Changes in PDB files used for clustering

Release 1.16 has 252 PDB files, release 1.17 has 257 PDB files, 251 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_42677.27
11HL_00311.17SSU Central Pseudoknot (forms helix 2)
12HL_06643.36tRNA D-loop. Sec tRNA
13HL_64543.46SSU Helix 31 (h31) Hairpin Loop
14HL_45018.46Hairpin-Hairpin Interacting HL
15HL_48254.46LSU Helix 84 (H84) Hairpin Loop.
16HL_72543.36LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
17HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
18HL_86115.25
19HL_08382.45
20HL_94364.15
21HL_72273.15tRNA D-loop
22HL_72372.15
23HL_00415.15GNRA-like. Closed by tSH UC.
24HL_55035.15SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
25HL_39203.15
26HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
27HL_79956.24GNRA-like with 5'-stacking of first unpaired base.
28HL_23182.24
29HL_25124.24tSW GA closed tetraloops
30HL_31147.14SSU Central Pseudoknot (forms helix 2)
31HL_66677.24
32HL_18587.34
33HL_19905.44LSU: Part of IL/3WJ between H55 and H56.
34HL_92706.14LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
35HL_96915.34
36HL_11376.14LSU Helix 8 (H8) Hairpin Loop
37HL_34954.14
38HL_48116.34GNRA-like with 5'-stacking of first unpaired base.
39HL_62881.14RNase P Structured Hairpin Loop
40HL_89131.14
41HL_01788.23LSU Yeast Hairpin Loop
42HL_13707.23cSH AA Platform containing Hairpin Loop
43HL_76766.43
44HL_06997.23
45HL_55684.13
46HL_91142.13Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
47HL_98833.33
48HL_18474.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
49HL_58083.33
50HL_74307.13
51HL_80492.23tRNA D-loop
52HL_91693.23
53HL_95969.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
54HL_94578.23
55HL_19033.13SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
56HL_78361.13
57HL_41827.13
58HL_15701.13
59HL_19221.23
60HL_21545.23LSU Helix 96 (H96) Hairpin Loop
61HL_28339.23
62HL_65249.23
63HL_06122.23
64HL_42094.23
65HL_60200.23
66HL_84911.13
67HL_19399.12
68HL_69907.12
69HL_98577.12
70HL_24711.12
71HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
72HL_49210.12
73HL_65924.12
74HL_70383.12GNRA-like
75HL_74026.12
76HL_77391.12
77HL_84172.12
78HL_93771.12tRNA T-loop distorted by RS binding
79HL_38130.22
80HL_42553.12
81HL_46388.12
82HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
83HL_23290.12
84HL_33451.12
85HL_64438.12Kink-turn-like Hairpin Loop
86HL_84548.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
87HL_92260.12
88HL_20004.12
89HL_41700.12
90HL_54719.12Two base, cross-stacked hairpin loop
91HL_27478.12
92HL_34912.12
93HL_50312.12
94HL_87554.12
95HL_01389.12
96HL_05361.12
97HL_42077.32LSU Helix 28 (H28) Hairpin Loop
98HL_50937.12
99HL_72489.12
100HL_82382.12
101HL_01766.12LSU Helix 35 (H35) Hairpin Loop from Yeast
102HL_15793.12UNCG-like. cWW Closing pair.
