Changes in PDB files used for clustering

Release 1.15 has 240 PDB files, release 1.16 has 253 PDB files, 239 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_89236.16LSU Helix 69 (H69) Hairpin Loop
6HL_06643.36tRNA D-loop. Sec tRNA
7HL_72543.36LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
8HL_08382.45
9HL_78731.25LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
10HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
11HL_72273.15tRNA D-loop
12HL_82418.14LSU Helix 8 (H8) Hairpin Loop
13HL_25124.24tSW GA closed tetraloops
14HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
15HL_19905.44LSU: Part of IL/3WJ between H55 and H56.
16HL_23182.24
17HL_92706.14LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
18HL_11376.14LSU Helix 8 (H8) Hairpin Loop
19HL_62881.14RNase P Structured Hairpin Loop
20HL_79956.24GNRA-like with 5'-stacking of first unpaired base.
21HL_48116.34GNRA-like with 5'-stacking of first unpaired base.
22HL_21545.23LSU Helix 96 (H96) Hairpin Loop
23HL_60200.23
24HL_64371.33SSU Central Pseudoknot (forms helix 2)
25HL_74307.13
26HL_84911.13
27HL_91142.13Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
28HL_98833.33
29HL_27429.43
30HL_41827.13
31HL_58083.33
32HL_65249.23
33HL_91693.23
34HL_76766.43
35HL_95969.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
36HL_06122.23
37HL_19033.13SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
38HL_55684.13
39HL_80492.23tRNA D-loop
40HL_06997.23
41HL_13707.23cSH AA Platform containing Hairpin Loop
42HL_19221.23
43HL_78361.13
44HL_34912.12
45HL_49210.12
46HL_98577.12
47HL_24711.12
48HL_41700.12
49HL_64438.12Kink-turn-like Hairpin Loop
50HL_93771.12tRNA T-loop distorted by RS binding
51HL_19399.12
52HL_27478.12
53HL_38130.22
54HL_42077.32LSU Helix 28 (H28) Hairpin Loop
55HL_84172.12
56HL_92635.12
57HL_05361.12
58HL_50312.12
59HL_65924.12
60HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
61HL_20004.12
62HL_23290.12
63HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
64HL_50937.12
65HL_26495.12
66HL_33451.12
67HL_38964.12LSU Helix 84 (H84) Hairpin Loop. E.coli.
68HL_42553.12
69HL_87554.12
70HL_24473.32tRNA D-loop
71HL_03785.11LSU Helix 8 (H8) Hairpin Loop
72HL_08203.11
73HL_13786.11
74HL_19226.11
75HL_24707.11
76HL_27236.11
77HL_39846.11
78HL_44390.11
79HL_53015.11
80HL_57217.11cHS platform Intercalation Site
81HL_68435.11
82HL_78389.11
83HL_82288.11
84HL_93567.11
85HL_04305.11
86HL_14536.11
87HL_19363.11
88HL_21695.11UNCG-like. cWW Closing pair.
89HL_27397.11
90HL_35865.11
91HL_45411.11
92HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
93HL_53116.11
94HL_57667.11
95HL_60203.11
96HL_68579.11
97HL_78507.11
98HL_85018.11
99HL_04979.11LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
100HL_10075.11
101HL_22461.11
102HL_37962.11
103HL_45740.11
104HL_49998.11
105HL_53789.11
106HL_70872.11
107HL_75624.11
108HL_83865.11
109HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
110HL_95049.11Two base, cross-stacked hairpin loop
111HL_99207.11Tetrahymena LSU hairpin poorly modeled
112HL_05113.11
113HL_10116.11Kink-turn-like Hairpin Loop
114HL_17537.11
115HL_19452.11tRNA D-loop
116HL_22533.11
117HL_25175.11
118HL_46055.11
119HL_50018.11
120HL_55202.11U2B"-U2A" binding hairpin loop
121HL_58223.11
122HL_62564.11LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
123HL_65802.11
124HL_70912.11
125HL_75984.11
126HL_79038.11LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
127HL_85982.11
128HL_99584.11
129HL_11337.11
130HL_25195.11
131HL_30008.11
132HL_38138.11
133HL_42345.11
134HL_46570.11
135HL_55272.11
136HL_59182.11
137HL_62880.11
138HL_79902.11
139HL_84289.11
140HL_99612.11
141HL_25197.11
142HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
143HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
144HL_47337.11
145HL_59225.11
146HL_66877.11cSH GU/cWS double platform, intercalation site
147HL_72389.11
148HL_77692.11tRNA D-loop
149HL_84720.11
150HL_87223.11
151HL_93263.11
152HL_96994.11
153HL_99779.11
154HL_12706.11
155HL_19132.11
156HL_20028.11
157HL_24108.11
158HL_52116.11
159HL_56775.11
160HL_59610.11
161HL_63997.11
162HL_67000.11
163HL_78228.11
164HL_84768.11
165HL_93428.11
166HL_97022.11
167HL_99932.11
168HL_20806.11
169HL_26579.11
170HL_33640.11
171HL_39422.11
172HL_48480.11
173HL_52540.11
174HL_56809.11
175HL_59982.11
176HL_64102.11LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
177HL_67761.11
178HL_73972.11
179HL_82243.11
180HL_84888.11T-loop like but without tWH UA
181HL_88960.11
182HL_93530.11
183HL_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_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_24544.410LSU Helix 53 (H53) Hairpin Loop. T-loop like.
