1.17 | 1.18

Changes in PDB files used for clustering

Release 1.17 has 263 PDB files, release 1.18 has 268 PDB files, 259 of them are identical.

2 equivalence classes changed representatives: 4TUX → 4TV0, 4LCK → 4TZZ.

7 new structures in release 1.18: 4PDB, 4QJD, 4QJH, 4R0D, 4TZX, 4W21, 4W23.

Obsolete: 1VWW → 4W1Z, 1VX2 → 4W28.

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 1.17 has 323 motif groups, release 1.18 has 316 motif groups, 212 of them are identical.

54 motif groups were updated, 57 groups are present only in release 1.17, 50 groups are only in release 1.18.

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_91226.7	23	Kissing Hairpin motif
2	HL_27271.4	15	LSU Helix 96 (H96) Hairpin Loop
3	HL_17723.6	10	LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
4	HL_15603.2	9	U1A protein-binding Hairpin Loop.
5	HL_39872.6	9	LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
6	HL_82538.5	7	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
7	HL_42677.2	7
8	HL_64543.4	6	SSU Helix 31 (h31) Hairpin Loop
9	HL_72543.3	6	LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
10	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
11	HL_06643.3	6	tRNA D-loop. Sec tRNA
12	HL_08382.4	5
13	HL_95720.1	5	Double tSH (double sheared) with bulged base \| LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
14	HL_72273.1	5	tRNA D-loop
15	HL_62881.1	4	RNase P Structured Hairpin Loop
16	HL_61547.5	4	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
17	HL_11376.1	4	LSU Helix 8 (H8) Hairpin Loop
18	HL_66677.2	4
19	HL_92706.1	4	LSU Helix 28 (H28) Hairpin Loop \| LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
20	HL_82418.2	4	LSU Helix 8 (H8) Hairpin Loop
21	HL_72846.1	4	LSU Helix 69 (H69) Hairpin Loop
22	HL_79956.2	4	GNRA-like with 5'-stacking of first unpaired base.
23	HL_25124.2	4	tSW GA closed tetraloops
24	HL_48116.3	4	GNRA-like with 5'-stacking of first unpaired base.
25	HL_18587.3	4
26	HL_19905.4	4	LSU: Part of IL/3WJ between H55 and H56.
27	HL_98833.3	3
28	HL_42094.2	3
29	HL_27429.5	3
30	HL_60200.2	3
31	HL_21419.2	3	UNCG-like. cWW Closing pair. \| UNCG-like. cWW Closing pair. \| LSU: Part of IL/3WJ between H55 and H56.
32	HL_95969.1	3	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
33	HL_58083.3	3
34	HL_84911.1	3
35	HL_65249.2	3
36	HL_06122.2	3
37	HL_41827.1	3
38	HL_19221.2	3
39	HL_80492.2	3	tRNA D-loop
40	HL_55684.1	3
41	HL_74307.1	3
42	HL_28339.2	3
43	HL_91142.1	3	Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
44	HL_91693.2	3
45	HL_21545.2	3	LSU Helix 96 (H96) Hairpin Loop
46	HL_59516.1	3	cHS GU/cWS Double Platform creates Intercalation site
47	HL_78361.1	3
48	HL_76766.4	3
49	HL_65924.1	2
50	HL_84172.1	2
51	HL_50312.1	2
52	HL_46388.1	2
53	HL_01766.1	2	LSU Helix 35 (H35) Hairpin Loop from Yeast
54	HL_38130.2	2
55	HL_19399.1	2
56	HL_87554.1	2
57	HL_54719.1	2	Two base, cross-stacked hairpin loop
58	HL_93771.1	2	tRNA T-loop distorted by RS binding
59	HL_49210.1	2
60	HL_26495.1	2
61	HL_05361.1	2
62	HL_98577.1	2
63	HL_20004.1	2
64	HL_77391.1	2
65	HL_57263.1	2
66	HL_64438.1	2	Kink-turn-like Hairpin Loop
67	HL_86123.2	2	SSU Helix 42 (h42) Hairpin Loop. T-loop like.
68	HL_42077.3	2	LSU Helix 28 (H28) Hairpin Loop
69	HL_01389.1	2
70	HL_42553.1	2
71	HL_35652.1	2	LSU Helix 84 (H84) Hairpin Loop. E.coli.
