1.16 | 1.17

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: 4NVV → 4QCN.

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

Obsolete: 4NVV → 4V9R.

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 id	Instances	Description
1	HL_46175.5	18	SSU Helix 43 (h43) Hairpin Loop E.coli \| 16S helix 23 and 24 hairpin loops \| 16S helix 23 and 24 hairpin loops
2	HL_74465.6	16	tRNA Anti-Codon loop
3	HL_27271.4	15	LSU Helix 96 (H96) Hairpin Loop
4	HL_82294.5	13	SSU Helix 37 (h37) Hairpin loop.
5	HL_48039.3	12	MS2 virus RNA Hairpin
6	HL_89482.2	10	LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. \| LSU Helix 80 (H80) P-site Hairpin Loop.
7	HL_15603.2	9	U1A protein-binding Hairpin Loop.
8	HL_57087.1	8	Two base, cross-stacked hairpin loop
9	HL_42677.2	7
10	HL_27353.1	7	UNCG-like. cWW Closing pair. \| UNCG-like. cWW Closing pair. \| UNCG-like. cWW Closing pair. \| LSU: Part of IL/3WJ between H55 and H56.
11	HL_00311.1	7	SSU Central Pseudoknot (forms helix 2)
12	HL_06643.3	6	tRNA D-loop. Sec tRNA
13	HL_72543.3	6	LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
14	HL_48254.4	6	LSU Helix 84 (H84) Hairpin Loop.
15	HL_45018.4	6	Hairpin-Hairpin Interacting HL
16	HL_64543.4	6	SSU Helix 31 (h31) Hairpin Loop
17	HL_08382.4	5
18	HL_00415.1	5	GNRA-like. Closed by tSH UC.
19	HL_72273.1	5	tRNA D-loop
20	HL_55035.1	5	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
21	HL_95720.1	5	Double tSH (double sheared) with bulged base \| LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
22	HL_72372.1	5
23	HL_86115.2	5
24	HL_39203.1	5
25	HL_94364.1	5
26	HL_61547.5	4	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
27	HL_92706.1	4	LSU Helix 28 (H28) Hairpin Loop \| LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
28	HL_11376.1	4	LSU Helix 8 (H8) Hairpin Loop
29	HL_66677.2	4
30	HL_19905.4	4	LSU: Part of IL/3WJ between H55 and H56.
31	HL_23182.2	4
32	HL_79956.2	4	GNRA-like with 5'-stacking of first unpaired base.
33	HL_31147.1	4	SSU Central Pseudoknot (forms helix 2)
34	HL_25124.2	4	tSW GA closed tetraloops
35	HL_48116.3	4	GNRA-like with 5'-stacking of first unpaired base.
36	HL_34954.1	4
37	HL_89131.1	4
38	HL_18587.3	4
39	HL_62881.1	4	RNase P Structured Hairpin Loop
40	HL_96915.3	4
41	HL_91142.1	3	Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
42	HL_41827.1	3
43	HL_15701.1	3
44	HL_80492.2	3	tRNA D-loop
45	HL_95969.1	3	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
46	HL_76766.4	3
47	HL_65249.2	3
48	HL_60200.2	3
49	HL_06122.2	3
50	HL_18474.1	3	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
51	HL_19033.1	3	SSU Helix 43 (h43) Hairpin Loop E.coli \| 16S helix 23 and 24 hairpin loops
52	HL_84911.1	3
53	HL_55684.1	3
54	HL_13707.2	3	cSH AA Platform containing Hairpin Loop
55	HL_91693.2	3
56	HL_94578.2	3
57	HL_42094.2	3
58	HL_58083.3	3
59	HL_06997.2	3
60	HL_21545.2	3	LSU Helix 96 (H96) Hairpin Loop
61	HL_01788.2	3	LSU Yeast Hairpin Loop
62	HL_19221.2	3
63	HL_98833.3	3
64	HL_28339.2	3
65	HL_78361.1	3
66	HL_74307.1	3
67	HL_72489.1	2
68	HL_24473.3	2	tRNA D-loop
69	HL_42553.1	2
70	HL_86123.2	2	SSU Helix 42 (h42) Hairpin Loop. T-loop like.
71	HL_33451.1	2
72	HL_41700.1	2
73	HL_50937.1	2
74	HL_65924.1	2
75	HL_38130.2	2
76	HL_50312.1	2
77	HL_93771.1	2	tRNA T-loop distorted by RS binding
78	HL_49210.1	2
79	HL_77391.1	2
80	HL_92260.1	2
81	HL_19399.1	2
82	HL_87554.1	2
83	HL_24711.1	2
84	HL_42077.3	2	LSU Helix 28 (H28) Hairpin Loop
85	HL_23290.1	2
86	HL_01389.1	2
87	HL_82382.1	2
88	HL_69907.1	2
89	HL_01766.1	2	LSU Helix 35 (H35) Hairpin Loop from Yeast
90	HL_98577.1	2
91	HL_84548.1	2	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
92	HL_46388.1	2
93	HL_29892.1	2
94	HL_20004.1	2
95	HL_54719.1	2	Two base, cross-stacked hairpin loop
96	HL_05361.1	2
97	HL_42436.1	2	Kissing Hairpin from di-GMP-II riboswitch
98	HL_44467.1	2
99	HL_64438.1	2	Kink-turn-like Hairpin Loop
100	HL_84172.1	2
