SASDE33: Unlabeled nuclear pore complex protein Nup153 (NUL) with denaturant

基本情報

• 登録情報: データベース: SASBDB / ID: SASDE33

試料

Unlabeled nuclear pore complex protein Nup153 (NUL) with denaturant

• Nuclear pore complex protein Nup153核膜孔 (protein), NUL, Homo sapiens

機能・相同性

分子機能:

negative regulation of RNA export from nucleus / nuclear pore complex assembly / Nuclear Pore Complex (NPC) Disassembly / nuclear inclusion body / nuclear pore nuclear basket / Transport of Ribonucleoproteins into the Host Nucleus / Regulation of Glucokinase by Glucokinase Regulatory Protein / Defective TPR may confer susceptibility towards thyroid papillary carcinoma (TPC) / Transport of the SLBP independent Mature mRNA / Transport of the SLBP Dependant Mature mRNA / NS1 Mediated Effects on Host Pathways / SUMOylation of SUMOylation proteins / Transport of Mature mRNA Derived from an Intronless Transcript / structural constituent of nuclear pore / Rev-mediated nuclear export of HIV RNA / 宿主 / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / RNA export from nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / nucleocytoplasmic transport / Viral Messenger RNA Synthesis / nuclear localization sequence binding / SUMOylation of ubiquitinylation proteins / Vpr-mediated nuclear import of PICs / SUMOylation of DNA replication proteins / Regulation of HSF1-mediated heat shock response / mRNA transport / SUMOylation of DNA damage response and repair proteins / 核膜孔 / protein-membrane adaptor activity / SUMOylation of chromatin organization proteins / nuclear periphery / HCMV Late Events / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / HCMV Early Events / protein import into nucleus / viral penetration into host nucleus / 核膜 / snRNP Assembly / 核膜 / symbiont entry into host cell / 核小体 / SARS-CoV-2 activates/modulates innate and adaptive immune responses / DNA binding / 核質 / 生体膜 / identical protein binding / metal ion binding / 細胞質基質

ドメイン・相同性:

Nucleoporin Nup153, N-terminal / Retro-transposon transporting motif / Nucleoporin Nup153-like / Retro-transposon transporting motif / Nuclear pore complex protein / Zinc finger domain / Zn-finger in Ran binding protein and others / Zinc finger RanBP2 type profile. / Zinc finger RanBP2-type signature. / Zinc finger, RanBP2-type superfamily / Zinc finger, RanBP2-type

構成要素:

Nuclear pore complex protein Nup153

• 生物種: Homo sapiens (ヒト)
• 引用: ジャーナル: Proc Natl Acad Sci U S A / 年: 2017; タイトル: Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements.; 著者: Gustavo Fuertes / Niccolò Banterle / Kiersten M Ruff / Aritra Chowdhury / Davide Mercadante / Christine Koehler / Michael Kachala / Gemma Estrada Girona / Sigrid Milles / Ankur Mishra / Patrick R Onck / Frauke Gräter / Santiago Esteban-Martín / Rohit V Pappu / Dmitri I Svergun / Edward A Lemke / ; 要旨: Unfolded states of proteins and native states of intrinsically disordered proteins (IDPs) populate heterogeneous conformational ensembles in solution. The average sizes of these heterogeneous systems, quantified by the radius of gyration ( ), can be measured by small-angle X-ray scattering (SAXS). Another parameter, the mean dye-to-dye distance ( ) for proteins with fluorescently labeled termini, can be estimated using single-molecule Förster resonance energy transfer (smFRET). A number of studies have reported inconsistencies in inferences drawn from the two sets of measurements for the dimensions of unfolded proteins and IDPs in the absence of chemical denaturants. These differences are typically attributed to the influence of fluorescent labels used in smFRET and to the impact of high concentrations and averaging features of SAXS. By measuring the dimensions of a collection of labeled and unlabeled polypeptides using smFRET and SAXS, we directly assessed the contributions of dyes to the experimental values and For chemically denatured proteins we obtain mutual consistency in our inferences based on and , whereas for IDPs under native conditions, we find substantial deviations. Using computations, we show that discrepant inferences are neither due to methodological shortcomings of specific measurements nor due to artifacts of dyes. Instead, our analysis suggests that chemical heterogeneity in heteropolymeric systems leads to a decoupling between and that is amplified in the absence of denaturants. Therefore, joint assessments of and combined with measurements of polymer shapes should provide a consistent and complete picture of the underlying ensembles.

登録者

• Gustavo Fuertes Vives (Institute of Biotechnology CAS v.v.i.)

モデル

• モデル #2295: ; タイプ: atomic / ソフトウェア: (CAMPARI); コメント: p-acetylphenylalanine was replaced with a cysteine.; カイ2乗値: 0.719 / P-value: 0.097643; 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 #2296: ; タイプ: atomic / ソフトウェア: (CAMPARI); コメント: p-acetylphenylalanine was replaced with a cysteine.; カイ2乗値: 0.719 / P-value: 0.097643; 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 #2297: ; タイプ: atomic / ソフトウェア: (CAMPARI); コメント: p-acetylphenylalanine was replaced with a cysteine.; カイ2乗値: 0.719 / P-value: 0.097643; 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 #2298: ; タイプ: atomic / ソフトウェア: (CAMPARI); コメント: p-acetylphenylalanine was replaced with a cysteine.; カイ2乗値: 0.719 / P-value: 0.097643; 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: Unlabeled nuclear pore complex protein Nup153 (NUL) with denaturant; 試料濃度: 10 mg/ml
• バッファ: 名称: PBS, 10 mM DTT, 6 M urea, 0.3 M KCl / pH: 7.4

要素 #1240

名称: NUL / タイプ: protein / 記述: Nuclear pore complex protein Nup153核膜孔 / 分子量: 11.717 / 分子数: 1 / 由来: Homo sapiens / 参照: UniProt: P49790
配列:

GCGFKGFDTS SSSSNSAASS SFKFGVSSSS SGPSQTLTST GNFKFGDQGG FKIGVSSDSG SINPMSEGFK FSKPIGDFKF GVSSESKPEE VKKDSKNDNF KFGLSSGLSN PVUA

実験情報

• ビーム: 設備名称: PETRA III EMBL P12 / 地域: Hamburg / 国: Germany / 線源: X-ray synchrotronシンクロトロン / 波長: 0.1 Å / スペクトロメータ・検出器間距離: 3 mm
• 検出器: 名称: Pilatus 2M

スキャン

タイトル: Unlabeled nuclear pore complex protein Nup153 (NUL) with denaturant (urea 6 M)
測定日: 2013年11月8日 / セル温度: 23 °C / 照射時間: 0.05 sec. / フレーム数: 20 / 単位: 1/nm /

	Min	Max
Q	0.0291	4.4884

距離分布関数 P(R)

ソフトウェア P(R): GNOM 5.0 / ポイント数: 543 /

	Min	Max
Q	0.0580383	1.48567
P(R) point	1	543
R	0	16

結果

カーブのタイプ: single_conc
コメント: The protein contains a penultimate non-canonical amino acid p-acetylphenylalanine (207 Da) that is represented as U (selenocysteine, 168 Da) in the amino acid sequence for the entry. Therefore, the calculated MW from sequence (MW(expected)) must be adjusted accordingly (ca. 40 Da).

	実験値	Porod
分子量	12 kDa	-
体積	-	53 nm3

	P(R)	P(R) error	Guinier	Guinier error
前方散乱 I0	825.1	8.5	807.4	4.3
慣性半径, Rg	3.947 nm	0.09	3.5 nm	0.3

	Min	Max
D	-	16
Guinier point	12	128