-binding protein 1 (protein), hGBP1, Homo sapiens

機能・相同性

分子機能:

GDP phosphatase activity / non-canonical inflammasome complex assembly / protein localization to vacuole / negative regulation of substrate adhesion-dependent cell spreading / symbiont cell surface / cytolysis in another organism / positive regulation of pyroptotic inflammatory response / vesicle membrane / negative regulation of T cell receptor signaling pathway / negative regulation of interleukin-2 production / spectrin binding / defense response to protozoan / cytokine binding / 加水分解酵素; 酸無水物に作用; リン含有酸無水物に作用 / cellular response to interleukin-1 / regulation of protein localization to plasma membrane / negative regulation of protein localization to plasma membrane / regulation of calcium-mediated signaling / lipopolysaccharide binding / Hsp90 protein binding / cytoplasmic vesicle membrane / cellular response to type II interferon / G protein activity / negative regulation of ERK1 and ERK2 cascade / Interferon gamma signaling / GDP binding / actin cytoskeleton / cellular response to tumor necrosis factor / actin binding / cytoplasmic vesicle / 加水分解酵素; 酸無水物に作用; GTPに作用・細胞または細胞小器官の運動に関与 / defense response to virus / defense response to bacterium / Golgi membrane / innate immune response / GTPase activity / GTP binding / Golgi apparatus / enzyme binding / protein homodimerization activity / extracellular region / identical protein binding / plasma membrane / cytosol / cytoplasm

ドメイン・相同性:

Guanylate-binding protein, C-terminal / Guanylate-binding protein/Atlastin, C-terminal / Guanylate-binding protein, C-terminal domain / Guanylate-binding protein, N-terminal / Guanylate-binding protein, C-terminal domain superfamily / Guanylate-binding protein, N-terminal domain / GB1/RHD3-type guanine nucleotide-binding (G) domain / GB1/RHD3-type guanine nucleotide-binding (G) domain profile. / P-loop containing nucleoside triphosphate hydrolase

構成要素:

Guanylate-binding protein 1

• 生物種: Homo sapiens (ヒト)
• 引用: ジャーナル: FEBS J / 年: 2020; タイトル: Farnesylation of human guanylate-binding protein 1 as safety mechanism preventing structural rearrangements and uninduced dimerization.; 著者: Charlotte Lorenz / Semra Ince / Tao Zhang / Anneliese Cousin / Renu Batra-Safferling / Luitgard Nagel-Steger / Christian Herrmann / Andreas M Stadler / ; 要旨: Human guanylate-binding protein 1 (hGBP1) belongs to the family of dynamin-like proteins and is activated by addition of nucleotides, leading to protein oligomerization and stimulated GTPase activity. In vivo, hGBP1 is post-translationally modified by attachment of a farnesyl group yielding farn-hGBP1. In this study, hydrodynamic differences in farn-hGBP1 and unmodified hGBP1 were investigated using dynamic light scattering (DLS), analytical ultracentrifugation (AUC) and analytical size-exclusion chromatography (SEC). In addition, we performed small-angle X-ray scattering (SAXS) experiments coupled with a SEC setup (SEC-SAXS) to investigate structural properties of nonmodified hGBP1 and farn-hGBP1 in solution. SEC-SAXS measurements revealed that farnesylation keeps hGBP1 in its inactive monomeric and crystal-like conformation in nucleotide-free solution, whereas unmodified hGBP1 forms a monomer-dimer equilibrium both in the inactive ground state in nucleotide-free solution as well as in the activated state that is trapped by addition of the nonhydrolysable GTP analogue GppNHp. Nonmodified hGBP1 is structurally perturbed as compared to farn-hGBP. In particular, GppNHp binding leads to large structural rearrangements and higher conformational flexibility of the monomer and the dimer. Structural changes observed in the nonmodified protein are prerequisites for further oligomer assemblies of farn-hGBP1 that occur in the presence of nucleotides. DATABASE: All SEC-SAXS data, corresponding fits to the data and structural models are deposited in the Small Angle Scattering Biological Data Bank [SASBDB (Nucleic Acids Res, 43, 2015, D357)] with project IDs: SASDEE8, SASDEF8, SASDEG8, SASDEH8, SASDEJ8, SASDEK8, SASDEL8 and SASDEM8.

