1.16 | 1.17

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: 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_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.
10	HL_42677.2	7
11	HL_00311.1	7	SSU Central Pseudoknot (forms helix 2)
12	HL_64543.4	6	SSU Helix 31 (h31) Hairpin Loop
13	HL_45018.4	6	Hairpin-Hairpin Interacting HL
14	HL_48254.4	6	LSU Helix 84 (H84) Hairpin Loop.
15	HL_72543.3	6	LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
16	HL_06643.3	6	tRNA D-loop. Sec tRNA
17	HL_08382.4	5
18	HL_94364.1	5
19	HL_72273.1	5	tRNA D-loop
20	HL_72372.1	5
21	HL_00415.1	5	GNRA-like. Closed by tSH UC.
22	HL_55035.1	5	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
23	HL_39203.1	5
24	HL_95720.1	5	Double tSH (double sheared) with bulged base \| LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
25	HL_86115.2	5
26	HL_23182.2	4
27	HL_25124.2	4	tSW GA closed tetraloops
28	HL_31147.1	4	SSU Central Pseudoknot (forms helix 2)
29	HL_66677.2	4
30	HL_18587.3	4
31	HL_19905.4	4	LSU: Part of IL/3WJ between H55 and H56.
32	HL_92706.1	4	LSU Helix 28 (H28) Hairpin Loop \| LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
33	HL_96915.3	4
34	HL_11376.1	4	LSU Helix 8 (H8) Hairpin Loop
35	HL_34954.1	4
36	HL_48116.3	4	GNRA-like with 5'-stacking of first unpaired base.
37	HL_62881.1	4	RNase P Structured Hairpin Loop
38	HL_89131.1	4
39	HL_61547.5	4	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
40	HL_79956.2	4	GNRA-like with 5'-stacking of first unpaired base.
41	HL_18474.1	3	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
42	HL_58083.3	3
43	HL_74307.1	3
44	HL_80492.2	3	tRNA D-loop
45	HL_91693.2	3
46	HL_95969.1	3	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
47	HL_94578.2	3
48	HL_19033.1	3	SSU Helix 43 (h43) Hairpin Loop E.coli \| 16S helix 23 and 24 hairpin loops
49	HL_78361.1	3
50	HL_41827.1	3
51	HL_15701.1	3
52	HL_19221.2	3
53	HL_21545.2	3	LSU Helix 96 (H96) Hairpin Loop
54	HL_28339.2	3
55	HL_65249.2	3
56	HL_06122.2	3
57	HL_42094.2	3
58	HL_60200.2	3
59	HL_84911.1	3
60	HL_01788.2	3	LSU Yeast Hairpin Loop
61	HL_13707.2	3	cSH AA Platform containing Hairpin Loop
62	HL_76766.4	3
63	HL_06997.2	3
64	HL_55684.1	3
65	HL_91142.1	3	Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
66	HL_98833.3	3
67	HL_38130.2	2
68	HL_42553.1	2
69	HL_46388.1	2
70	HL_86123.2	2	SSU Helix 42 (h42) Hairpin Loop. T-loop like.
71	HL_23290.1	2
72	HL_33451.1	2
73	HL_64438.1	2	Kink-turn-like Hairpin Loop
74	HL_84548.1	2	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
75	HL_92260.1	2
76	HL_20004.1	2
77	HL_41700.1	2
78	HL_54719.1	2	Two base, cross-stacked hairpin loop
79	HL_27478.1	2
80	HL_34912.1	2
81	HL_50312.1	2
82	HL_87554.1	2
83	HL_01389.1	2
84	HL_05361.1	2
85	HL_42077.3	2	LSU Helix 28 (H28) Hairpin Loop
86	HL_50937.1	2
87	HL_72489.1	2
88	HL_82382.1	2
89	HL_01766.1	2	LSU Helix 35 (H35) Hairpin Loop from Yeast
90	HL_15793.1	2	UNCG-like. cWW Closing pair.
91	HL_24473.3	2	tRNA D-loop
92	HL_26495.1	2
93	HL_29892.1	2
94	HL_19399.1	2
95	HL_69907.1	2
96	HL_98577.1	2
97	HL_24711.1	2
98	HL_42436.1	2	Kissing Hairpin from di-GMP-II riboswitch
99	HL_49210.1	2
100	HL_65924.1	2
101	HL_70383.1	2	GNRA-like
102	HL_74026.1	2
103	HL_77391.1	2
104	HL_84172.1	2
105	HL_93771.1	2	tRNA T-loop distorted by RS binding
106	HL_04305.1	1
107	HL_14524.1	1
108	HL_19673.1	1
109	HL_40070.1	1
110	HL_49492.1	1	Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
111	HL_53015.1	1
112	HL_56775.1	1
113	HL_61871.1	1
114	HL_63997.1	1
115	HL_70912.1	1
116	HL_77692.1	1	tRNA D-loop
117	HL_84289.1	1
118	HL_98834.1	1
119	HL_04584.1	1
120	HL_10075.1	1
121	HL_14536.1	1
122	HL_25175.1	1
123	HL_38138.1	1
124	HL_40731.1	1
125	HL_46570.1	1
126	HL_50018.1	1
127	HL_53789.1	1
128	HL_56809.1	1
129	HL_58223.1	1
130	HL_62500.1	1
131	HL_66877.1	1	cSH GU/cWS double platform, intercalation site
132	HL_74451.1	1
133	HL_78228.1	1
134	HL_81994.1	1
135	HL_87172.1	1
136	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.