72	HL_42436.1	2	Kissing Hairpin from di-GMP-II riboswitch
73	HL_44467.1	2
74	HL_15793.1	2	UNCG-like. cWW Closing pair.
75	HL_50937.1	2
76	HL_24711.1	2
77	HL_51271.1	2
78	HL_33451.1	2
79	HL_34912.1	2
80	HL_27478.1	2
81	HL_24473.3	2	tRNA D-loop
82	HL_70383.1	2	GNRA-like
83	HL_41700.1	2
84	HL_38898.1	1
85	HL_33640.1	1
86	HL_99932.1	1
87	HL_50018.1	1
88	HL_98834.1	1
89	HL_21695.1	1	UNCG-like. cWW Closing pair.
90	HL_45411.1	1
91	HL_52540.1	1
92	HL_05113.1	1
93	HL_19132.1	1
94	HL_15291.1	1	GNRA with one bulged base
95	HL_70912.1	1
96	HL_03785.1	1	LSU Helix 8 (H8) Hairpin Loop
97	HL_82288.1	1
98	HL_97022.1	1
99	HL_59225.1	1
100	HL_22533.1	1
101	HL_89473.1	1
102	HL_17008.1	1	Nova-2 KH3 domain binding hairpin
103	HL_84768.1	1
104	HL_35865.1	1
105	HL_53789.1	1
106	HL_20806.1	1
107	HL_95049.1	1	Two base, cross-stacked hairpin loop
108	HL_84888.1	1	T-loop like but without tWH UA
109	HL_88960.1	1
110	HL_30731.1	1
111	HL_78228.1	1
112	HL_74451.1	1
113	HL_17537.1	1
114	HL_99584.1	1
115	HL_96012.1	1
116	HL_14384.1	1
117	HL_38138.1	1
118	HL_62564.1	1	LSU Helix 28 (H28) Hairpin Loop \| LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
119	HL_04305.1	1
120	HL_46055.1	1
121	HL_14524.1	1
122	HL_45740.1	1
123	HL_60203.1	1
124	HL_45358.1	1	Double hairpin loop based on GGA triple
125	HL_66877.1	1	cSH GU/cWS double platform, intercalation site
126	HL_68579.1	1
127	HL_67000.1	1
128	HL_55272.1	1
129	HL_99207.1	1	Tetrahymena LSU hairpin poorly modeled
130	HL_84720.1	1
131	HL_85018.1	1
132	HL_08203.1	1
133	HL_23080.1	1
134	HL_19074.1	1
135	HL_57644.1	1
136	HL_25195.1	1
137	HL_78507.1	1
138	HL_87223.1	1
139	HL_68435.1	1
140	HL_66880.1	1
141	HL_91613.1	1
142	HL_93263.1	1
143	HL_53015.1	1
144	HL_97784.1	1
145	HL_39846.1	1
146	HL_19452.1	1	tRNA D-loop
147	HL_30008.1	1
148	HL_14536.1	1
149	HL_56775.1	1
150	HL_77692.1	1	tRNA D-loop
151	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.
152	HL_85044.1	1	LSU Helix 10 (H10) Hairpin E.coli
153	HL_19363.1	1
154	HL_00721.1	1
155	HL_58223.1	1
156	HL_55450.1	1
157	HL_10116.1	1	Kink-turn-like Hairpin Loop
158	HL_98233.1	1
159	HL_42345.1	1
160	HL_72389.1	1
161	HL_78422.1	1	SSU Central Pseudoknot (forms helix 2)
162	HL_36151.1	1	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
163	HL_65802.1	1
164	HL_93428.1	1
165	HL_04979.1	1	LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
166	HL_24707.1	1
167	HL_48480.1	1
168	HL_26579.1	1
169	HL_84289.1	1
170	HL_44390.1	1
171	HL_47337.1	1
172	HL_11257.1	1
173	HL_46570.1	1
174	HL_22461.1	1
175	HL_21839.1	1
176	HL_96994.1	1
177	HL_42255.1	1
178	HL_52116.1	1
179	HL_99612.1	1
180	HL_27236.1	1
181	HL_99779.1	1
182	HL_37962.1	1
183	HL_63997.1	1
184	HL_39422.1	1
185	HL_56809.1	1
186	HL_67761.1	1
187	HL_93530.1	1
188	HL_83865.1	1
189	HL_57667.1	1
190	HL_79038.1	1	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
191	HL_24108.1	1
192	HL_62374.1	1
193	HL_55202.1	1	U2B"-U2A" binding hairpin loop
194	HL_59610.1	1
195	HL_73972.1	1
196	HL_10075.1	1
197	HL_57339.1	1
198	HL_93567.1	1
199	HL_57923.1	1
200	HL_30366.1	1	LSU Helix 10 (H10) Hairpin E.coli
201	HL_57217.1	1	cHS platform Intercalation Site
202	HL_79902.1	1
203	HL_27397.1	1
204	HL_12706.1	1
205	HL_13786.1	1
206	HL_25175.1	1
207	HL_78389.1	1
208	HL_75624.1	1
209	HL_49492.1	1	Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
210	HL_20028.1	1
211	HL_59182.1	1
212	HL_28776.1	1

