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)	Category	Clashscore	DI	INF all	INF nwc	INF stacking	INF wc	MCQ	RMSD
1	Bujnicki Group (Bujnicki )	2	Human	12.380	2.805	0.820	0.000	0.794	0.919	23.750	2.300
2	Bujnicki Group (Bujnicki )	3	Human	0.310	2.854	0.816	0.000	0.783	0.919	23.690	2.329
3	Das Group (Das )	1	Human	14.230	2.861	0.872	0.000	0.863	0.961	13.560	2.496
4	Dokholyan Group (Dokholyan )	1	Human	12.100	3.074	0.827	0.000	0.806	0.904	12.610	2.543
5	Bujnicki Group (Bujnicki )	1	Human	10.520	2.968	0.894	-	0.873	0.961	17.130	2.653
6	Chen Group (Chen )	1	Human	16.790	3.722	0.760	-	0.699	0.904	24.180	2.830
7	Das Group (Das )	4	Human	16.710	3.415	0.830	0.000	0.797	0.973	14.410	2.834
8	Major Group (Major )	1	Human	125.890	3.785	0.787	-	0.717	0.946	25.380	2.980
9	Das Group (Das )	3	Human	17.330	3.656	0.830	0.000	0.803	0.973	13.350	3.034
10	Das Group (Das )	2	Human	16.710	3.672	0.830	0.000	0.819	0.973	13.630	3.048
11	Das Group (Das )	5	Human	17.950	4.166	0.832	0.000	0.813	0.959	13.040	3.464
12	Wildauer Group (Wildauer )	1	Human	153.530	4.403	0.790	0.000	0.772	0.889	24.750	3.479
13	Santalucia Group (Santalucia )	1	Human	18.910	4.515	0.809	-	0.759	0.922	18.710	3.650

Group (User)

Model(s)

Metric	Webserver category		Human category
Metric	Median	Mean	Median	Mean
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

Puzzle PZ2