101	HL_74026.1	2
102	HL_26495.1	2
103	HL_34912.1	2
104	HL_70383.1	2	GNRA-like
105	HL_27478.1	2
106	HL_15793.1	2	UNCG-like. cWW Closing pair.
107	HL_38898.1	1
108	HL_84768.1	1
109	HL_33640.1	1
110	HL_99932.1	1
111	HL_50018.1	1
112	HL_94639.1	1
113	HL_62500.1	1
114	HL_58052.1	1
115	HL_65428.1	1
116	HL_24707.1	1
117	HL_37962.1	1
118	HL_63997.1	1
119	HL_39422.1	1
120	HL_79902.1	1
121	HL_95822.1	1
122	HL_56809.1	1
123	HL_67761.1	1
124	HL_47337.1	1
125	HL_11257.1	1
126	HL_10116.1	1	Kink-turn-like Hairpin Loop
127	HL_39846.1	1
128	HL_85018.1	1
129	HL_30008.1	1
130	HL_23080.1	1
131	HL_17008.1	1	Nova-2 KH3 domain binding hairpin
132	HL_38138.1	1
133	HL_35865.1	1
134	HL_19673.1	1
135	HL_16822.1	1
136	HL_65107.1	1
137	HL_39035.1	1
138	HL_63001.1	1
139	HL_87172.1	1
140	HL_21695.1	1	UNCG-like. cWW Closing pair.
141	HL_25197.1	1
142	HL_19363.1	1
143	HL_57217.1	1	cHS platform Intercalation Site
144	HL_19132.1	1
145	HL_27397.1	1
146	HL_12706.1	1
147	HL_13786.1	1
148	HL_93530.1	1
149	HL_46570.1	1
150	HL_19452.1	1	tRNA D-loop
151	HL_42345.1	1
152	HL_14536.1	1
153	HL_36151.1	1	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
154	HL_62564.1	1	LSU Helix 28 (H28) Hairpin Loop \| LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
155	HL_04305.1	1
156	HL_46055.1	1
157	HL_40731.1	1
158	HL_76004.1	1
159	HL_61871.1	1
160	HL_83263.1	1
161	HL_63323.1	1
162	HL_57339.1	1
163	HL_48480.1	1
164	HL_99779.1	1
165	HL_52540.1	1
166	HL_05113.1	1
167	HL_88960.1	1
168	HL_15291.1	1	GNRA with one bulged base
169	HL_70912.1	1
170	HL_03785.1	1	LSU Helix 8 (H8) Hairpin Loop
171	HL_25175.1	1
172	HL_78389.1	1
173	HL_83865.1	1
174	HL_75984.1	1
175	HL_98233.1	1
176	HL_96994.1	1
177	HL_72389.1	1
178	HL_56775.1	1
179	HL_77692.1	1	tRNA D-loop
180	HL_50954.1	1
181	HL_24422.1	1
182	HL_98834.1	1
183	HL_93567.1	1
184	HL_57923.1	1
185	HL_30366.1	1	LSU Helix 10 (H10) Hairpin E.coli
186	HL_95049.1	1	Two base, cross-stacked hairpin loop
187	HL_84888.1	1	T-loop like but without tWH UA
188	HL_66877.1	1	cSH GU/cWS double platform, intercalation site
189	HL_30731.1	1
190	HL_62880.1	1
191	HL_82288.1	1
192	HL_75624.1	1
193	HL_22461.1	1
194	HL_79038.1	1	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
195	HL_24108.1	1
196	HL_63642.1	1
197	HL_59610.1	1
198	HL_39943.1	1
199	HL_45411.1	1
200	HL_20806.1	1
201	HL_60203.1	1
202	HL_45358.1	1	Double hairpin loop based on GGA triple
203	HL_66880.1	1
204	HL_68579.1	1
205	HL_67000.1	1
206	HL_78228.1	1
207	HL_57667.1	1
208	HL_20028.1	1
209	HL_59182.1	1
210	HL_94981.1	1
211	HL_52116.1	1
212	HL_65802.1	1
213	HL_96515.1	1	LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. \| LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
214	HL_93428.1	1
215	HL_04979.1	1	LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
216	HL_04584.1	1
217	HL_81994.1	1
218	HL_05350.1	1
219	HL_14524.1	1
220	HL_45740.1	1
221	HL_87223.1	1
222	HL_68435.1	1
223	HL_55450.1	1
224	HL_91613.1	1
225	HL_93263.1	1
226	HL_55272.1	1
227	HL_11337.1	1
228	HL_49492.1	1	Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
229	HL_59225.1	1
230	HL_42255.1	1
231	HL_78422.1	1	SSU Central Pseudoknot (forms helix 2)
232	HL_73972.1	1
233	HL_27236.1	1
234	HL_23628.1	1
235	HL_57644.1	1
236	HL_53789.1	1
237	HL_78507.1	1
238	HL_00721.1	1
239	HL_58223.1	1
240	HL_84289.1	1
241	HL_53015.1	1
242	HL_99207.1	1	Tetrahymena LSU hairpin poorly modeled
243	HL_74451.1	1
244	HL_97022.1	1
245	HL_99584.1	1
246	HL_22533.1	1
247	HL_62374.1	1
248	HL_55202.1	1	U2B"-U2A" binding hairpin loop
249	HL_38897.1	1	S8 operon binding Hairpin Loop. T-loop like with purine stacking.
250	HL_99612.1	1
251	HL_10075.1	1
252	HL_25947.1	1
253	HL_50078.1	1
254	HL_94813.1	1
255	HL_40070.1	1
256	HL_85044.1	1	LSU Helix 10 (H10) Hairpin E.coli
257	HL_25195.1	1
258	HL_26579.1	1
259	HL_44390.1	1
260	HL_97784.1	1
261	HL_84720.1	1
262	HL_17537.1	1
263	HL_08203.1	1
264	HL_96012.1	1

