Bioisis

"U2AF65 RRM1-RRM2, with N- and C-terminal flanking sequences"

Experimental SAS Curve

Your browser doesn't support canvas.

Low_res_thumbnail

Experimental Mass

23,420 Da

Experimental Details for BID:  2U2FKP
Experiment ID: 86
Collected at: ALS BL 12.3.1
Contributors: Jenkins, JL ,  Kielkopf, CL ,  Laird, KM
SAXS profile of human U2AF65 RRM1-RRM2, residues 136-347, with N-terminal 'GPLGS' sequence from protease site. This residue range includes 12 residues N-terminal to RRM1 and 11 residues C-terminal to RRM2. Sample was purified by gel filtration and homogeneity was verified by dynamic light scattering prior to data collection.
Samples at 5 or 10 mg/mL were used for 6s and 60s exposures, followed by a 6s exposure to check for radiation damage. Appropriate resolution ranges of the exposures and concentrations were merged in the final data file.

Electron Pair Distribution

Your browser doesn't support canvas.

       Dmax → 85 Å


Guinier Plot

Your browser doesn't support canvas.

     Guinier Rg → 24.6 Å

Real Space Rg → 25.6 Å

The Guinier plot is used to estimate the radius of gyration, Rg, which is taken from the slope of a line observed at low scattering angles (typically in the range where q* Rg < 1.3). This should be in reasonable agreement with the real space Rg.


Kratky Plot

Your browser doesn't support canvas.

The Kratky plot can be used to visually assess the degree of "unfoldedness" of a protein or RNA sample. The plot of a well-behaved folded protein approaches the baseline at high q values creating a parabolic shape.


Ensemble Model

A ENSEMBLE model was determined using the following:

Simulation MethodGAJOE 
Simulation AlgorithmGenetic Algorithm Judging Optimization of Ensembles 
Ensemble Size10000 
Selection MethodEOM 
Member Size
Scoring FunctionChi Squared 
Score1.1 

Ensemble Fit

Med_res_ensemble_fit

The red line is the calculated SAXS profile from the ENSEMBLE model scaled to the experimental SAXS curve (cyan).

Supportive Diagnostic Figure for ENSEMBLE Selection

Diagnostic

Fig: The radii of gyration (RG) of the structures are plotted on the x-axis, against the frequency with which a structure of a given RG occurs in the selected ensemble on the y-axis. Gray dashed lines represent the randomized starting pool of structures. Solid lines are the selected pool (2 PDB ensemble - best fit when compared with 3,4,5,20-PDB) showing the presence of two major types of conformations


Additional Experimental Details
Title

U2AF65 RRM1-RRM2, with N- and C-terminal flanking sequences

Description

SAXS profile of human U2AF65 RRM1-RRM2, residues 136-347, with N-terminal 'GPLGS' sequence from protease site. This residue range includes 12 residues N-terminal to RRM1 and 11 residues C-terminal to RRM2. Sample was purified by gel filtration and homogeneity was verified by dynamic light scattering prior to data collection.

Publication

Major Contribution of Elongated Conformations to the Solution Ensemble of the Essential Splicing Factor U2AF65, submitted

Contributors

Jenkins, JL ,  Kielkopf, CL ,  Laird, KM

Genomics and Proteomics

The experiment is composed of a single gene/ORF

Abbreviated name: U2AF65FIR

Annotation: RNA recognition motif domains RRM1 and RRM2 of essential pre-mRNA splicing factor U2AF65, with 11-12 flanking residues and 'GPLGS' from cloning site

GPLGSPVPVV GSQMTRQARR LYVGNIPFGI TEEAMMDFFN AQMRLGGLTQ APGNPVLAVQ INQDKNFAFL EFRSVDETTQ AMAFDGIIFQ GQSLKIRRPH DYQPLPGMSE NPSVYVPGVV STVVPDSAHK LFIGGLPNYL NDDQVKELLT SFGPLKAFNL VKDSATGLSK GYAFCEYVDI NVTDQAIAGL NGMQLGDKKL LVQRASVGAK NATLVSP
categoryamino acid composition(%)
HydrophobicI(4.1) V(9.2) L(9.7) M(3.2) A(7.8) G(9.7) P(6.9)
AromaticF(5.5) W(0.0) Y(2.8)
HydrophilicR(3.7) K(4.6) E(3.2) D(5.5) Q(6.5) N(5.5) H(0.9) S(6.0) T(4.6) C(0.5)