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_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
9HL_08382.45
10HL_78731.25LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
11HL_72273.15tRNA D-loop
12HL_11376.14LSU Helix 8 (H8) Hairpin Loop
13HL_48116.34GNRA-like with 5'-stacking of first unpaired base.
14HL_82418.14LSU Helix 8 (H8) Hairpin Loop
15HL_25124.24tSW GA closed tetraloops
16HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
17HL_92706.14LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
18HL_23182.24
19HL_79956.24GNRA-like with 5'-stacking of first unpaired base.
20HL_19905.44LSU: Part of IL/3WJ between H55 and H56.
21HL_62881.14RNase P Structured Hairpin Loop
22HL_19033.13SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
23HL_06122.23
24HL_78361.13
25HL_84911.13
26HL_91142.13Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
27HL_98833.33
28HL_13707.23cSH AA Platform containing Hairpin Loop
29HL_19221.23
30HL_21545.23LSU Helix 96 (H96) Hairpin Loop
31HL_60200.23
32HL_64371.33SSU Central Pseudoknot (forms helix 2)
33HL_74307.13
34HL_91693.23
35HL_06997.23
36HL_27429.43
37HL_41827.13
38HL_58083.33
39HL_65249.23
40HL_95969.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
41HL_76766.43
42HL_55684.13
43HL_80492.23tRNA D-loop
44HL_05361.12
45HL_20004.12
46HL_26495.12
47HL_33451.12
48HL_38964.12LSU Helix 84 (H84) Hairpin Loop. E.coli.
49HL_42553.12
50HL_98577.12
51HL_24473.32tRNA D-loop
52HL_93771.12tRNA T-loop distorted by RS binding
53HL_34912.12
54HL_49210.12
55HL_24711.12
56HL_41700.12
57HL_64438.12Kink-turn-like Hairpin Loop
58HL_92635.12
59HL_84172.12
60HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
61HL_19399.12
62HL_27478.12
63HL_38130.22
64HL_42077.32LSU Helix 28 (H28) Hairpin Loop
65HL_50312.12
66HL_65924.12
67HL_87554.12
68HL_23290.12
69HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
70HL_50937.12
71HL_24108.11
72HL_52116.11
73HL_56775.11
74HL_59610.11
75HL_63997.11
76HL_67000.11
77HL_78228.11
78HL_82243.11
79HL_84888.11T-loop like but without tWH UA
80HL_93567.11
81HL_12706.11
82HL_19132.11
83HL_20806.11
84HL_26579.11
85HL_33640.11
86HL_39422.11
87HL_48480.11
88HL_52540.11
89HL_56809.11
90HL_59982.11
91HL_64102.11LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
92HL_67761.11
93HL_73972.11
94HL_82288.11
95HL_24707.11
96HL_27236.11
97HL_39846.11
98HL_44390.11
99HL_53015.11
100HL_57217.11cHS platform Intercalation Site
101HL_68435.11
102HL_78389.11
103HL_85018.11
104HL_95049.11Two base, cross-stacked hairpin loop
105HL_99207.11Tetrahymena LSU hairpin poorly modeled
106HL_13786.11
107HL_19226.11
108HL_21695.11UNCG-like. cWW Closing pair.
109HL_27397.11
110HL_35865.11
111HL_45411.11
112HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
113HL_53116.11
114HL_57667.11
115HL_60203.11
116HL_68579.11
117HL_78507.11
118HL_83865.11
119HL_85982.11
120HL_99612.11
121HL_14536.11
122HL_19363.11
123HL_22461.11
124HL_37962.11
125HL_45740.11
126HL_49998.11
127HL_53789.11
128HL_70872.11
129HL_75624.11
130HL_99932.11
131HL_03785.11LSU Helix 8 (H8) Hairpin Loop
132HL_10075.11
133HL_22533.11
134HL_25175.11
135HL_46055.11
136HL_50018.11
137HL_55202.11U2B"-U2A" binding hairpin loop
138HL_58223.11
139HL_62564.11LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
140HL_65802.11
141HL_70912.11
142HL_75984.11
143HL_79902.11
144HL_84289.11
145HL_87223.11
146HL_93263.11
147HL_96994.11
148HL_04305.11
149HL_10116.11Kink-turn-like Hairpin Loop
150HL_17537.11
151HL_19452.11tRNA D-loop
152HL_25195.11
153HL_30008.11
154HL_38138.11
155HL_42345.11
156HL_46570.11
157HL_55272.11
158HL_59182.11
159HL_62880.11
160HL_84720.11
161HL_93428.11
162HL_97022.11
163HL_04979.11LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
164HL_11337.11
165HL_25197.11
166HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
167HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
168HL_47337.11
169HL_59225.11
170HL_66877.11cSH GU/cWS double platform, intercalation site
171HL_72389.11
172HL_77692.11tRNA D-loop
173HL_84768.11
174HL_88960.11
175HL_93530.11
176HL_97784.11