Updated motif groups

#	Motif id	Instances	Description
1	HL_67042.16	321	GNRA Hairpin motifs
2	HL_72498.16	76	T-loops with two bulged bases
3	HL_39895.10	45	UNCG Hairpin motifs
4	HL_18781.8	30	Double sheared (tSH) with U-turn
5	HL_91226.7	23	Kissing Hairpin motif
6	HL_97270.7	21	T-loops with 1 bulged base
7	HL_37020.2	20	LSU 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.
8	HL_74411.2	18	GNRA 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
9	HL_75759.8	16
10	HL_33402.7	14	LSU Helix 13 (H13) Hairpin loop. GNRA-like.
11	HL_56824.6	14	LSU Helix 60A. LSU Helix 63A.
12	HL_68081.7	13	LSU Helix 20 Hairpin loop
13	HL_11547.6	11	LSU 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.
14	HL_34027.6	11	5S Loop C - Upper part of Hairpin Loop.
15	HL_48507.2	11	LSU 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
16	HL_80459.7	11
17	HL_17723.6	10	LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
18	HL_18156.6	10	LSU Helix 72 (H72) Hairpin Loop
19	HL_34108.6	10	LSU Helix 37 (H37) Hairpin Loop.
20	HL_87136.6	10	LSU Helix 39A Hairpin loop
21	HL_75579.6	10
22	HL_24544.5	10	LSU Helix 53 (H53) Hairpin Loop. T-loop like.
23	HL_41833.6	10	LSU Helix 81 (H81) Hairpin Loop
24	HL_46489.6	9	LSU H89 Hairpin Loop
25	HL_70420.6	9	LSU Helix 97 Hairpin loop
26	HL_85534.5	9	LSU Helix 65 (H65) Hairpin Loop. T-loop like.
27	HL_39872.6	9	LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
28	HL_01926.7	9	LSU Helix 71 (H71) Hairpin Loop.
29	HL_88311.6	8	LSU Helix 35 (H35) Hairpin Loop
30	HL_11509.6	8	LSU Helix 6 (H6) Hairpin Loop.
31	HL_82538.5	7	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
32	HL_19626.3	7	LSU 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
33	HL_62228.6	7	LSU Helix 35A (H35A) Hairpin Loop
34	HL_99908.4	7	LSU Helix 69 (H69) Hairpin Loop
35	HL_66174.3	6	cHS GU/cWS Double Platform creates Intercalation site
36	HL_86077.3	5	GNRA with one bulged base \| GNRA-like with bulged base.
37	HL_28422.2	4
38	HL_43357.2	4	SSU Central Pseudoknot (forms helix 2)
39	HL_82418.2	4	LSU Helix 8 (H8) Hairpin Loop
40	HL_21419.2	3	UNCG-like. cWW Closing pair. \| UNCG-like. cWW Closing pair. \| LSU: Part of IL/3WJ between H55 and H56.
41	HL_64371.4	3	SSU Central Pseudoknot (forms helix 2)
42	HL_27429.5	3

Removed motif groups

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

Added motif groups

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