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_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_72273.15tRNA D-loop
11HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
12HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
13HL_82418.14LSU Helix 8 (H8) Hairpin Loop
14HL_25124.24tSW GA closed tetraloops
15HL_11376.14LSU Helix 8 (H8) Hairpin Loop
16HL_19905.44LSU: Part of IL/3WJ between H55 and H56.
17HL_48116.34GNRA-like with 5'-stacking of first unpaired base.
18HL_62881.14RNase P Structured Hairpin Loop
19HL_23182.24
20HL_79956.24GNRA-like with 5'-stacking of first unpaired base.
21HL_92706.14LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
22HL_21545.23LSU Helix 96 (H96) Hairpin Loop
23HL_74307.13
24HL_84911.13
25HL_58083.33
26HL_65249.23
27HL_91142.13Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
28HL_27429.43
29HL_55684.13
30HL_91693.23
31HL_06122.23
32HL_76766.43
33HL_98833.33
34HL_19033.13SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
35HL_41827.13
36HL_95969.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
37HL_06997.23
38HL_13707.23cSH AA Platform containing Hairpin Loop
39HL_80492.23tRNA D-loop
40HL_19221.23
41HL_60200.23
42HL_64371.33SSU Central Pseudoknot (forms helix 2)
43HL_78361.13
44HL_24473.32tRNA D-loop
45HL_33451.12
46HL_64438.12Kink-turn-like Hairpin Loop
47HL_38964.12LSU Helix 84 (H84) Hairpin Loop. E.coli.
48HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
49HL_19399.12
50HL_24711.12
51HL_34912.12
52HL_42553.12
53HL_50312.12
54HL_93771.12tRNA T-loop distorted by RS binding
55HL_05361.12
56HL_50937.12
57HL_65924.12
58HL_84172.12
59HL_98577.12
60HL_27478.12
61HL_41700.12
62HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
63HL_92635.12
64HL_20004.12
65HL_38130.22
66HL_44467.12
67HL_23290.12
68HL_42077.32LSU Helix 28 (H28) Hairpin Loop
69HL_49210.12
70HL_87554.12
71HL_26495.12
72HL_04305.11
73HL_14536.11
74HL_19226.11
75HL_26579.11
76HL_38898.11
77HL_42345.11
78HL_45740.11
79HL_49998.11
80HL_53789.11
81HL_57923.11
82HL_60203.11
83HL_68435.11
84HL_78389.11
85HL_82288.11
86HL_93530.11
87HL_97022.11
88HL_99779.11
89HL_04979.11LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
90HL_10075.11
91HL_19363.11
92HL_21695.11UNCG-like. cWW Closing pair.
93HL_24707.11
94HL_27236.11
95HL_33640.11
96HL_46055.11
97HL_50018.11
98HL_55202.11U2B"-U2A" binding hairpin loop
99HL_68579.11
100HL_78507.11
101HL_85018.11
102HL_93567.11
103HL_97784.11
104HL_99932.11
105HL_05113.11
106HL_10116.11Kink-turn-like Hairpin Loop
107HL_17008.11Nova-2 KH3 domain binding hairpin
108HL_22461.11
109HL_27397.11
110HL_39422.11
111HL_46570.11
112HL_55272.11
113HL_58223.11
114HL_62564.11LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
115HL_65802.11
116HL_70872.11
117HL_75624.11
118HL_83865.11
119HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
120HL_91613.11
121HL_98233.11
122HL_11337.11
123HL_17537.11
124HL_19452.11tRNA D-loop
125HL_22533.11
126HL_35865.11
127HL_39846.11
128HL_47337.11
129HL_59182.11
130HL_62880.11
131HL_70912.11
132HL_75984.11
133HL_79038.11LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
134HL_85982.11
135HL_95049.11Two base, cross-stacked hairpin loop
136HL_23080.11
137HL_25175.11
138HL_37962.11
139HL_44390.11
140HL_52116.11
141HL_56775.11
142HL_59225.11
143HL_66877.11cSH GU/cWS double platform, intercalation site
144HL_79902.11
145HL_84289.11
146HL_12706.11
147HL_25195.11
148HL_30008.11
149HL_48480.11
150HL_52540.11
151HL_56809.11
152HL_59610.11
153HL_63997.11
154HL_66880.11
155HL_72389.11
156HL_77692.11tRNA D-loop
157HL_84720.11
158HL_87223.11
159HL_99207.11Tetrahymena LSU hairpin poorly modeled
160HL_00721.11
161HL_19132.11
162HL_20028.11
163HL_25197.11
164HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
165HL_38138.11
166HL_45358.11Double hairpin loop based on GGA triple
167HL_53015.11
168HL_57217.11cHS platform Intercalation Site
169HL_59982.11
170HL_64102.11LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
171HL_67000.11
172HL_78228.11
173HL_84768.11
174HL_93263.11
175HL_96012.11
176HL_99584.11
177HL_03785.11LSU Helix 8 (H8) Hairpin Loop
178HL_08203.11
179HL_13786.11
180HL_20806.11
181HL_24108.11
182HL_30731.11
183HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
184HL_42255.11
185HL_45411.11
186HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
187HL_53116.11
188HL_57667.11
189HL_67761.11
190HL_73972.11
191HL_82243.11
192HL_84888.11T-loop like but without tWH UA
193HL_88960.11
194HL_93428.11
195HL_96994.11
196HL_99612.11

