Changes in PDB files used for clustering

Release 1.15 has 239 PDB files, release 1.16 has 252 PDB files, 238 of them are identical.

1 equivalence classes changed representatives: 4L8R4TUX.

13 new structures in release 1.16: 1VWW, 1VX2, 1VX6, 3J7A, 3WQY, 4KZD, 4LX6, 4OJI, 4PLX, 4QI2, 4QIL, 4UN3, 4UN5.

No equivalence class representatives have been obsoleted.

Help Every Motif Atlas release is based on a representative set of PDB files. When comparing two releases, it's important to know how the input data changed.

Representative sets are quite stable in time, but PDB files from the older releases can be replaced by newer PDB files or removed from the set altogether if the structure is obsoleted by PDB without replacement.

PDB files from the newer release either replace representatives in the existing equivalence classes or come from new equivalence classes.

Redistribution of motif instances

Loading the Sankey diagram...

Changes in motif groups

Release 1.15 has 285 motif groups, release 1.16 has 324 motif groups, 196 of them are identical.

48 motif groups were updated, 41 groups are present only in release 1.15, 80 groups are only in release 1.16.

Help The Sankey diagram shows redistribution of motif instances (loops) between two releases. The rectangles represent the motif groups and are colored as follows:

Added motif groups: green
Removed motif groups: grey
Updated motif groups: orange
Added motif instances: green
Removed motif instances: grey

Hover over the links connecting the motif groups to see which motif instances were exchanged.


Identical motif groups

#Motif idInstancesDescription
1HL_74465.616tRNA Anti-Codon loop
2HL_17723.510LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
3HL_15603.29U1A protein-binding Hairpin Loop.
4HL_42677.27
5HL_72543.36LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
6HL_89236.16LSU Helix 69 (H69) Hairpin Loop
7HL_06643.36tRNA D-loop. Sec tRNA
8HL_72273.15tRNA D-loop
9HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
10HL_08382.45
11HL_78731.25LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
12HL_23182.24
13HL_79956.24GNRA-like with 5'-stacking of first unpaired base.
14HL_19905.44LSU: Part of IL/3WJ between H55 and H56.
15HL_62881.14RNase P Structured Hairpin Loop
16HL_11376.14LSU Helix 8 (H8) Hairpin Loop
17HL_48116.34GNRA-like with 5'-stacking of first unpaired base.
18HL_82418.14LSU Helix 8 (H8) Hairpin Loop
19HL_25124.24tSW GA closed tetraloops
20HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
21HL_92706.14LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
22HL_76766.43
23HL_55684.13
24HL_80492.23tRNA D-loop
25HL_19033.13SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
26HL_06122.23
27HL_78361.13
28HL_84911.13
29HL_91142.13Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
30HL_98833.33
31HL_13707.23cSH AA Platform containing Hairpin Loop
32HL_19221.23
33HL_21545.23LSU Helix 96 (H96) Hairpin Loop
34HL_60200.23
35HL_64371.33SSU Central Pseudoknot (forms helix 2)
36HL_74307.13
37HL_91693.23
38HL_06997.23
39HL_27429.43
40HL_41827.13
41HL_58083.33
42HL_65249.23
43HL_95969.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
44HL_50312.12
45HL_65924.12
46HL_87554.12
47HL_23290.12
48HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
49HL_50937.12
50HL_05361.12
51HL_20004.12
52HL_26495.12
53HL_33451.12
54HL_38964.12LSU Helix 84 (H84) Hairpin Loop. E.coli.
55HL_42553.12
56HL_98577.12
57HL_24473.32tRNA D-loop
58HL_93771.12tRNA T-loop distorted by RS binding
59HL_34912.12
60HL_49210.12
61HL_24711.12
62HL_41700.12
63HL_64438.12Kink-turn-like Hairpin Loop
64HL_92635.12
65HL_84172.12
66HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
67HL_19399.12
68HL_27478.12
69HL_38130.22
70HL_42077.32LSU Helix 28 (H28) Hairpin Loop
71HL_04305.11
72HL_10116.11Kink-turn-like Hairpin Loop
73HL_17537.11
74HL_19452.11tRNA D-loop
75HL_25195.11
76HL_30008.11
77HL_38138.11
78HL_42345.11
79HL_46570.11
80HL_55272.11
81HL_59182.11
82HL_62880.11
83HL_84720.11
84HL_93428.11
85HL_97022.11
86HL_04979.11LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
87HL_11337.11
88HL_25197.11
89HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
90HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
91HL_47337.11
92HL_59225.11
93HL_66877.11cSH GU/cWS double platform, intercalation site
94HL_72389.11
95HL_77692.11tRNA D-loop
96HL_84768.11
97HL_88960.11
98HL_93530.11
99HL_97784.11
100HL_24108.11
101HL_52116.11
102HL_56775.11
103HL_59610.11
104HL_63997.11
105HL_67000.11
106HL_78228.11
107HL_82243.11
108HL_84888.11T-loop like but without tWH UA
109HL_93567.11
110HL_12706.11
111HL_19132.11
112HL_20806.11
113HL_26579.11
114HL_33640.11
115HL_39422.11
116HL_48480.11
117HL_52540.11
118HL_56809.11
119HL_59982.11
120HL_64102.11LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
121HL_67761.11
122HL_73972.11
123HL_82288.11
124HL_24707.11
125HL_27236.11
126HL_39846.11
127HL_44390.11
128HL_53015.11
129HL_57217.11cHS platform Intercalation Site
130HL_68435.11
131HL_78389.11
132HL_85018.11
133HL_95049.11Two base, cross-stacked hairpin loop
134HL_99207.11Tetrahymena LSU hairpin poorly modeled
135HL_13786.11
136HL_19226.11
137HL_21695.11UNCG-like. cWW Closing pair.
138HL_27397.11
139HL_35865.11
140HL_45411.11
141HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
142HL_53116.11
143HL_57667.11
144HL_60203.11
145HL_68579.11
146HL_78507.11
147HL_83865.11
148HL_85982.11
149HL_99612.11
150HL_14536.11
151HL_19363.11
152HL_22461.11
153HL_37962.11
154HL_45740.11
155HL_49998.11
156HL_53789.11
157HL_70872.11
158HL_75624.11
159HL_99932.11
160HL_03785.11LSU Helix 8 (H8) Hairpin Loop
161HL_10075.11
162HL_22533.11
163HL_25175.11
164HL_46055.11
165HL_50018.11
166HL_55202.11U2B"-U2A" binding hairpin loop
167HL_58223.11
168HL_62564.11LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
169HL_65802.11
170HL_70912.11
171HL_75984.11
172HL_79902.11
173HL_84289.11
174HL_87223.11
175HL_93263.11
176HL_96994.11