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_56824.514LSU Helix 60A. LSU Helix 63A.
11HL_33402.614LSU Helix 13 (H13) Hairpin loop. GNRA-like.
12HL_68081.613LSU Helix 20 Hairpin loop
13HL_82294.513SSU Helix 37 (h37) 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_34108.510LSU Helix 37 (H37) Hairpin Loop.
19HL_24544.410LSU Helix 53 (H53) Hairpin Loop. T-loop like.
20HL_41833.510LSU Helix 81 (H81) Hairpin Loop
21HL_75579.510
22HL_87136.510LSU Helix 39A Hairpin loop
23HL_89482.210LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop.
24HL_18156.510LSU Helix 72 (H72) Hairpin Loop
25HL_85534.49LSU Helix 65 (H65) Hairpin Loop. T-loop like.
26HL_39872.59LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
27HL_70420.59LSU Helix 97 Hairpin loop
28HL_01926.69LSU Helix 71 (H71) Hairpin Loop.
29HL_46489.59LSU H89 Hairpin Loop
30HL_88311.58LSU Helix 35 (H35) Hairpin Loop
31HL_11509.58LSU Helix 6 (H6) Hairpin Loop.
32HL_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
33HL_99908.37LSU Helix 69 (H69) Hairpin Loop
34HL_62228.57LSU Helix 35A (H35A) Hairpin Loop
35HL_82538.47LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
36HL_48254.46LSU Helix 84 (H84) Hairpin Loop.
37HL_64543.46SSU Helix 31 (h31) Hairpin Loop
38HL_45018.46Hairpin-Hairpin Interacting HL
39HL_66174.26cHS GU/cWS Double Platform creates Intercalation site
40HL_86077.25GNRA with one bulged base | GNRA-like with bulged base.
41HL_86115.25
42HL_18587.34
43HL_96915.34
44HL_66677.24
45HL_01788.23LSU Yeast Hairpin Loop
46HL_42094.23
47HL_28339.23
48HL_94578.23

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_86398.23
9HL_99633.23
10HL_33223.13SSU Central Pseudoknot (forms helix 2)
11HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
12HL_74559.23Two base, cross-stacked hairpin loop
13HL_54751.33
14HL_35619.33
15HL_64803.12
16HL_65386.12UNCG-like. cWW Closing pair.
17HL_09641.12SSU Central Pseudoknot (forms helix 2)
18HL_91872.12
19HL_19528.12
20HL_53745.12
21HL_94189.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
22HL_78660.12
23HL_94309.12GNRA with one bulged base
24HL_23129.12
25HL_84967.12
26HL_44485.1116S helix 23 and 24 hairpin loops
27HL_01418.11
28HL_29196.11
29HL_44522.11
30HL_90541.11LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
31HL_69403.11GNRA-like
32HL_10894.11
33HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
34HL_73465.11
35HL_20920.11
36HL_34491.11
37HL_82622.11SSU Central Pseudoknot (forms helix 2)
38HL_95079.11
39HL_23195.11
40HL_64209.11UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
41HL_95716.11

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_00311.17SSU Central Pseudoknot (forms helix 2)
6HL_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.
7HL_55035.15SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
8HL_72372.15
9HL_94364.15
10HL_00415.15GNRA-like. Closed by tSH UC.
11HL_39203.15
12HL_89131.14
13HL_31147.14SSU Central Pseudoknot (forms helix 2)
14HL_34954.14
15HL_43357.14SSU Central Pseudoknot (forms helix 2)
16HL_28422.14
17HL_18474.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
18HL_15701.13
19HL_29892.12
20HL_53358.1216S helix 23 and 24 hairpin loops
21HL_69907.12
22HL_77391.12
23HL_54719.12Two base, cross-stacked hairpin loop
24HL_70383.12GNRA-like
25HL_92260.12
26HL_09697.12
27HL_21419.12UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
28HL_35425.12
29HL_72489.12
30HL_82049.12
31HL_46388.12
32HL_74026.12
33HL_82382.12
34HL_01389.12
35HL_01766.12LSU Helix 35 (H35) Hairpin Loop from Yeast
36HL_15793.12UNCG-like. cWW Closing pair.
37HL_84548.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
38HL_04584.11
39HL_39943.11
40HL_61871.11
41HL_98834.11
42HL_05350.11
43HL_19673.11
44HL_40070.11
45HL_62500.11
46HL_78422.11SSU Central Pseudoknot (forms helix 2)
47HL_40731.11
48HL_63001.11
49HL_81994.11
50HL_14524.11
51HL_23628.11
52HL_55450.11
53HL_63323.11
54HL_94639.11
55HL_15291.11GNRA with one bulged base
56HL_24422.11
57HL_36151.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
58HL_63642.11
59HL_94813.11
60HL_25947.11
61HL_57339.11
62HL_65107.11
63HL_83263.11
64HL_94981.11
65HL_39035.11
66HL_50078.11
67HL_57644.11
68HL_65428.11
69HL_74451.11
70HL_95822.11
71HL_04382.11
72HL_16822.11
73HL_50954.11
74HL_58052.11
75HL_68904.11
76HL_76004.11
77HL_87172.11
78HL_96515.11LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like.