Changes in PDB files used for clustering

Release 1.15 has 245 PDB files, release 1.16 has 258 PDB files, 244 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_06643.36tRNA D-loop. Sec tRNA
6HL_72543.36LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
7HL_89236.16LSU Helix 69 (H69) Hairpin Loop
8HL_78731.25LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
9HL_72273.15tRNA D-loop
10HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
11HL_08382.45
12HL_25124.24tSW GA closed tetraloops
13HL_11376.14LSU Helix 8 (H8) Hairpin Loop
14HL_19905.44LSU: Part of IL/3WJ between H55 and H56.
15HL_48116.34GNRA-like with 5'-stacking of first unpaired base.
16HL_62881.14RNase P Structured Hairpin Loop
17HL_23182.24
18HL_79956.24GNRA-like with 5'-stacking of first unpaired base.
19HL_92706.14LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
20HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
21HL_82418.14LSU Helix 8 (H8) Hairpin Loop
22HL_27429.43
23HL_55684.13
24HL_91693.23
25HL_06122.23
26HL_76766.43
27HL_98833.33
28HL_19033.13SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
29HL_41827.13
30HL_95969.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
31HL_06997.23
32HL_13707.23cSH AA Platform containing Hairpin Loop
33HL_80492.23tRNA D-loop
34HL_19221.23
35HL_60200.23
36HL_64371.33SSU Central Pseudoknot (forms helix 2)
37HL_78361.13
38HL_21545.23LSU Helix 96 (H96) Hairpin Loop
39HL_74307.13
40HL_84911.13
41HL_58083.33
42HL_65249.23
43HL_91142.13Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
44HL_19399.12
45HL_24711.12
46HL_34912.12
47HL_42553.12
48HL_50312.12
49HL_93771.12tRNA T-loop distorted by RS binding
50HL_05361.12
51HL_50937.12
52HL_65924.12
53HL_84172.12
54HL_98577.12
55HL_27478.12
56HL_41700.12
57HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
58HL_92635.12
59HL_20004.12
60HL_38130.22
61HL_44467.12
62HL_23290.12
63HL_42077.32LSU Helix 28 (H28) Hairpin Loop
64HL_49210.12
65HL_87554.12
66HL_26495.12
67HL_24473.32tRNA D-loop
68HL_33451.12
69HL_64438.12Kink-turn-like Hairpin Loop
70HL_38964.12LSU Helix 84 (H84) Hairpin Loop. E.coli.
71HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
72HL_05113.11
73HL_10116.11Kink-turn-like Hairpin Loop
74HL_17008.11Nova-2 KH3 domain binding hairpin
75HL_22461.11
76HL_27397.11
77HL_39422.11
78HL_46570.11
79HL_55272.11
80HL_58223.11
81HL_62564.11LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
82HL_65802.11
83HL_70872.11
84HL_75624.11
85HL_83865.11
86HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
87HL_91613.11
88HL_98233.11
89HL_11337.11
90HL_17537.11
91HL_19452.11tRNA D-loop
92HL_22533.11
93HL_35865.11
94HL_39846.11
95HL_47337.11
96HL_59182.11
97HL_62880.11
98HL_70912.11
99HL_75984.11
100HL_79038.11LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
101HL_85982.11
102HL_95049.11Two base, cross-stacked hairpin loop
103HL_23080.11
104HL_25175.11
105HL_37962.11
106HL_44390.11
107HL_52116.11
108HL_56775.11
109HL_59225.11
110HL_66877.11cSH GU/cWS double platform, intercalation site
111HL_79902.11
112HL_84289.11
113HL_12706.11
114HL_25195.11
115HL_30008.11
116HL_48480.11
117HL_52540.11
118HL_56809.11
119HL_59610.11
120HL_63997.11
121HL_66880.11
122HL_72389.11
123HL_77692.11tRNA D-loop
124HL_84720.11
125HL_87223.11
126HL_99207.11Tetrahymena LSU hairpin poorly modeled
127HL_00721.11
128HL_19132.11
129HL_20028.11
130HL_25197.11
131HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
132HL_38138.11
133HL_45358.11Double hairpin loop based on GGA triple
134HL_53015.11
135HL_57217.11cHS platform Intercalation Site
136HL_59982.11
137HL_64102.11LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
138HL_67000.11
139HL_78228.11
140HL_84768.11
141HL_93263.11
142HL_96012.11
143HL_99584.11
144HL_03785.11LSU Helix 8 (H8) Hairpin Loop
145HL_08203.11
146HL_13786.11
147HL_20806.11
148HL_24108.11
149HL_30731.11
150HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
151HL_42255.11
152HL_45411.11
153HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
154HL_53116.11
155HL_57667.11
156HL_67761.11
157HL_73972.11
158HL_82243.11
159HL_84888.11T-loop like but without tWH UA
160HL_88960.11
161HL_93428.11
162HL_96994.11
163HL_99612.11
164HL_04305.11
165HL_14536.11
166HL_19226.11
167HL_26579.11
168HL_38898.11
169HL_42345.11
170HL_45740.11
171HL_49998.11
172HL_53789.11
173HL_57923.11
174HL_60203.11
175HL_68435.11
176HL_78389.11
177HL_82288.11
178HL_93530.11
179HL_97022.11
180HL_99779.11
181HL_04979.11LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
182HL_10075.11
183HL_19363.11
184HL_21695.11UNCG-like. cWW Closing pair.
185HL_24707.11
186HL_27236.11
187HL_33640.11
188HL_46055.11
189HL_50018.11
190HL_55202.11U2B"-U2A" binding hairpin loop
191HL_68579.11
192HL_78507.11
193HL_85018.11
194HL_93567.11
195HL_97784.11
196HL_99932.11

