1.15 | 1.16

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: 4L8R → 4TUX.

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 id	Instances	Description
1	HL_74465.6	16	tRNA Anti-Codon loop
2	HL_17723.5	10	LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
3	HL_15603.2	9	U1A protein-binding Hairpin Loop.
4	HL_42677.2	7
5	HL_06643.3	6	tRNA D-loop. Sec tRNA
6	HL_89236.1	6	LSU Helix 69 (H69) Hairpin Loop
7	HL_72543.3	6	LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
8	HL_72273.1	5	tRNA D-loop
9	HL_95720.1	5	Double tSH (double sheared) with bulged base \| LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
10	HL_78731.2	5	LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
11	HL_08382.4	5
12	HL_23182.2	4
13	HL_48116.3	4	GNRA-like with 5'-stacking of first unpaired base.
14	HL_19905.4	4	LSU: Part of IL/3WJ between H55 and H56.
15	HL_79956.2	4	GNRA-like with 5'-stacking of first unpaired base.
16	HL_62881.1	4	RNase P Structured Hairpin Loop
17	HL_61547.5	4	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
18	HL_92706.1	4	LSU Helix 28 (H28) Hairpin Loop \| LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
19	HL_11376.1	4	LSU Helix 8 (H8) Hairpin Loop
20	HL_25124.2	4	tSW GA closed tetraloops
21	HL_82418.1	4	LSU Helix 8 (H8) Hairpin Loop
22	HL_78361.1	3
23	HL_84911.1	3
24	HL_76766.4	3
25	HL_06122.2	3
26	HL_91693.2	3
27	HL_65249.2	3
28	HL_19033.1	3	SSU Helix 43 (h43) Hairpin Loop E.coli \| 16S helix 23 and 24 hairpin loops
29	HL_58083.3	3
30	HL_27429.4	3
31	HL_55684.1	3
32	HL_13707.2	3	cSH AA Platform containing Hairpin Loop
33	HL_19221.2	3
34	HL_74307.1	3
35	HL_91142.1	3	Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
36	HL_98833.3	3
37	HL_95969.1	3	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
38	HL_06997.2	3
39	HL_21545.2	3	LSU Helix 96 (H96) Hairpin Loop
40	HL_64371.3	3	SSU Central Pseudoknot (forms helix 2)
41	HL_80492.2	3	tRNA D-loop
42	HL_41827.1	3
43	HL_60200.2	3
44	HL_86123.2	2	SSU Helix 42 (h42) Hairpin Loop. T-loop like.
45	HL_50937.1	2
46	HL_93771.1	2	tRNA T-loop distorted by RS binding
47	HL_24711.1	2
48	HL_42077.3	2	LSU Helix 28 (H28) Hairpin Loop
49	HL_38130.2	2
50	HL_20004.1	2
51	HL_50312.1	2
52	HL_42436.1	2	Kissing Hairpin from di-GMP-II riboswitch
53	HL_44467.1	2
54	HL_64438.1	2	Kink-turn-like Hairpin Loop
55	HL_84172.1	2
56	HL_05361.1	2
57	HL_27478.1	2
58	HL_26495.1	2
59	HL_19399.1	2
60	HL_98577.1	2
61	HL_49210.1	2
62	HL_92635.1	2
63	HL_41700.1	2
64	HL_65924.1	2
65	HL_23290.1	2
66	HL_24473.3	2	tRNA D-loop
67	HL_42553.1	2
68	HL_38964.1	2	LSU Helix 84 (H84) Hairpin Loop. E.coli.
69	HL_33451.1	2
70	HL_34912.1	2
71	HL_87554.1	2
72	HL_56775.1	1
73	HL_77692.1	1	tRNA D-loop
74	HL_10075.1	1
75	HL_21695.1	1	UNCG-like. cWW Closing pair.
76	HL_57923.1	1
77	HL_99779.1	1
78	HL_37962.1	1