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_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_11509.58LSU Helix 6 (H6) Hairpin Loop.
31HL_88311.58LSU Helix 35 (H35) 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_45018.46Hairpin-Hairpin Interacting HL
37HL_66174.26cHS GU/cWS Double Platform creates Intercalation site
38HL_48254.46LSU Helix 84 (H84) Hairpin Loop.
39HL_64543.46SSU Helix 31 (h31) 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_28339.23
46HL_94578.23
47HL_01788.23LSU Yeast Hairpin Loop
48HL_42094.23

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_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_19528.12
16HL_53745.12
17HL_94189.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
18HL_78660.12
19HL_94309.12GNRA with one bulged base
20HL_23129.12
21HL_84967.12
22HL_64803.12
23HL_65386.12UNCG-like. cWW Closing pair.
24HL_09641.12SSU Central Pseudoknot (forms helix 2)
25HL_91872.12
26HL_10894.11
27HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
28HL_73465.11
29HL_20920.11
30HL_34491.11
31HL_82622.11SSU Central Pseudoknot (forms helix 2)
32HL_95079.11
33HL_23195.11
34HL_64209.11UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
35HL_95716.11
36HL_44485.1116S helix 23 and 24 hairpin loops
37HL_01418.11
38HL_29196.11
39HL_44522.11
40HL_90541.11LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
41HL_69403.11GNRA-like

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_15701.13
18HL_18474.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
19HL_01389.12
20HL_46388.12
21HL_72489.12
22HL_82049.12
23HL_01766.12LSU Helix 35 (H35) Hairpin Loop from Yeast
24HL_74026.12
25HL_82382.12
26HL_15793.12UNCG-like. cWW Closing pair.
27HL_84548.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
28HL_29892.12
29HL_53358.1216S helix 23 and 24 hairpin loops
30HL_09697.12
31HL_54719.12Two base, cross-stacked hairpin loop
32HL_69907.12
33HL_77391.12
34HL_21419.12UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
35HL_70383.12GNRA-like
36HL_92260.12
37HL_35425.12
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_63323.11
42HL_94639.11
43HL_25947.11
44HL_57339.11
45HL_63642.11
46HL_94813.11
47HL_04382.11
48HL_39035.11
49HL_50078.11
50HL_57644.11
51HL_65107.11
52HL_83263.11
53HL_94981.11
54HL_04584.11
55HL_16822.11
56HL_50954.11
57HL_58052.11
58HL_65428.11
59HL_74451.11
60HL_95822.11
61HL_05350.11
62HL_39943.11
63HL_61871.11
64HL_68904.11
65HL_76004.11
66HL_87172.11
67HL_96515.11LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
68HL_19673.11
69HL_40070.11
70HL_62374.11
71HL_98834.11
72HL_11257.11
73HL_40731.11
74HL_62500.11
75HL_78422.11SSU Central Pseudoknot (forms helix 2)
76HL_14524.11
77HL_23628.11
78HL_55450.11
79HL_63001.11
80HL_81994.11