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_34027.5115S Loop C - Upper part of Hairpin Loop.
16HL_80459.611
17HL_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.
18HL_18156.510LSU Helix 72 (H72) Hairpin Loop
19HL_34108.510LSU Helix 37 (H37) Hairpin Loop.
20HL_24544.410LSU Helix 53 (H53) Hairpin Loop. T-loop like.
21HL_41833.510LSU Helix 81 (H81) Hairpin Loop
22HL_75579.510
23HL_87136.510LSU Helix 39A Hairpin loop
24HL_89482.210LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop.
25HL_46489.59LSU H89 Hairpin Loop
26HL_85534.49LSU Helix 65 (H65) Hairpin Loop. T-loop like.
27HL_39872.59LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
28HL_70420.59LSU Helix 97 Hairpin loop
29HL_01926.69LSU Helix 71 (H71) 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_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_94578.23
46HL_01788.23LSU Yeast Hairpin Loop
47HL_42094.23
48HL_28339.23

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_57514.26Two base, cross-stacked hairpin loop
5HL_31318.26SSU Central Pseudoknot (forms helix 2)
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_54751.33
9HL_35619.33
10HL_86398.23
11HL_99633.23
12HL_33223.13SSU Central Pseudoknot (forms helix 2)
13HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
14HL_74559.23Two base, cross-stacked hairpin loop
15HL_78660.12
16HL_94309.12GNRA with one bulged base
17HL_23129.12
18HL_84967.12
19HL_64803.12
20HL_65386.12UNCG-like. cWW Closing pair.
21HL_09641.12SSU Central Pseudoknot (forms helix 2)
22HL_91872.12
23HL_19528.12
24HL_53745.12
25HL_94189.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
26HL_20920.11
27HL_34491.11
28HL_82622.11SSU Central Pseudoknot (forms helix 2)
29HL_95079.11
30HL_23195.11
31HL_64209.11UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
32HL_95716.11
33HL_44485.1116S helix 23 and 24 hairpin loops
34HL_01418.11
35HL_29196.11
36HL_44522.11
37HL_90541.11LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
38HL_69403.11GNRA-like
39HL_10894.11
40HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
41HL_73465.11

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_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_39203.15
8HL_55035.15SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
9HL_00415.15GNRA-like. Closed by tSH UC.
10HL_72372.15
11HL_94364.15
12HL_28422.14
13HL_31147.14SSU Central Pseudoknot (forms helix 2)
14HL_89131.14
15HL_34954.14
16HL_43357.14SSU Central Pseudoknot (forms helix 2)
17HL_18474.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
18HL_15701.13
19HL_15793.12UNCG-like. cWW Closing pair.
20HL_84548.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
21HL_29892.12
22HL_53358.1216S helix 23 and 24 hairpin loops
23HL_09697.12
24HL_54719.12Two base, cross-stacked hairpin loop
25HL_69907.12
26HL_77391.12
27HL_21419.12UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
28HL_70383.12GNRA-like
29HL_92260.12
30HL_35425.12
31HL_01389.12
32HL_46388.12
33HL_72489.12
34HL_82049.12
35HL_01766.12LSU Helix 35 (H35) Hairpin Loop from Yeast
36HL_74026.12
37HL_82382.12
38HL_04382.11
39HL_39035.11
40HL_50078.11
41HL_57644.11
42HL_65107.11
43HL_83263.11
44HL_94981.11
45HL_04584.11
46HL_16822.11
47HL_50954.11
48HL_58052.11
49HL_65428.11
50HL_74451.11
51HL_95822.11
52HL_05350.11
53HL_39943.11
54HL_61871.11
55HL_68904.11
56HL_76004.11
57HL_87172.11
58HL_96515.11LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
59HL_19673.11
60HL_40070.11
61HL_62374.11
62HL_98834.11
63HL_11257.11
64HL_40731.11
65HL_62500.11
66HL_78422.11SSU Central Pseudoknot (forms helix 2)
67HL_14524.11
68HL_23628.11
69HL_55450.11
70HL_63001.11
71HL_81994.11
72HL_15291.11GNRA with one bulged base
73HL_24422.11
74HL_36151.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
75HL_63323.11
76HL_94639.11
77HL_25947.11
78HL_57339.11
79HL_63642.11
80HL_94813.11