79	HL_63997.1	1
80	HL_39422.1	1
81	HL_68579.1	1
82	HL_67000.1	1
83	HL_78228.1	1
84	HL_97784.1	1
85	HL_19452.1	1	tRNA D-loop
86	HL_42345.1	1
87	HL_14536.1	1
88	HL_42255.1	1
89	HL_99612.1	1
90	HL_50018.1	1
91	HL_93567.1	1
92	HL_45411.1	1
93	HL_30366.1	1	LSU Helix 10 (H10) Hairpin E.coli
94	HL_57217.1	1	cHS platform Intercalation Site
95	HL_79902.1	1
96	HL_91613.1	1
97	HL_93263.1	1
98	HL_55272.1	1
99	HL_10116.1	1	Kink-turn-like Hairpin Loop
100	HL_75984.1	1
101	HL_98233.1	1
102	HL_96994.1	1
103	HL_72389.1	1
104	HL_59610.1	1
105	HL_52116.1	1
106	HL_65802.1	1
107	HL_46055.1	1
108	HL_52540.1	1
109	HL_05113.1	1
110	HL_19132.1	1
111	HL_53015.1	1
112	HL_46570.1	1
113	HL_22461.1	1
114	HL_79038.1	1	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
115	HL_24108.1	1
116	HL_49998.1	1
117	HL_73972.1	1
118	HL_99932.1	1
119	HL_53789.1	1
120	HL_20806.1	1
121	HL_19226.1	1
122	HL_95049.1	1	Two base, cross-stacked hairpin loop
123	HL_84888.1	1	T-loop like but without tWH UA
124	HL_88960.1	1
125	HL_44390.1	1
126	HL_93530.1	1
127	HL_83865.1	1
128	HL_57667.1	1
129	HL_20028.1	1
130	HL_59182.1	1
131	HL_64102.1	1	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
132	HL_38897.1	1	S8 operon binding Hairpin Loop. T-loop like with purine stacking.
133	HL_35865.1	1
134	HL_04979.1	1	LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
135	HL_85044.1	1	LSU Helix 10 (H10) Hairpin E.coli
136	HL_25195.1	1
137	HL_45740.1	1
138	HL_45358.1	1	Double hairpin loop based on GGA triple
139	HL_66877.1	1	cSH GU/cWS double platform, intercalation site
140	HL_56809.1	1
141	HL_67761.1	1
142	HL_47337.1	1
143	HL_82243.1	1
144	HL_75624.1	1
145	HL_49492.1	1	Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
146	HL_59225.1	1
147	HL_85982.1	1
148	HL_55202.1	1	U2B"-U2A" binding hairpin loop
149	HL_84768.1	1
150	HL_33640.1	1
151	HL_04305.1	1
152	HL_78507.1	1
153	HL_60203.1	1
154	HL_68435.1	1
155	HL_66880.1	1
156	HL_12706.1	1
157	HL_13786.1	1
158	HL_78389.1	1
159	HL_11337.1	1
160	HL_97022.1	1
161	HL_99584.1	1
162	HL_22533.1	1
163	HL_53116.1	1
164	HL_38898.1	1
165	HL_38138.1	1
166	HL_93428.1	1
167	HL_24707.1	1
168	HL_19363.1	1
169	HL_87223.1	1
170	HL_58223.1	1
171	HL_27397.1	1
172	HL_70912.1	1
173	HL_03785.1	1	LSU Helix 8 (H8) Hairpin Loop
174	HL_25175.1	1
175	HL_82288.1	1
176	HL_84720.1	1
177	HL_17537.1	1
178	HL_08203.1	1
179	HL_96012.1	1
180	HL_59982.1	1
181	HL_17008.1	1	Nova-2 KH3 domain binding hairpin
182	HL_62564.1	1	LSU Helix 28 (H28) Hairpin Loop \| LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
183	HL_27236.1	1
184	HL_25197.1	1
185	HL_48480.1	1
186	HL_00721.1	1
187	HL_26579.1	1
188	HL_84289.1	1
189	HL_30731.1	1
190	HL_62880.1	1
191	HL_99207.1	1	Tetrahymena LSU hairpin poorly modeled
192	HL_39846.1	1
193	HL_85018.1	1
194	HL_30008.1	1
195	HL_23080.1	1
196	HL_70872.1	1