Updated motif groups

#	Motif id	Instances	Description
1	HL_67042.17	328	GNRA Hairpin motifs
2	HL_72498.17	78	T-loops with two bulged bases
3	HL_39895.11	46	UNCG Hairpin motifs
4	HL_18781.9	30	Double sheared (tSH) with U-turn
5	HL_97270.8	21	T-loops with 1 bulged base
6	HL_74411.3	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
7	HL_74465.7	18	tRNA Anti-Codon loop
8	HL_46175.6	17	SSU Helix 43 (h43) Hairpin Loop E.coli \| 16S helix 23 and 24 hairpin loops \| 16S helix 23 and 24 hairpin loops
9	HL_75759.9	16
10	HL_33402.8	15	LSU Helix 13 (H13) Hairpin loop. GNRA-like.
11	HL_56824.7	14	LSU Helix 60A. LSU Helix 63A.
12	HL_68081.8	13	LSU Helix 20 Hairpin loop
13	HL_82294.6	13	SSU Helix 37 (h37) Hairpin loop.
14	HL_48507.3	12	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_48039.4	12	MS2 virus RNA Hairpin
16	HL_01926.8	11	LSU Helix 71 (H71) Hairpin Loop.
17	HL_11547.7	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.
18	HL_24544.6	11	LSU Helix 53 (H53) Hairpin Loop. T-loop like.
19	HL_34027.7	11	5S Loop C - Upper part of Hairpin Loop.
20	HL_80459.8	11
21	HL_70420.7	10	LSU Helix 97 Hairpin loop
22	HL_41833.7	10	LSU Helix 81 (H81) Hairpin Loop
23	HL_87136.7	10	LSU Helix 39A Hairpin loop
24	HL_18156.7	10	LSU Helix 72 (H72) Hairpin Loop
25	HL_75579.7	10
26	HL_46489.7	10	LSU H89 Hairpin Loop
27	HL_34108.7	10	LSU Helix 37 (H37) Hairpin Loop.
28	HL_85534.6	9	LSU Helix 65 (H65) Hairpin Loop. T-loop like.
29	HL_11509.7	8	LSU Helix 6 (H6) Hairpin Loop.
30	HL_57087.2	8	Two base, cross-stacked hairpin loop
31	HL_88311.7	8	LSU Helix 35 (H35) Hairpin Loop
32	HL_19626.4	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_27353.2	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.
34	HL_99908.5	7	LSU Helix 69 (H69) Hairpin Loop
35	HL_45018.5	7	Hairpin-Hairpin Interacting HL
36	HL_62228.7	7	LSU Helix 35A (H35A) Hairpin Loop
37	HL_00311.2	7	SSU Central Pseudoknot (forms helix 2)
38	HL_66174.4	7	cHS GU/cWS Double Platform creates Intercalation site
39	HL_48254.5	6	LSU Helix 84 (H84) Hairpin Loop.
40	HL_12908.2	6	LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
41	HL_39203.2	5
42	HL_96915.4	5
43	HL_86077.4	5	GNRA with one bulged base \| GNRA-like with bulged base.
44	HL_43357.3	5	SSU Central Pseudoknot (forms helix 2)
45	HL_86115.3	5
46	HL_94364.2	5
47	HL_13707.3	4	cSH AA Platform containing Hairpin Loop
48	HL_31147.2	4	SSU Central Pseudoknot (forms helix 2)
49	HL_89131.2	4
50	HL_19033.2	4	SSU Helix 43 (h43) Hairpin Loop E.coli \| 16S helix 23 and 24 hairpin loops
51	HL_23290.2	3
52	HL_01788.3	3	LSU Yeast Hairpin Loop
53	HL_94578.3	2
54	HL_64371.5	2	SSU Central Pseudoknot (forms helix 2)