Updated motif groups

#Motif idInstancesDescription
1HL_67042.15318GNRA Hairpin motifs
2HL_72498.1576T-loops with two bulged bases
3HL_39895.943UNCG Hairpin motifs
4HL_18781.730Double sheared (tSH) with U-turn
5HL_91226.622Kissing Hairpin motif
6HL_97270.621T-loops with 1 bulged base
7HL_46175.518SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops | 16S helix 23 and 24 hairpin loops
8HL_75759.716
9HL_27271.415LSU Helix 96 (H96) Hairpin Loop
10HL_33402.614LSU Helix 13 (H13) Hairpin loop. GNRA-like.
11HL_56824.514LSU Helix 60A. LSU Helix 63A.
12HL_82294.513SSU Helix 37 (h37) Hairpin loop.
13HL_68081.613LSU Helix 20 Hairpin loop
14HL_48039.312MS2 virus RNA Hairpin
15HL_80459.611
16HL_11547.511LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop. | LSU Helix 80 (H80) P-site Hairpin Loop.
17HL_34027.5115S Loop C - Upper part of Hairpin Loop.
18HL_89482.210LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop.
19HL_18156.510LSU Helix 72 (H72) Hairpin Loop
20HL_34108.510LSU Helix 37 (H37) Hairpin Loop.
21HL_24544.410LSU Helix 53 (H53) Hairpin Loop. T-loop like.
22HL_41833.510LSU Helix 81 (H81) Hairpin Loop
23HL_75579.510
24HL_87136.510LSU Helix 39A Hairpin loop
25HL_01926.69LSU Helix 71 (H71) Hairpin Loop.
26HL_46489.59LSU H89 Hairpin Loop
27HL_85534.49LSU Helix 65 (H65) Hairpin Loop. T-loop like.
28HL_39872.59LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
29HL_70420.59LSU Helix 97 Hairpin loop
30HL_88311.58LSU Helix 35 (H35) Hairpin Loop
31HL_11509.58LSU Helix 6 (H6) Hairpin Loop.
32HL_82538.47LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
33HL_19626.27LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
34HL_99908.37LSU Helix 69 (H69) Hairpin Loop
35HL_62228.57LSU Helix 35A (H35A) Hairpin Loop
36HL_64543.46SSU Helix 31 (h31) Hairpin Loop
37HL_45018.46Hairpin-Hairpin Interacting HL
38HL_66174.26cHS GU/cWS Double Platform creates Intercalation site
39HL_48254.46LSU Helix 84 (H84) Hairpin Loop.
40HL_86077.25GNRA with one bulged base | GNRA-like with bulged base.
41HL_86115.25
42HL_66677.24
43HL_18587.34
44HL_96915.34
45HL_42094.23
46HL_28339.23
47HL_94578.23
48HL_01788.23LSU Yeast Hairpin Loop