137	HL_99207.1	1	Tetrahymena LSU hairpin poorly modeled
138	HL_04979.1	1	LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
139	HL_10116.1	1	Kink-turn-like Hairpin Loop
140	HL_15291.1	1	GNRA with one bulged base
141	HL_23628.1	1
142	HL_25195.1	1
143	HL_27397.1	1
144	HL_33640.1	1
145	HL_38897.1	1	S8 operon binding Hairpin Loop. T-loop like with purine stacking.
146	HL_44390.1	1
147	HL_47337.1	1
148	HL_50078.1	1
149	HL_59182.1	1
150	HL_62564.1	1	LSU Helix 28 (H28) Hairpin Loop \| LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
151	HL_67000.1	1
152	HL_82288.1	1
153	HL_84720.1	1
154	HL_87223.1	1
155	HL_94639.1	1
156	HL_99612.1	1
157	HL_05350.1	1
158	HL_11337.1	1
159	HL_19132.1	1
160	HL_20806.1	1
161	HL_24108.1	1
162	HL_25197.1	1
163	HL_39035.1	1
164	HL_57217.1	1	cHS platform Intercalation Site
165	HL_59225.1	1
166	HL_62880.1	1
167	HL_65107.1	1
168	HL_67761.1	1
169	HL_72389.1	1
170	HL_75624.1	1
171	HL_78389.1	1
172	HL_84768.1	1
173	HL_93263.1	1
174	HL_94813.1	1
175	HL_96994.1	1
176	HL_99932.1	1
177	HL_24422.1	1
178	HL_25947.1	1
179	HL_45411.1	1
180	HL_55202.1	1	U2B"-U2A" binding hairpin loop
181	HL_57339.1	1
182	HL_59610.1	1
183	HL_68435.1	1
184	HL_75984.1	1
185	HL_78422.1	1	SSU Central Pseudoknot (forms helix 2)
186	HL_84888.1	1	T-loop like but without tWH UA
187	HL_88960.1	1
188	HL_93428.1	1
189	HL_94981.1	1
190	HL_97022.1	1
191	HL_12706.1	1
192	HL_19363.1	1
193	HL_21695.1	1	UNCG-like. cWW Closing pair.
194	HL_35865.1	1
195	HL_39422.1	1
196	HL_45740.1	1
197	HL_50954.1	1
198	HL_55272.1	1
199	HL_57644.1	1
200	HL_63001.1	1
201	HL_65428.1	1
202	HL_68579.1	1
203	HL_76004.1	1
204	HL_78507.1	1
205	HL_83263.1	1
206	HL_93530.1	1
207	HL_95049.1	1	Two base, cross-stacked hairpin loop
208	HL_97784.1	1
209	HL_16822.1	1
210	HL_22461.1	1
211	HL_24707.1	1
212	HL_26579.1	1
213	HL_30008.1	1
214	HL_36151.1	1	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
215	HL_39846.1	1
216	HL_42345.1	1
217	HL_46055.1	1
218	HL_48480.1	1
219	HL_52116.1	1
220	HL_55450.1	1
221	HL_57667.1	1
222	HL_60203.1	1
223	HL_63323.1	1
224	HL_65802.1	1
225	HL_73972.1	1
226	HL_79902.1	1
227	HL_83865.1	1
228	HL_85018.1	1
229	HL_93567.1	1
230	HL_03785.1	1	LSU Helix 8 (H8) Hairpin Loop
231	HL_13786.1	1
232	HL_17537.1	1
233	HL_19452.1	1	tRNA D-loop
234	HL_22533.1	1
235	HL_27236.1	1
236	HL_30366.1	1	LSU Helix 10 (H10) Hairpin E.coli
