SASDET2: Unlabeled Importin Beta Binding Domain (IBB) from importin subuni...

Basic information

• Entry: Database: SASBDB / ID: SASDET2

Sample

Unlabeled Importin Beta Binding Domain (IBB) from importin subunit alpha-1 with denaturant

• Importin subunit alpha-1 (protein), IBB, Homo sapiens

Function / homology

Function:

Sensing of DNA Double Strand Breaks / regulation of DNA recombination / entry of viral genome into host nucleus through nuclear pore complex via importin / positive regulation of viral life cycle / NS1 Mediated Effects on Host Pathways / NLS-dependent protein nuclear import complex / host cell / CREB1 phosphorylation through the activation of CaMKII/CaMKK/CaMKIV cascasde / nuclear import signal receptor activity / nuclear localization sequence binding / DNA metabolic process / CaMK IV-mediated phosphorylation of CREB / NLS-bearing protein import into nucleus / ISG15 antiviral mechanism / protein import into nucleus / histone deacetylase binding / SARS-CoV-1 activates/modulates innate immune responses / nuclear membrane / Estrogen-dependent gene expression / Golgi membrane / endoplasmic reticulum membrane / SARS-CoV-2 activates/modulates innate and adaptive immune responses / RNA binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm

Domain/homology:

Importin subunit alpha / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain superfamily / Importin beta binding domain / Atypical Arm repeat / Importin-alpha, importin-beta-binding domain / IBB domain profile. / Armadillo/plakoglobin ARM repeat profile. / Armadillo/beta-catenin-like repeat / Armadillo/beta-catenin-like repeats / Armadillo / Armadillo-like helical / Armadillo-type fold

Component:

Importin subunit alpha-1

• 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 #2276: ; Type: atomic / Software: (CAMPARI); Comment: p-acetylphenylalanine was replaced with a cysteine.; Chi-square value: 1.037 / P-value: 0.098745; Search similar-shape structures of this assembly by Omokage search (details)
• Model #2277: ; Type: atomic / Software: (CAMPARI); Comment: p-acetylphenylalanine was replaced with a cysteine.; Chi-square value: 1.037 / P-value: 0.098745; Search similar-shape structures of this assembly by Omokage search (details)
• Model #2278: ; Type: atomic; Comment: p-acetylphenylalanine was replaced with a cysteine.; Chi-square value: 1.037 / P-value: 0.098745; Search similar-shape structures of this assembly by Omokage search (details)
• Model #2279: ; Type: atomic; Comment: p-acetylphenylalanine was replaced with a cysteine.; Chi-square value: 1.037 / P-value: 0.098745; Search similar-shape structures of this assembly by Omokage search (details)
• Model #2280: ; Type: atomic; Comment: p-acetylphenylalanine was replaced with a cysteine.; Chi-square value: 1.037 / P-value: 0.098745; Search similar-shape structures of this assembly by Omokage search (details)
• Model #2281: ; Type: atomic / Software: (CAMPARI); Comment: p-acetylphenylalanine was replaced with a cysteine.; Chi-square value: 1.037 / P-value: 0.098745; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Unlabeled Importin Beta Binding Domain (IBB) from importin subunit alpha-1 with denaturant; Specimen concentration: 10 mg/ml
• Buffer: Name: PBS, 10 mM DTT, 6 M urea, 0.3 M KCl / pH: 7.4

Entity #1234

Name: IBB / Type: protein / Description: Importin subunit alpha-1 / Formula weight: 11.275 / Num. of mol.: 1 / Source: Homo sapiens / References: UniProt: P52292
Sequence:

GCTNENANTP AARLHRFKNK GKDSTEMRRR RIEVNVELRK AKKDDQMLKR RNVSSFPDDA TSPLQENRNN QGTVNWSVDD IVKGINSSNV ENQLQATUA

Experimental information

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

Scan

Title: Unlabeled Importin Beta Binding Domain (IBB) from importin subunit alpha-1 with denaturant (urea 6 M)
Measurement date: Jun 15, 2013 / Cell temperature: 23 °C / Exposure time: 0.05 sec. / Number of frames: 20 / Unit: 1/nm /

	Min	Max
Q	0.0768	4.5832

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 624 /

	Min	Max
Q	0.0951749	1.73414
P(R) point	1	624
R	0	15.32

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	17.4 kDa	-
Volume	-	33.92 nm3

	P(R)	P(R) error	Guinier	Guinier error
Forward scattering, I0	647.5	2.3	631.4	2
Radius of gyration, Rg	3.493 nm	0.03	3.12 nm	0.07

	Min	Max
D	-	15.32
Guinier point	8	130