Changes in PDB files used for clustering

Release 1.16 has 258 PDB files, release 1.17 has 263 PDB files, 257 of them are identical.

1 equivalence classes changed representatives: 4NVV4QCN.

5 new structures in release 1.17: 1VY9, 4QK8, 4QK9, 4QLM, 4U7U.

Obsolete: 4NVV4V9R.

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 1.16 has 324 motif groups, release 1.17 has 323 motif groups, 264 of them are identical.

42 motif groups were updated, 18 groups are present only in release 1.16, 17 groups are only in release 1.17.

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_46175.518SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops | 16S helix 23 and 24 hairpin loops
2HL_74465.616tRNA Anti-Codon loop
3HL_27271.415LSU Helix 96 (H96) Hairpin Loop
4HL_82294.513SSU Helix 37 (h37) Hairpin loop.
5HL_48039.312MS2 virus RNA Hairpin
6HL_89482.210LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop.
7HL_15603.29U1A protein-binding Hairpin Loop.
8HL_57087.18Two base, cross-stacked hairpin loop
9HL_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.
10HL_00311.17SSU Central Pseudoknot (forms helix 2)
11HL_42677.27
12HL_45018.46Hairpin-Hairpin Interacting HL
13HL_64543.46SSU Helix 31 (h31) Hairpin Loop
14HL_06643.36tRNA D-loop. Sec tRNA
15HL_72543.36LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
16HL_48254.46LSU Helix 84 (H84) Hairpin Loop.
17HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
18HL_72372.15
19HL_86115.25
20HL_39203.15
21HL_94364.15
22HL_08382.45
23HL_00415.15GNRA-like. Closed by tSH UC.
24HL_72273.15tRNA D-loop
25HL_55035.15SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
26HL_79956.24GNRA-like with 5'-stacking of first unpaired base.
27HL_31147.14SSU Central Pseudoknot (forms helix 2)
28HL_25124.24tSW GA closed tetraloops
29HL_48116.34GNRA-like with 5'-stacking of first unpaired base.
30HL_34954.14
31HL_89131.14
32HL_18587.34
33HL_62881.14RNase P Structured Hairpin Loop
34HL_96915.34
35HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
36HL_92706.14LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
37HL_11376.14LSU Helix 8 (H8) Hairpin Loop
38HL_66677.24
39HL_19905.44LSU: Part of IL/3WJ between H55 and H56.
40HL_23182.24
41HL_06122.23
42HL_18474.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
43HL_19033.13SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
44HL_84911.13
45HL_55684.13
46HL_13707.23cSH AA Platform containing Hairpin Loop
47HL_91693.23
48HL_94578.23
49HL_42094.23
50HL_58083.33
51HL_06997.23
52HL_21545.23LSU Helix 96 (H96) Hairpin Loop
53HL_01788.23LSU Yeast Hairpin Loop
54HL_19221.23
55HL_98833.33
56HL_28339.23
57HL_78361.13
58HL_74307.13
59HL_91142.13Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
60HL_41827.13
61HL_15701.13
62HL_80492.23tRNA D-loop
63HL_95969.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
64HL_76766.43
65HL_65249.23
66HL_60200.23
67HL_24711.12
68HL_42077.32LSU Helix 28 (H28) Hairpin Loop
69HL_23290.12
70HL_01389.12
71HL_82382.12
72HL_69907.12
73HL_01766.12LSU Helix 35 (H35) Hairpin Loop from Yeast
74HL_98577.12
75HL_84548.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
76HL_46388.12
77HL_29892.12
78HL_20004.12
79HL_54719.12Two base, cross-stacked hairpin loop
80HL_05361.12
81HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
82HL_44467.12
83HL_64438.12Kink-turn-like Hairpin Loop
84HL_84172.12
85HL_74026.12
86HL_26495.12
87HL_34912.12
88HL_70383.12GNRA-like
89HL_27478.12
90HL_15793.12UNCG-like. cWW Closing pair.
91HL_72489.12
92HL_24473.32tRNA D-loop
93HL_42553.12
94HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
95HL_33451.12
96HL_41700.12
97HL_50937.12
98HL_65924.12
99HL_38130.22
100HL_50312.12
101HL_93771.12tRNA T-loop distorted by RS binding
102HL_49210.12
103HL_77391.12
104HL_92260.12
105HL_19399.12
106HL_87554.12
107HL_59610.11
108HL_39943.11
109HL_45411.11
110HL_20806.11
111HL_60203.11
112HL_45358.11Double hairpin loop based on GGA triple
113HL_66880.11
114HL_68579.11
115HL_67000.11
116HL_78228.11
117HL_57667.11
118HL_20028.11
119HL_59182.11
120HL_94981.11
121HL_52116.11
122HL_65802.11
123HL_96515.11LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
124HL_93428.11
125HL_04979.11LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
126HL_04584.11
127HL_81994.11
128HL_05350.11
129HL_14524.11
130HL_45740.11
131HL_87223.11
132HL_68435.11
133HL_55450.11
134HL_91613.11
135HL_93263.11
136HL_55272.11
137HL_11337.11
138HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
139HL_59225.11
140HL_42255.11
141HL_78422.11SSU Central Pseudoknot (forms helix 2)
142HL_73972.11
143HL_27236.11
144HL_23628.11
145HL_57644.11
146HL_53789.11
147HL_78507.11
148HL_00721.11
149HL_58223.11
150HL_84289.11
151HL_53015.11
152HL_99207.11Tetrahymena LSU hairpin poorly modeled
153HL_74451.11
154HL_97022.11
155HL_99584.11
156HL_22533.11
157HL_62374.11
158HL_55202.11U2B"-U2A" binding hairpin loop
159HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
160HL_99612.11
161HL_10075.11
162HL_25947.11
163HL_50078.11
164HL_94813.11
165HL_40070.11
166HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
167HL_25195.11
168HL_26579.11
169HL_44390.11
170HL_97784.11
171HL_84720.11
172HL_17537.11
173HL_08203.11
174HL_96012.11
175HL_38898.11
176HL_84768.11
177HL_33640.11
178HL_99932.11
179HL_50018.11
180HL_94639.11
181HL_62500.11
182HL_58052.11
183HL_65428.11
184HL_24707.11
185HL_37962.11
186HL_63997.11
187HL_39422.11
188HL_79902.11
189HL_95822.11
190HL_56809.11
191HL_67761.11
192HL_47337.11
193HL_11257.11
194HL_10116.11Kink-turn-like Hairpin Loop
195HL_39846.11
196HL_85018.11
197HL_30008.11
198HL_23080.11
199HL_17008.11Nova-2 KH3 domain binding hairpin
200HL_38138.11
201HL_35865.11
202HL_19673.11
203HL_16822.11
204HL_65107.11
205HL_39035.11
206HL_63001.11
207HL_87172.11
208HL_21695.11UNCG-like. cWW Closing pair.
209HL_25197.11
210HL_19363.11
211HL_57217.11cHS platform Intercalation Site
212HL_19132.11
213HL_27397.11
214HL_12706.11
215HL_13786.11
216HL_93530.11
217HL_46570.11
218HL_19452.11tRNA D-loop
219HL_42345.11
220HL_14536.11
221HL_36151.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
222HL_62564.11LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
223HL_04305.11
224HL_46055.11
225HL_40731.11
226HL_76004.11
227HL_61871.11
228HL_83263.11
229HL_63323.11
230HL_57339.11
231HL_48480.11
232HL_99779.11
233HL_52540.11
234HL_05113.11
235HL_88960.11
236HL_15291.11GNRA with one bulged base
237HL_70912.11
238HL_03785.11LSU Helix 8 (H8) Hairpin Loop
239HL_25175.11
240HL_78389.11
241HL_83865.11
242HL_75984.11
243HL_98233.11
244HL_96994.11
245HL_72389.11
246HL_56775.11
247HL_77692.11tRNA D-loop
248HL_50954.11
249HL_24422.11
250HL_98834.11
251HL_93567.11
252HL_57923.11
253HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
254HL_95049.11Two base, cross-stacked hairpin loop
255HL_84888.11T-loop like but without tWH UA
256HL_66877.11cSH GU/cWS double platform, intercalation site
257HL_30731.11
258HL_62880.11
259HL_82288.11
260HL_75624.11
261HL_22461.11
262HL_79038.11LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
263HL_24108.11
264HL_63642.11