Updated motif groups

#	Motif id	Instances	Description
1	HL_67042.15	318	GNRA Hairpin motifs
2	HL_72498.15	76	T-loops with two bulged bases
3	HL_39895.9	43	UNCG Hairpin motifs
4	HL_18781.7	30	Double sheared (tSH) with U-turn
5	HL_91226.6	22	Kissing Hairpin motif
6	HL_97270.6	21	T-loops with 1 bulged base
7	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
8	HL_75759.7	16
9	HL_27271.4	15	LSU Helix 96 (H96) Hairpin Loop
10	HL_56824.5	14	LSU Helix 60A. LSU Helix 63A.
11	HL_33402.6	14	LSU Helix 13 (H13) Hairpin loop. GNRA-like.
12	HL_82294.5	13	SSU Helix 37 (h37) Hairpin loop.
13	HL_68081.6	13	LSU Helix 20 Hairpin loop
14	HL_48039.3	12	MS2 virus RNA Hairpin
15	HL_80459.6	11
16	HL_11547.5	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_34027.5	11	5S Loop C - Upper part of Hairpin Loop.
18	HL_24544.4	10	LSU Helix 53 (H53) Hairpin Loop. T-loop like.
19	HL_41833.5	10	LSU Helix 81 (H81) Hairpin Loop
20	HL_75579.5	10
21	HL_87136.5	10	LSU Helix 39A Hairpin loop
22	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.
23	HL_18156.5	10	LSU Helix 72 (H72) Hairpin Loop
24	HL_34108.5	10	LSU Helix 37 (H37) Hairpin Loop.
25	HL_39872.5	9	LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
26	HL_70420.5	9	LSU Helix 97 Hairpin loop
27	HL_01926.6	9	LSU Helix 71 (H71) Hairpin Loop.
28	HL_46489.5	9	LSU H89 Hairpin Loop
29	HL_85534.4	9	LSU Helix 65 (H65) Hairpin Loop. T-loop like.
30	HL_88311.5	8	LSU Helix 35 (H35) Hairpin Loop
31	HL_11509.5	8	LSU Helix 6 (H6) Hairpin Loop.
32	HL_19626.2	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_99908.3	7	LSU Helix 69 (H69) Hairpin Loop
34	HL_62228.5	7	LSU Helix 35A (H35A) Hairpin Loop
35	HL_82538.4	7	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
36	HL_48254.4	6	LSU Helix 84 (H84) Hairpin Loop.
37	HL_64543.4	6	SSU Helix 31 (h31) Hairpin Loop
38	HL_45018.4	6	Hairpin-Hairpin Interacting HL
39	HL_66174.2	6	cHS GU/cWS Double Platform creates Intercalation site
40	HL_86077.2	5	GNRA with one bulged base \| GNRA-like with bulged base.
41	HL_86115.2	5
42	HL_66677.2	4
43	HL_18587.3	4
44	HL_96915.3	4
45	HL_01788.2	3	LSU Yeast Hairpin Loop
46	HL_42094.2	3
47	HL_28339.2	3
48	HL_94578.2	3

Removed motif groups

#	Motif id	Instances	Description
1	HL_92565.1	16	LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. \| LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
2	HL_49036.5	13	LSU Helix 11 (H11) Hairpin Loop. GNRA-like. \| GNRA with one bulged base
3	HL_39942.4	8	LSU Helix 91 (H91) Hairpin Loop
4	HL_57514.2	6	Two base, cross-stacked hairpin loop
5	HL_31318.2	6	SSU Central Pseudoknot (forms helix 2)
6	HL_25878.1	5	UNCG-like. cWW Closing pair. \| UNCG-like. cWW Closing pair. \| LSU: Part of IL/3WJ between H55 and H56.
7	HL_98523.2	4	GNRA-like. Closed by tSH UC.
8	HL_54751.3	3
9	HL_35619.3	3
10	HL_86398.2	3
11	HL_99633.2	3
12	HL_33223.1	3	SSU Central Pseudoknot (forms helix 2)
13	HL_33875.1	3	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
14	HL_74559.2	3	Two base, cross-stacked hairpin loop
15	HL_78660.1	2
16	HL_94309.1	2	GNRA with one bulged base
17	HL_23129.1	2
18	HL_84967.1	2
19	HL_64803.1	2
20	HL_65386.1	2	UNCG-like. cWW Closing pair.
21	HL_09641.1	2	SSU Central Pseudoknot (forms helix 2)
22	HL_91872.1	2
23	HL_19528.1	2
24	HL_53745.1	2
25	HL_94189.1	2	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
26	HL_20920.1	1
27	HL_34491.1	1
28	HL_82622.1	1	SSU Central Pseudoknot (forms helix 2)
29	HL_95079.1	1
30	HL_23195.1	1
31	HL_64209.1	1	UNCG-like. cWW Closing pair. \| UNCG-like. cWW Closing pair. \| LSU: Part of IL/3WJ between H55 and H56.
32	HL_95716.1	1
33	HL_44485.1	1	16S helix 23 and 24 hairpin loops
34	HL_01418.1	1
35	HL_29196.1	1
36	HL_44522.1	1
37	HL_90541.1	1	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
38	HL_69403.1	1	GNRA-like
39	HL_10894.1	1
40	HL_50059.1	1	LSU Helix 35 (H35) Hairpin Loop from Yeast
41	HL_73465.1	1

