RNA-Puzzles

Description

The crystal structure shows a 100 nt square that assembles from four inner and four outer strands. The secondary structure shown was used for the design of the square. Actual base pairing in the crystal may deviate. 3D coordinates of the nucleotides in the inner strands (B,D,F,H) were provided. What are the structures of the outer strands (A,C,E,G)?

RNA sequence (5' to 3')

CCGGAGGAACUACUG-CCGGCAGCCU-CCGGAGGAACUACUG-CCGGCAGCCU-CCGGAGGAACUACUG-CCGGCAGCCU-CCGGAGGAACUACUG-CCGGCAGCCU

Experimental structure(s)

Z5r1hJd6Jz3CYuEPCWYu3hVn6EUvL07g-solutionPZ2.pdb

References

S.M. Dibrov, J. McLean, J. Parsons and T. Hermann (2011). Self-assembling RNA square. PNAS 108: 6405-6408.

PDB ID:

3p59

Opening date:

19 Oct 2020, 23:24

Closing date (Human category):

19 Oct 2020, 23:24

#	Group (User)	Model(s)	Clashscore	DI	INF all	INF nwc	INF stacking	INF wc	MCQ	RMSD
1	Bujnicki Group (Bujnicki )	2	12.380	2.805	0.820	0.000	0.794	0.919	23.750	2.300
2	Bujnicki Group (Bujnicki )	3	0.310	2.854	0.816	0.000	0.783	0.919	23.690	2.329
3	Das Group (Das )	1	14.230	2.861	0.872	0.000	0.863	0.961	13.560	2.496
4	Dokholyan Group (Dokholyan )	1	12.100	3.074	0.827	0.000	0.806	0.904	12.610	2.543
5	Bujnicki Group (Bujnicki )	1	10.520	2.968	0.894	-	0.873	0.961	17.130	2.653
6	Chen Group (Chen )	1	16.790	3.722	0.760	-	0.699	0.904	24.180	2.830
7	Das Group (Das )	4	16.710	3.415	0.830	0.000	0.797	0.973	14.410	2.834
8	Major Group (Major )	1	125.890	3.785	0.787	-	0.717	0.946	25.380	2.980
9	Das Group (Das )	3	17.330	3.656	0.830	0.000	0.803	0.973	13.350	3.034
10	Das Group (Das )	2	16.710	3.672	0.830	0.000	0.819	0.973	13.630	3.048

Group (User)

Model(s)

Clashscore

INF all

INF nwc

INF stacking

INF wc

MCQ

P-Value

RMSD

Details

Bujnicki Group (Bujnicki )

12.380

2.805

0.820

0.000

0.794

0.919

23.750

0.000

2.300

Bujnicki Group (Bujnicki )

0.310

2.854

0.816

0.000

0.783

0.919

23.690

0.000

2.329

Das Group (Das )

14.230

2.861

0.872

0.000

0.863

0.961

13.560

0.000

2.496

Dokholyan Group (Dokholyan )

12.100

3.074

0.827

0.000

0.806

0.904

12.610

0.000

2.543

Bujnicki Group (Bujnicki )

10.520

2.968

0.894

0.873

0.961

17.130

0.000

2.653

Chen Group (Chen )

16.790

3.722

0.760

0.699

0.904

24.180

0.000

2.830

Das Group (Das )

16.710

3.415

0.830

0.000

0.797

0.973

14.410

0.000

2.834

Major Group (Major )

125.890

3.785

0.787

0.717

0.946

25.380

0.000

2.980

Das Group (Das )

17.330

3.656

0.830

0.000

0.803

0.973

13.350

0.000

3.034

Das Group (Das )

16.710

3.672

0.830

0.000

0.819

0.973

13.630

0.000

3.048

Metric	Webserver category	Human category
Clashscore	-	-	16.710	33.335
DI	-	-	3.656	3.530
INF all	-	-	0.827	0.823
INF nwc	-	-	0.000	0.000
INF stacking	-	-	0.797	0.792
INF wc	-	-	0.946	0.939
MCQ	-	-	17.130	18.322
P-Value	-	-	0.000	0.000
RMSD	-	-	2.834	2.895

Metric

Webserver category

Human category

Median

Mean

Median

Mean

Clashscore

16.710

33.335

3.656

3.530

INF all

0.827

0.823

INF nwc

0.000

INF stacking

0.797

0.792

INF wc

0.946

0.939

MCQ

17.130

18.322

P-Value

0.000

RMSD

2.834

2.895

Puzzle PZ2