19HL_41833.510LSU Helix 81 (H81) Hairpin Loop
20HL_75579.510
21HL_87136.510LSU Helix 39A Hairpin loop
22HL_89482.210LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop.
23HL_18156.510LSU Helix 72 (H72) Hairpin Loop
24HL_34108.510LSU Helix 37 (H37) 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_62228.57LSU Helix 35A (H35A) Hairpin Loop
33HL_82538.47LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
34HL_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
35HL_99908.37LSU Helix 69 (H69) 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_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_99633.23
9HL_33223.13SSU Central Pseudoknot (forms helix 2)
10HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
11HL_74559.23Two base, cross-stacked hairpin loop
12HL_54751.33
13HL_35619.33
14HL_86398.23
15HL_65386.12UNCG-like. cWW Closing pair.
16HL_09641.12SSU Central Pseudoknot (forms helix 2)
17HL_91872.12
18HL_19528.12
19HL_53745.12
20HL_94189.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
21HL_78660.12
22HL_94309.12GNRA with one bulged base
23HL_23129.12
24HL_84967.12
25HL_64803.12
26HL_01418.11
27HL_29196.11
28HL_44522.11
29HL_90541.11LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
30HL_69403.11GNRA-like
31HL_10894.11
32HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
33HL_73465.11
34HL_20920.11
35HL_34491.11
36HL_82622.11SSU Central Pseudoknot (forms helix 2)
37HL_95079.11
38HL_23195.11
39HL_64209.11UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
40HL_95716.11
41HL_44485.1116S helix 23 and 24 hairpin loops

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_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_43357.14SSU Central Pseudoknot (forms helix 2)
13HL_28422.14
14HL_89131.14
15HL_31147.14SSU Central Pseudoknot (forms helix 2)
16HL_34954.14
17HL_15701.13
18HL_18474.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
19HL_35425.12
20HL_72489.12
21HL_82049.12
22HL_46388.12
23HL_74026.12
24HL_82382.12
25HL_01389.12
26HL_01766.12LSU Helix 35 (H35) Hairpin Loop from Yeast
27HL_15793.12UNCG-like. cWW Closing pair.
28HL_84548.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
29HL_29892.12
30HL_53358.1216S helix 23 and 24 hairpin loops
31HL_69907.12
32HL_77391.12
33HL_54719.12Two base, cross-stacked hairpin loop
34HL_70383.12GNRA-like
35HL_92260.12
36HL_09697.12
37HL_21419.12UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
38HL_14524.11
39HL_23628.11
40HL_55450.11
41HL_63323.11
42HL_94639.11
43HL_15291.11GNRA with one bulged base
44HL_24422.11
45HL_36151.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
46HL_63642.11
47HL_94813.11
48HL_25947.11
49HL_57339.11
50HL_65107.11
51HL_83263.11
52HL_94981.11
53HL_39035.11
54HL_50078.11
55HL_57644.11
56HL_65428.11
57HL_74451.11
58HL_95822.11
59HL_04382.11
60HL_16822.11
61HL_50954.11
62HL_58052.11
63HL_68904.11
64HL_76004.11
65HL_87172.11
66HL_96515.11LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
67HL_04584.11
68HL_39943.11
69HL_61871.11
70HL_98834.11
71HL_05350.11
72HL_19673.11
73HL_40070.11
74HL_62500.11
75HL_78422.11SSU Central Pseudoknot (forms helix 2)
76HL_40731.11
77HL_63001.11
78HL_81994.11