Added motif groups

#	Motif id	Instances	Description
1	HL_37020.1	19	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.
2	HL_74411.1	17	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
3	HL_48507.1	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
4	HL_57087.1	8	Two base, cross-stacked hairpin loop
5	HL_00311.1	7	SSU Central Pseudoknot (forms helix 2)
6	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.
7	HL_55035.1	5	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
8	HL_00415.1	5	GNRA-like. Closed by tSH UC.
9	HL_72372.1	5
10	HL_94364.1	5
11	HL_39203.1	5
12	HL_31147.1	4	SSU Central Pseudoknot (forms helix 2)
13	HL_89131.1	4
14	HL_34954.1	4
15	HL_43357.1	4	SSU Central Pseudoknot (forms helix 2)
16	HL_28422.1	4
17	HL_15701.1	3
18	HL_18474.1	3	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
19	HL_09697.1	2
20	HL_54719.1	2	Two base, cross-stacked hairpin loop
21	HL_69907.1	2
22	HL_77391.1	2
23	HL_21419.1	2	UNCG-like. cWW Closing pair. \| UNCG-like. cWW Closing pair. \| LSU: Part of IL/3WJ between H55 and H56.
24	HL_70383.1	2	GNRA-like
25	HL_92260.1	2
26	HL_35425.1	2
27	HL_01389.1	2
28	HL_46388.1	2
29	HL_72489.1	2
30	HL_82049.1	2
31	HL_01766.1	2	LSU Helix 35 (H35) Hairpin Loop from Yeast
32	HL_74026.1	2
33	HL_82382.1	2
34	HL_15793.1	2	UNCG-like. cWW Closing pair.
35	HL_84548.1	2	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
36	HL_29892.1	2
37	HL_53358.1	2	16S helix 23 and 24 hairpin loops
38	HL_19673.1	1
39	HL_40070.1	1
40	HL_62374.1	1
41	HL_98834.1	1
42	HL_11257.1	1
43	HL_40731.1	1
44	HL_62500.1	1
45	HL_78422.1	1	SSU Central Pseudoknot (forms helix 2)
46	HL_14524.1	1
47	HL_23628.1	1
48	HL_55450.1	1
49	HL_63001.1	1
50	HL_81994.1	1
51	HL_15291.1	1	GNRA with one bulged base
52	HL_24422.1	1
53	HL_36151.1	1	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
54	HL_63323.1	1
55	HL_94639.1	1
56	HL_25947.1	1
57	HL_57339.1	1
58	HL_63642.1	1
59	HL_94813.1	1
60	HL_04382.1	1
61	HL_39035.1	1
62	HL_50078.1	1
63	HL_57644.1	1
64	HL_65107.1	1
65	HL_83263.1	1
66	HL_94981.1	1
67	HL_04584.1	1
68	HL_16822.1	1
69	HL_50954.1	1
70	HL_58052.1	1
71	HL_65428.1	1
72	HL_74451.1	1
73	HL_95822.1	1
74	HL_05350.1	1
75	HL_39943.1	1
76	HL_61871.1	1
77	HL_68904.1	1
78	HL_76004.1	1
79	HL_87172.1	1
80	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.