Removed motif groups

#	Motif id	Instances	Description
1	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.
2	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.
3	HL_55035.1	5	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
4	HL_72372.1	5
5	HL_00415.1	5	GNRA-like. Closed by tSH UC.
6	HL_23182.2	4
7	HL_28422.2	4
8	HL_34954.1	4
9	HL_06997.2	3
10	HL_15701.1	3
11	HL_18474.1	3	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
12	HL_92260.1	2
13	HL_94212.1	2	16S helix 23 and 24 hairpin loops
14	HL_69907.1	2
15	HL_82382.1	2
16	HL_72489.1	2
17	HL_84548.1	2	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
18	HL_29892.1	2
19	HL_49961.1	2
20	HL_74026.1	2
21	HL_05350.1	1
22	HL_50954.1	1
23	HL_63642.1	1
24	HL_76004.1	1
25	HL_23628.1	1
26	HL_38897.1	1	S8 operon binding Hairpin Loop. T-loop like with purine stacking.
27	HL_65107.1	1
28	HL_79541.1	1	16S helix 23 and 24 hairpin loops
29	HL_92594.1	1
30	HL_08388.1	1
31	HL_24422.1	1
32	HL_39035.1	1
33	HL_58052.1	1
34	HL_65428.1	1
35	HL_81994.1	1
36	HL_11337.1	1
37	HL_25197.1	1
38	HL_39943.1	1
39	HL_61871.1	1
40	HL_94639.1	1
41	HL_25947.1	1
42	HL_40070.1	1
43	HL_62500.1	1
44	HL_83263.1	1
45	HL_94813.1	1
46	HL_16822.1	1
47	HL_40731.1	1
48	HL_62880.1	1
49	HL_94981.1	1
50	HL_63001.1	1
51	HL_87172.1	1
52	HL_95822.1	1
53	HL_04584.1	1
54	HL_19673.1	1
55	HL_50078.1	1
56	HL_63323.1	1
57	HL_75984.1	1

Added motif groups

#	Motif id	Instances	Description
1	HL_71179.1	20	LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. \| LSU Helix 80 (H80) P-site Hairpin Loop. \| 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_90506.1	9	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.
3	HL_80263.1	5
4	HL_57963.1	4	GNRA-like. Closed by tSH UC.
5	HL_13352.1	4
6	HL_90792.1	4
7	HL_19066.1	4	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
8	HL_85551.1	4
9	HL_01475.1	4
10	HL_82098.1	3	16S helix 23 and 24 hairpin loops
11	HL_57225.1	3
12	HL_22952.1	2
13	HL_43821.1	2
14	HL_57621.1	2
15	HL_23337.1	2
16	HL_45343.1	2
17	HL_05894.1	2
18	HL_08494.1	2	LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. \| LSU Helix 80 (H80) P-site Hairpin Loop.
19	HL_52338.1	2
20	HL_53279.1	2
21	HL_84575.1	2
22	HL_91125.1	2
23	HL_00394.1	2
24	HL_72388.1	2	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
25	HL_96309.1	2	S8 operon binding Hairpin Loop. T-loop like with purine stacking.
26	HL_03007.1	1
27	HL_87958.1	1
28	HL_04735.1	1
29	HL_81815.1	1
30	HL_88259.1	1	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
31	HL_31261.1	1
32	HL_45777.1	1
33	HL_61400.1	1
34	HL_89958.1	1	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
35	HL_33822.1	1
36	HL_49013.1	1
37	HL_64778.1	1
38	HL_83609.1	1
39	HL_36554.1	1
40	HL_64859.1	1
41	HL_84030.1	1
42	HL_16959.1	1
43	HL_38777.1	1
44	HL_70061.1	1
45	HL_40222.1	1
46	HL_56596.1	1
47	HL_91581.1	1
48	HL_19755.1	1
49	HL_42161.1	1
50	HL_85802.1	1