SASDD25: 1:1 Mixture between Protein sex-lethal mutant (Sxl10GS) and RNA d...

基本情報

• 登録情報: データベース: SASBDB / ID: SASDD25

試料

1:1 Mixture between Protein sex-lethal mutant (Sxl10GS) and RNA decaneucleotide UGU8

• Protein sex-lethal mutant (protein), Sxl10GS, Drosophila melanogaster
• RNA decaneucleotide UGU8 (RNA), UGU8, synthetic construct

機能・相同性

分子機能:

sex determination, primary response to X:A ratio / germarium-derived cystoblast division / epithelium regeneration / female sex determination / somatic sex determination / female germ-line sex determination / oocyte differentiation / imaginal disc growth / regulation of stem cell division / sex determination / negative regulation of RNA export from nucleus / poly-pyrimidine tract binding / sex-chromosome dosage compensation / sex differentiation / alternative mRNA splicing, via spliceosome / negative regulation of receptor signaling pathway via JAK-STAT / poly(A) binding / positive regulation of smoothened signaling pathway / pre-mRNA binding / regulation of mRNA splicing, via spliceosome / reciprocal meiotic recombination / poly(U) RNA binding / regulation of alternative mRNA splicing, via spliceosome / oogenesis / negative regulation of mRNA splicing, via spliceosome / negative regulation of translational initiation / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / mRNA 3'-UTR binding / mRNA 5'-UTR binding / negative regulation of translation / protein stabilization / ribonucleoprotein complex / mRNA binding / protein-containing complex / RNA binding / nucleus / cytosol / cytoplasm

ドメイン・相同性:

Sex-lethal splicing factor / Paraneoplastic encephalomyelitis antigen / RNA recognition motif / RNA recognition motif / Eukaryotic RNA Recognition Motif (RRM) profile. / RNA recognition motif domain / RNA-binding domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily

構成要素:

Protein sex-lethal

• 生物種: Drosophila melanogaster (キイロショウジョウバエ); synthetic construct (人工物)
• 引用: ジャーナル: ACS Comb Sci / 年: 2018; タイトル: A General Small-Angle X-ray Scattering-Based Screening Protocol Validated for Protein-RNA Interactions.; 著者: Po-Chia Chen / Pawel Masiewicz / Vladimir Rybin / Dmitri Svergun / Janosch Hennig / ; 要旨: We present a screening protocol utilizing small-angle X-ray scattering (SAXS) to obtain structural information on biomolecular interactions independent of prior knowledge, so as to complement affinity-based screening and provide leads for further exploration. This protocol categorizes ligand titrations by computing pairwise agreement between curves, and separately estimates affinities by quantifying complex formation as a departure from the linear sum properties of solution SAXS. The protocol is validated by sparse sequence search around the native poly uridine RNA motifs of the two-RRM domain Sex-lethal protein (Sxl). The screening of 35 RNA motifs between 4 to 10 nucleotides reveals a strong variation of resulting complexes, revealed to be preference-switching between 1:1 and 2:2 binding stoichiometries upon addition of structural modeling. Validation of select sequences in isothermal calorimetry and NMR titration retrieves domain-specific roles and function of a guanine anchor. These findings reinforce the suitability of SAXS as a complement in lead identification.

登録者

• Po-chia Chen (EMBL, European Molecular Biology Laboratory (EMBL) - Heidelberg, Heidelberg, Germany)

モデル

• モデル #1877: ; タイプ: mix / ソフトウェア: (2.1) / ダミー原子の半径: 1.90 A / カイ2乗値: 0.777 / P-value: 0.240677; 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 #1878: ; タイプ: mix / ソフトウェア: (2.1) / ダミー原子の半径: 1.90 A / カイ2乗値: 0.777 / P-value: 0.240677; 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 #1879: ; タイプ: mix / ソフトウェア: (2.1) / ダミー原子の半径: 1.90 A / カイ2乗値: 0.777 / P-value: 0.240677; 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: 1:1 Mixture between Protein sex-lethal mutant (Sxl10GS) and RNA decaneucleotide UGU8; 試料濃度: 1 mg/ml / Entity id: 1008 / 1009
• バッファ: 名称: 50% dilution of protein buffer {10 mM KP, 50 mM NaCl, 10 mM DTT pH 6} with {milliQ-water pH 7} suspended RNA; pH: 6

要素 #1008

名称: Sxl10GS / タイプ: protein / 記述: Protein sex-lethal mutant / 分子量: 20.432 / 分子数: 2 / 由来: Drosophila melanogaster / 参照: UniProt: P19339
配列:

GAMASNTNLI VNYLPQDMTD RELYALFRAI GPINTCRIMR DYKTGYSFGY AFVDFTSEMD SQRAIKVLNG ITVRNKRLKV SYARPGGGSG SGGGGSGESI KDTNLYVTNL PRTITDDQLD TIFGKYGSIV QKNILRDKLT GRPRGVAFVR YNKREEAQEA ISALNNVIPE GGSQPLSVRL AEEHGK

要素 #1009

名称: UGU8 / タイプ: RNA / 記述: RNA decaneucleotide UGU8 / 分子量: 3.119 / 分子数: 2 / 由来: synthetic construct
配列:

UGUUUUUUUU

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

スキャン

タイトル: 1:1 Mixture between Protein sex-lethal mutant (Sxl10GS) and RNA decaneucleotide UGU8
測定日: 2017年4月12日 / 保管温度: 20 °C / セル温度: 20 °C / 照射時間: 0.5 sec. / フレーム数: 10 / 単位: 1/nm /

	Min	Max
Q	0.0308	4.9444

距離分布関数 P(R)

ソフトウェア P(R): GNOM 4.5a / ポイント数: 295 /

	Min	Max
Q	0.2087	2.997
P(R) point	1	295
R	0	8.878

結果

カーブのタイプ: single_conc
コメント: This synchrotron session suffered from misalignment of the beamstop resulting in parasitic scattering at low angles. Note that the uploaded EOM ensemble is chosen as the 2:2-complex with one RNA monomer as fully bound by two Sxl10GS molecules in the canonical position from Protein data bankk (PDB) entry 1B7F.pdb. The second RNA monomer is placed in the canonical position bound to the free RRM2, resulting in three rigid bodies: RRM2+RNA, RRM1+RRM2+RNA, and RRM1.

	実験値	Porod
分子量	24 kDa	-
体積	-	40.96 nm3

	P(R)	P(R) error	Guinier	Guinier error
前方散乱 I0	77.67	0.08	76.65	0.13
慣性半径, Rg	2.63 nm	0.004	2.54 nm	0.07

	Min	Max
D	-	8.88
Guinier point	51	92