SASDEB3: Unlabeled nuclear pore complex protein Nup98-Nup96 (N98) without ...

基本情報

登録情報

データベース: SASBDB / ID: SASDEB3

試料

Unlabeled nuclear pore complex protein Nup98-Nup96 (N98) without denaturant

• Nuclear pore complex protein Nup98-Nup96 (protein), N98, Homo sapiens

機能・相同性

分子機能:

nuclear pore organization / nuclear pore outer ring / nuclear pore complex assembly / telomere tethering at nuclear periphery / post-transcriptional tethering of RNA polymerase II gene DNA at nuclear periphery / nuclear pore cytoplasmic filaments / 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 / SUMOylation of RNA binding proteins / Nuclear import of Rev protein / RNA export from nucleus / NEP/NS2 Interacts with the Cellular Export Machinery / tRNA processing in the nucleus / Transport of Mature mRNA derived from an Intron-Containing Transcript / Postmitotic nuclear pore complex (NPC) reformation / positive regulation of mRNA splicing, via spliceosome / 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 / 加水分解酵素; プロテアーゼ; ペプチド結合加水分解酵素; セリンエンドペプチターゼ / Regulation of HSF1-mediated heat shock response / mRNA transport / nuclear pore / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / SUMOylation of DNA damage response and repair proteins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / serine-type peptidase activity / SUMOylation of chromatin organization proteins / nuclear periphery / HCMV Late Events / promoter-specific chromatin binding / RHO GTPases Activate Formins / molecular condensate scaffold activity / Transcriptional regulation by small RNAs / ISG15 antiviral mechanism / HCMV Early Events / protein import into nucleus / Separation of Sister Chromatids / nuclear envelope / snRNP Assembly / nuclear membrane / transcription coactivator activity / nuclear body / ribonucleoprotein complex / mRNA binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / proteolysis / RNA binding / nucleoplasm / cytosol

ドメイン・相同性:

Nup98, Gle2-binding sequence / Nuclear pore complex protein NUP96, C-terminal domain / Nuclear protein 96 / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain / Nuclear pore complex protein Nup98-Nup96-like, autopeptidase S59 domain superfamily / Nucleoporin peptidase S59-like / Nucleoporin autopeptidase / NUP C-terminal domain profile.

構成要素:

Nuclear pore complex protein Nup98-Nup96

• 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

試料

• 試料: 名称: Unlabeled nuclear pore complex protein Nup98-Nup96 (N98) without denaturant; 試料濃度: 1.00-10.00
• バッファ: 名称: PBS, 10 mM DTT / pH: 7.4

要素 #1248

名称: N98 / タイプ: protein / 記述: Nuclear pore complex protein Nup98-Nup96 / 分子量: 14.763 / 分子数: 1 / 由来: Homo sapiens / 参照: UniProt: P52948
配列:

GCFNKSFGTP FGGGTGGFGT TSTFGQNTGF GTTSGGAFGT SAFGSSNNTG GLFGNSQTKP GGLFGTSSFS QPATSTSTGF GFGTSTGTAN TLFGTASTGT SLFSSQNNAF AQNKPTGFGN FGTSTSSGGL FGTTNTTSNP FGSTSGSLFG PUA

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 / 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 Nup98-Nup96, Nup98 (N98), without denaturant
測定日: 2015年6月24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	0.1799	4.5256

距離分布関数 P(R)

ソフトウェア P(R): GNOM 5.0 / ポイント数: 992 /

	Min	Max
Q	0.179883	2.79627
P(R) point	1	992
R	0	10.4

結果

カーブのタイプ: extrapolated
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	20 kDa	-
体積	-	27.41 nm3

	P(R)	P(R) error	Guinier	Guinier error
前方散乱 I0	6279	13.6	6123.1	54.7
慣性半径, Rg	3.073 nm	0.01	2.86 nm	0.06

	Min	Max
D	-	10.4
Guinier point	1	105