Removed motif groups

#Motif idInstancesDescription
1HL_92565.116LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
2HL_49036.513LSU Helix 11 (H11) Hairpin Loop. GNRA-like. | GNRA with one bulged base
3HL_39942.48LSU Helix 91 (H91) Hairpin Loop
4HL_31318.26SSU Central Pseudoknot (forms helix 2)
5HL_57514.26Two base, cross-stacked hairpin loop
6HL_25878.15UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
7HL_98523.24GNRA-like. Closed by tSH UC.
8HL_33223.13SSU Central Pseudoknot (forms helix 2)
9HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
10HL_74559.23Two base, cross-stacked hairpin loop
11HL_54751.33
12HL_35619.33
13HL_86398.23
14HL_99633.23
15HL_09641.12SSU Central Pseudoknot (forms helix 2)
16HL_91872.12
17HL_19528.12
18HL_53745.12
19HL_94189.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
20HL_78660.12
21HL_94309.12GNRA with one bulged base
22HL_23129.12
23HL_84967.12
24HL_64803.12
25HL_65386.12UNCG-like. cWW Closing pair.
26HL_69403.11GNRA-like
27HL_10894.11
28HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
29HL_73465.11
30HL_20920.11
31HL_34491.11
32HL_82622.11SSU Central Pseudoknot (forms helix 2)
33HL_95079.11
34HL_23195.11
35HL_64209.11UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
36HL_95716.11
37HL_44485.1116S helix 23 and 24 hairpin loops
38HL_01418.11
39HL_29196.11
40HL_44522.11
41HL_90541.11LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base

Added motif groups

#Motif idInstancesDescription
1HL_37020.119LSU Helix 91 (H91) Hairpin Loop | LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like. | LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop.
2HL_74411.117GNRA with one bulged base | GNRA-like with bulged base. | GNRA with one bulged base | GNRA Hairpin motifs | LSU Helix 11 (H11) Hairpin Loop. GNRA-like. | GNRA with one bulged base
3HL_48507.111LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like. | GNRA with one bulged base
4HL_57087.18Two base, cross-stacked hairpin loop
5HL_27353.17UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
6HL_00311.17SSU Central Pseudoknot (forms helix 2)
7HL_00415.15GNRA-like. Closed by tSH UC.
8HL_39203.15
9HL_55035.15SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
10HL_72372.15
11HL_94364.15
12HL_28422.14
13HL_89131.14
14HL_31147.14SSU Central Pseudoknot (forms helix 2)
15HL_34954.14
16HL_43357.14SSU Central Pseudoknot (forms helix 2)
17HL_15701.13
18HL_18474.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
19HL_46388.12
20HL_74026.12
21HL_82382.12
22HL_01389.12
23HL_01766.12LSU Helix 35 (H35) Hairpin Loop from Yeast
24HL_15793.12UNCG-like. cWW Closing pair.
25HL_84548.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
26HL_29892.12
27HL_53358.1216S helix 23 and 24 hairpin loops
28HL_69907.12
29HL_77391.12
30HL_54719.12Two base, cross-stacked hairpin loop
31HL_70383.12GNRA-like
32HL_92260.12
33HL_09697.12
34HL_21419.12UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
35HL_35425.12
36HL_72489.12
37HL_82049.12
38HL_15291.11GNRA with one bulged base
39HL_24422.11
40HL_36151.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
41HL_63642.11
42HL_94813.11
43HL_25947.11
44HL_57339.11
45HL_65107.11
46HL_83263.11
47HL_94981.11
48HL_39035.11
49HL_50078.11
50HL_57644.11
51HL_65428.11
52HL_74451.11
53HL_95822.11
54HL_04382.11
55HL_16822.11
56HL_50954.11
57HL_58052.11
58HL_68904.11
59HL_76004.11
60HL_87172.11
61HL_96515.11LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
62HL_04584.11
63HL_39943.11
64HL_61871.11
65HL_98834.11
66HL_05350.11
67HL_19673.11
68HL_40070.11
69HL_62500.11
70HL_78422.11SSU Central Pseudoknot (forms helix 2)
71HL_40731.11
72HL_63001.11
73HL_81994.11
74HL_14524.11
75HL_23628.11
76HL_55450.11
77HL_63323.11
78HL_94639.11