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

Basic information

• Entry: Database: SASBDB / ID: SASDE33

Sample

Unlabeled nuclear pore complex protein Nup153 (NUL) with denaturant

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

Function / homology

Function:

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 / Nuclear import of Rev protein / SUMOylation of RNA binding proteins / 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 / 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 / nuclear pore / SUMOylation of DNA damage response and repair proteins / protein-membrane adaptor activity / SUMOylation of chromatin organization proteins / nuclear periphery / HCMV Late Events / Transcriptional regulation by small RNAs / molecular condensate scaffold activity / ISG15 antiviral mechanism / HCMV Early Events / viral penetration into host nucleus / protein import into nucleus / host cell / nuclear envelope / snRNP Assembly / nuclear membrane / amyloid fibril formation / symbiont entry into host cell / nucleolus / SARS-CoV-2 activates/modulates innate and adaptive immune responses / DNA binding / nucleoplasm / identical protein binding / membrane / metal ion binding / cytosol

Domain/homology:

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

Component:

Nuclear pore complex protein Nup153

• Biological species: Homo sapiens (human)
• Citation: Journal: Proc Natl Acad Sci U S A / Year: 2017; Title: Decoupling of size and shape fluctuations in heteropolymeric sequences reconciles discrepancies in SAXS vs. FRET measurements.; Authors: 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 / ; Abstract: 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.

Contact author

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

Models

• Model #2295: ; Type: atomic / Software: (CAMPARI); Comment: p-acetylphenylalanine was replaced with a cysteine.; Chi-square value: 0.719 / P-value: 0.097643; Search similar-shape structures of this assembly by Omokage search (details)
• Model #2296: ; Type: atomic / Software: (CAMPARI); Comment: p-acetylphenylalanine was replaced with a cysteine.; Chi-square value: 0.719 / P-value: 0.097643; Search similar-shape structures of this assembly by Omokage search (details)
• Model #2297: ; Type: atomic / Software: (CAMPARI); Comment: p-acetylphenylalanine was replaced with a cysteine.; Chi-square value: 0.719 / P-value: 0.097643; Search similar-shape structures of this assembly by Omokage search (details)
• Model #2298: ; Type: atomic / Software: (CAMPARI); Comment: p-acetylphenylalanine was replaced with a cysteine.; Chi-square value: 0.719 / P-value: 0.097643; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Unlabeled nuclear pore complex protein Nup153 (NUL) with denaturant; Specimen concentration: 10 mg/ml
• Buffer: Name: PBS, 10 mM DTT, 6 M urea, 0.3 M KCl / pH: 7.4

Entity #1240

Name: NUL / Type: protein / Description: Nuclear pore complex protein Nup153 / Formula weight: 11.717 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: P49790
Sequence:

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

Experimental information

• Beam: Instrument name: PETRA III EMBL P12 / City: Hamburg / 国: Germany / Type of source: X-ray synchrotron / Wavelength: 0.1 Å / Dist. spec. to detc.: 3 mm
• Detector: Name: Pilatus 2M

Scan

Title: Unlabeled nuclear pore complex protein Nup153 (NUL) with denaturant (urea 6 M)
Measurement date: Nov 8, 2013 / Cell temperature: 23 °C / Exposure time: 0.05 sec. / Number of frames: 20 / Unit: 1/nm /

	Min	Max
Q	0.0291	4.4884

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 543 /

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

Result

Type of curve: single_conc
Comments: 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).

	Experimental	Porod
MW	12 kDa	-
Volume	-	53 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	825.1	8.5	807.4	4.3
Radius of gyration, Rg	3.947 nm	0.09	3.5 nm	0.3

	Min	Max
D	-	16
Guinier point	12	128