登録者

• Charlotte Lorenz (Forschungszentrum Jülich, Germany)

モデル

• モデル #2217: ; タイプ: atomic / カイ2乗値: 12.841; 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 #2220: ; タイプ: atomic / カイ2乗値: 0.91 / P-value: 0.000001; 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 Guanylate Binding Protein 1 (hGBP1), dimer from SEC-SAXS; 試料濃度: 16 mg/ml
• バッファ: 名称: 50 mM Tris-HCl, 5 mM MgCl2, 150 mM NaCl / pH: 7.9

要素 #1224

名称: hGBP1 / タイプ: protein / 記述: human Guanylate-binding protein 1 / 分子量: 69.169 / 分子数: 2 / 由来: Homo sapiens / 参照: UniProt: P32455
配列:

MRGSHHHHHH GSASEIHMTG PMCLIENTNG RLMANPEALK ILSAITQPMV VVAIVGLYRT GKSYLMNKLA GKKKGFSLGS TVQSHTKGIW MWCVPHPKKP GHILVLLDTE GLGDVEKGDN QNDSWIFALA VLLSSTFVYN SIGTINQQAM DQLYYVTELT HRIRSKSSPD ENENEVEDSA DFVSFFPDFV WTLRDFSLDL EADGQPLTPD EYLTYSLKLK KGTSQKDETF NLPRLCIRKF FPKKKCFVFD RPVHRRKLAQ LEKLQDEELD PEFVQQVADF CSYIFSNSKT KTLSGGIQVN GPRLESLVLT YVNAISSGDL PCMENAVLAL AQIENSAAVQ KAIAHYEQQM GQKVQLPTES LQELLDLHRD SEREAIEVFI RSSFKDVDHL FQKELAAQLE KKRDDFCKQN QEASSDRCSG LLQVIFSPLE EEVKAGIYSK PGGYRLFVQK LQDLKKKYYE EPRKGIQAEE ILQTYLKSKE SMTDAILQTD QTLTEKEKEI EVERVKAESA QASAKMLQEM QRKNEQMMEQ KERSYQEHLK QLTEKMENDR VQLLKEQERT LALKLQEQEQ LLKEGFQKES RIMKNEIQDL QTKMRRRKAC TIS

実験情報

• ビーム: 設備名称: ESRF BM29 / 地域: Grenoble / 国: France / 線源: X-ray synchrotron / 波長: 0.09919 Å / スペクトロメータ・検出器間距離: 2.867 mm
• 検出器: 名称: Pilatus 1M / タイプ: Dectris / Pixsize x: 172 mm

スキャン

タイトル: Human Guanylate Binding Protein 1 (hGBP1), dimer from SEC-SAXS
測定日: 2017年4月30日 / 保管温度: 20 °C / セル温度: 20 °C / 照射時間: 1 sec. / フレーム数: 3600 / 単位: 1/nm /

	Min	Max
Q	0.0327	4.9445

距離分布関数 P(R)

ソフトウェア P(R): GNOM 5.0 / ポイント数: 777 /

	Min	Max
Q	0.141078	3.799
P(R) point	1	777
R	0	15.61

結果

カーブのタイプ: single_conc

	実験値	Porod
分子量	130.95 kDa	132.01 kDa
体積	-	211.21 nm3

	P(R)	Guinier	Guinier error
前方散乱 I0	30.41	30.77	0.048
慣性半径, Rg	4.725 nm	4.79 nm	1.56

	Min	Max
D	-	15.61
Guinier point	24	41