103HL_24473.32tRNA D-loop
104HL_26495.12
105HL_29892.12
106HL_16822.11
107HL_22461.11
108HL_24707.11
109HL_26579.11
110HL_30008.11
111HL_36151.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
112HL_39846.11
113HL_42345.11
114HL_46055.11
115HL_48480.11
116HL_52116.11
117HL_55450.11
118HL_57667.11
119HL_60203.11
120HL_63323.11
121HL_65802.11
122HL_73972.11
123HL_79902.11
124HL_83865.11
125HL_85018.11
126HL_93567.11
127HL_03785.11LSU Helix 8 (H8) Hairpin Loop
128HL_13786.11
129HL_17537.11
130HL_19452.11tRNA D-loop
131HL_22533.11
132HL_27236.11
133HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
134HL_37962.11
135HL_39943.11
136HL_52540.11
137HL_58052.11
138HL_63642.11
139HL_95822.11
140HL_04305.11
141HL_14524.11
142HL_19673.11
143HL_40070.11
144HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
145HL_53015.11
146HL_56775.11
147HL_61871.11
148HL_63997.11
149HL_70912.11
150HL_77692.11tRNA D-loop
151HL_84289.11
152HL_98834.11
153HL_04584.11
154HL_10075.11
155HL_14536.11
156HL_25175.11
157HL_38138.11
158HL_40731.11
159HL_46570.11
160HL_50018.11
161HL_53789.11
162HL_56809.11
163HL_58223.11
164HL_62500.11
165HL_66877.11cSH GU/cWS double platform, intercalation site
166HL_74451.11
167HL_78228.11
168HL_81994.11
169HL_87172.11
170HL_96515.11LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
171HL_99207.11Tetrahymena LSU hairpin poorly modeled
172HL_04979.11LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
173HL_10116.11Kink-turn-like Hairpin Loop
174HL_15291.11GNRA with one bulged base
175HL_23628.11
176HL_25195.11
177HL_27397.11
178HL_33640.11
179HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
180HL_44390.11
181HL_47337.11
182HL_50078.11
183HL_59182.11
184HL_62564.11LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
185HL_67000.11
186HL_82288.11
187HL_84720.11
188HL_87223.11
189HL_94639.11
190HL_99612.11
191HL_05350.11
192HL_11337.11
193HL_19132.11
194HL_20806.11
195HL_24108.11
196HL_25197.11
197HL_39035.11
198HL_57217.11cHS platform Intercalation Site
199HL_59225.11
200HL_62880.11
201HL_65107.11
202HL_67761.11
203HL_72389.11
204HL_75624.11
205HL_78389.11
206HL_84768.11
207HL_93263.11
208HL_94813.11
209HL_96994.11
210HL_99932.11
211HL_24422.11
212HL_25947.11
213HL_45411.11
214HL_55202.11U2B"-U2A" binding hairpin loop
215HL_57339.11
216HL_59610.11
217HL_68435.11
218HL_75984.11
219HL_78422.11SSU Central Pseudoknot (forms helix 2)
220HL_84888.11T-loop like but without tWH UA
221HL_88960.11
222HL_93428.11
223HL_94981.11
224HL_97022.11
225HL_12706.11
226HL_19363.11
227HL_21695.11UNCG-like. cWW Closing pair.
228HL_35865.11
229HL_39422.11
230HL_45740.11
231HL_50954.11
232HL_55272.11
233HL_57644.11
234HL_63001.11
235HL_65428.11
236HL_68579.11
237HL_76004.11
238HL_78507.11
239HL_83263.11
240HL_93530.11
241HL_95049.11Two base, cross-stacked hairpin loop
242HL_97784.11

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_34027.6115S Loop C - Upper part of Hairpin Loop.
14HL_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
15HL_80459.711
16HL_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.
17HL_18156.610LSU Helix 72 (H72) Hairpin Loop
18HL_34108.610LSU Helix 37 (H37) Hairpin Loop.
19HL_87136.610LSU Helix 39A Hairpin loop
20HL_75579.610
21HL_24544.510LSU Helix 53 (H53) Hairpin Loop. T-loop like.
22HL_41833.610LSU Helix 81 (H81) Hairpin Loop
23HL_17723.610LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
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_38964.12LSU Helix 84 (H84) Hairpin Loop. E.coli.
4HL_82049.12
5HL_53358.1216S helix 23 and 24 hairpin loops
6HL_09697.12
7HL_92635.12
8HL_35425.12
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_79541.1116S helix 23 and 24 hairpin loops
11HL_28776.11
12HL_89473.11
13HL_92594.11
14HL_08388.11
15HL_14384.11
16HL_19074.11