Updated motif groups

#Motif idInstancesDescription
1HL_67042.16321GNRA Hairpin motifs
2HL_72498.1676T-loops with two bulged bases
3HL_39895.1045UNCG Hairpin motifs
4HL_18781.830Double sheared (tSH) with U-turn
5HL_91226.723Kissing Hairpin motif
6HL_97270.721T-loops with 1 bulged base
7HL_37020.220LSU 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.
8HL_74411.218GNRA 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
9HL_75759.816
10HL_56824.614LSU Helix 60A. LSU Helix 63A.
11HL_33402.714LSU Helix 13 (H13) Hairpin loop. GNRA-like.
12HL_68081.713LSU Helix 20 Hairpin loop
13HL_80459.711
14HL_11547.611LSU 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.
15HL_34027.6115S Loop C - Upper part of Hairpin Loop.
16HL_48507.211LSU 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
17HL_34108.610LSU Helix 37 (H37) Hairpin Loop.
18HL_87136.610LSU Helix 39A Hairpin loop
19HL_75579.610
20HL_24544.510LSU Helix 53 (H53) Hairpin Loop. T-loop like.
21HL_41833.610LSU Helix 81 (H81) Hairpin Loop
22HL_17723.610LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
23HL_18156.610LSU Helix 72 (H72) Hairpin Loop
24HL_39872.69LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
25HL_01926.79LSU Helix 71 (H71) Hairpin Loop.
26HL_46489.69LSU H89 Hairpin Loop
27HL_70420.69LSU Helix 97 Hairpin loop
28HL_85534.59LSU Helix 65 (H65) Hairpin Loop. T-loop like.
29HL_88311.68LSU Helix 35 (H35) Hairpin Loop
30HL_11509.68LSU Helix 6 (H6) Hairpin Loop.
31HL_19626.37LSU 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
32HL_62228.67LSU Helix 35A (H35A) Hairpin Loop
33HL_99908.47LSU Helix 69 (H69) Hairpin Loop
34HL_82538.57LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
35HL_66174.36cHS GU/cWS Double Platform creates Intercalation site
36HL_86077.35GNRA with one bulged base | GNRA-like with bulged base.
37HL_82418.24LSU Helix 8 (H8) Hairpin Loop
38HL_28422.24
39HL_43357.24SSU Central Pseudoknot (forms helix 2)
40HL_21419.23UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
41HL_64371.43SSU Central Pseudoknot (forms helix 2)
42HL_27429.53

Removed motif groups

#Motif idInstancesDescription
1HL_89236.16LSU Helix 69 (H69) Hairpin Loop
2HL_78731.25LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
3HL_82049.12
4HL_53358.1216S helix 23 and 24 hairpin loops
5HL_09697.12
6HL_92635.12
7HL_35425.12
8HL_38964.12LSU Helix 84 (H84) Hairpin Loop. E.coli.
9HL_49998.11
10HL_53116.11
11HL_82243.11
12HL_85982.11
13HL_04382.11
14HL_59982.11
15HL_64102.11LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
16HL_19226.11
17HL_68904.11
18HL_70872.11

Added motif groups

#Motif idInstancesDescription
1HL_20199.16SSU Central Pseudoknot (forms helix 2) | LSU Helix 69 (H69) Hairpin Loop | LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
2HL_12908.14LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
3HL_72846.14LSU Helix 69 (H69) Hairpin Loop
4HL_59516.13cHS GU/cWS Double Platform creates Intercalation site
5HL_35652.12LSU Helix 84 (H84) Hairpin Loop. E.coli.
6HL_49961.12
7HL_94212.1216S helix 23 and 24 hairpin loops
8HL_51271.12
9HL_57263.12
10HL_21839.11
11HL_79541.1116S helix 23 and 24 hairpin loops
12HL_28776.11
13HL_89473.11
14HL_92594.11
15HL_08388.11
16HL_14384.11
17HL_19074.11