. Author manuscript; available in PMC: 2013 Jun 6.

Published in final edited form as: Structure. 2012 May 10;20(6):1097–1106. doi: 10.1016/j.str.2012.03.022

Table 2.

Matching NMA conformers

a) Four groups of conformers of U5 snRNP within U4/U6.U5 tri-snRNP.

Conformer information			Body domain pose
Mode A (amplitude)^a	Mode B (amplitude)^a	Matching score^b	Rank	Score
2 (−0.62)	3 (+0.12)	3776
2 (−0.62)	3 (+0.41)	3410	67	2660
2 (−1.00)	1 (−0.13)	2561

2 (−0.62)	4 (+1.00)	3479
2 (−0.23)	4 (+0.29)	2628	1	5147
2 (−0.62)	4 (+0.29)	2476

1 (+0.58)	2 (−0.23)	2318	183	1325
1 (+0.58)	-	1043	183	1325

2 (−0.23)	1 (+0.17)	2054	1	5147
2 (−0.23)	3 (+0.12)	1428	1	5147
1 (+0.58)	4 (+0.29)	1158	183	1325

b) Conformers of U4/U6.U5 tri-snRNP within the native spliceosome^c

Conformer information			Body domain pose
Mode A (amplitude)^a	Mode B (amplitude)^a	Matching score^b	Rank	Score
6 (−1.00)	3 (−0.57)	3193	193	1313
	5 (−0.57)	3143
	3 (−0.35)	3119
	5 (−0.35)	3081

c) Conformers of U5 snRNP within “bound” U4.U6/U5 tri-snRNP

Conformer information			Body domain pose
Mode A (amplitude)^a	Mode B (amplitude)^a	Matching score^b	Rank	Score
5 (−1.00)	7 (−0.38)	5465	67	2660
5 (−1.00)	3 (+0.41)	3398	67	2660

d) Conformers of U2-SF3b within spliceosomeΔ[U4/U6.U5]^d

Conformer Information			Unperturbed particle pose
Mode A (amplitude)^a	Mode B (amplitude)^a	Matching score^b	Rank	Score
1 (+0.13)	3 (+0.13)	4270	1	3674

4 (−0.25)	3 (−0.15)	2611	9	1017

^a)

The normal modes numbering excludes the 6 rigid body modes. The amplitude is given as a fraction of the maximal amplitude determined by the number of clashes and level of distortions (see Methods). The direction of the perturbation from the starting geometry is given by + or −.

^b)

w was set to the calculated value + 0.3.

^c)

The cluster includes 63 configurations. We listed the four configurations with scores exceeding 1185, the limit set for the U4/U6.U5 tri-snRNP body matching.

^d)

Only the two configurations that comply with experimental contact data (see text) are listed.