237	HL_37962.1	1
238	HL_39943.1	1
239	HL_52540.1	1
240	HL_58052.1	1
241	HL_63642.1	1
242	HL_95822.1	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_56824.6	14	LSU Helix 60A. LSU Helix 63A.
11	HL_33402.7	14	LSU Helix 13 (H13) Hairpin loop. GNRA-like.
12	HL_68081.7	13	LSU Helix 20 Hairpin loop
13	HL_34027.6	11	5S Loop C - Upper part of Hairpin Loop.
14	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
15	HL_80459.7	11
16	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.
17	HL_18156.6	10	LSU Helix 72 (H72) Hairpin Loop
18	HL_34108.6	10	LSU Helix 37 (H37) Hairpin Loop.
19	HL_87136.6	10	LSU Helix 39A Hairpin loop
20	HL_75579.6	10
21	HL_24544.5	10	LSU Helix 53 (H53) Hairpin Loop. T-loop like.
22	HL_41833.6	10	LSU Helix 81 (H81) Hairpin Loop
23	HL_17723.6	10	LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
24	HL_39872.6	9	LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
25	HL_01926.7	9	LSU Helix 71 (H71) Hairpin Loop.
26	HL_46489.6	9	LSU H89 Hairpin Loop
27	HL_70420.6	9	LSU Helix 97 Hairpin loop
28	HL_85534.5	9	LSU Helix 65 (H65) Hairpin Loop. T-loop like.
29	HL_88311.6	8	LSU Helix 35 (H35) Hairpin Loop
30	HL_11509.6	8	LSU Helix 6 (H6) Hairpin Loop.
31	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
32	HL_62228.6	7	LSU Helix 35A (H35A) Hairpin Loop
33	HL_99908.4	7	LSU Helix 69 (H69) Hairpin Loop
34	HL_82538.5	7	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
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_82418.2	4	LSU Helix 8 (H8) Hairpin Loop
38	HL_28422.2	4
39	HL_43357.2	4	SSU Central Pseudoknot (forms helix 2)
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_38964.1	2	LSU Helix 84 (H84) Hairpin Loop. E.coli.
4	HL_82049.1	2
5	HL_53358.1	2	16S helix 23 and 24 hairpin loops
6	HL_09697.1	2
7	HL_92635.1	2
8	HL_35425.1	2
9	HL_49998.1	1
10	HL_53116.1	1
11	HL_82243.1	1
12	HL_85982.1	1
13	HL_04382.1	1
14	HL_59982.1	1
15	HL_64102.1	1	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
16	HL_19226.1	1
17	HL_68904.1	1
18	HL_70872.1	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_35652.1	2	LSU Helix 84 (H84) Hairpin Loop. E.coli.
6	HL_49961.1	2
7	HL_94212.1	2	16S helix 23 and 24 hairpin loops
8	HL_51271.1	2
9	HL_57263.1	2
10	HL_79541.1	1	16S helix 23 and 24 hairpin loops
11	HL_28776.1	1
12	HL_89473.1	1
13	HL_92594.1	1
14	HL_08388.1	1
15	HL_14384.1	1
16	HL_19074.1	1