1.0 | 1.1

Changes in PDB files used for clustering

Release 1.0 has 211 PDB files, release 1.1 has 213 PDB files, 209 of them are identical.

2 equivalence classes changed representatives: 3ZD3 → 3ZP8, 2ZJR → 4IOA.

2 new structures in release 1.1: 4ILL, 4ILM.

Obsolete: 3ZD3 → 3ZP8.

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 1.0 has 252 motif groups, release 1.1 has 254 motif groups, 190 of them are identical.

40 motif groups were updated, 22 groups are present only in release 1.0, 24 groups are only in release 1.1.

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_74465.2	12	tRNA Anti-Codon loop
2	HL_48039.1	11	MS2 virus RNA Hairpin
3	HL_46175.1	10	16S helix 23 and 24 hairpin loops
4	HL_15603.1	8	U1A protein-binding Hairpin Loop.
5	HL_82294.2	8	SSU Helix 37 (h37) Hairpin loop.
6	HL_24544.1	8	LSU Helix 53 (H53) Hairpin Loop. T-loop like.
7	HL_42677.1	6
8	HL_06643.2	5	tRNA D-loop. Sec tRNA
9	HL_45018.3	5	Hairpin-Hairpin Interacting HL
10	HL_66174.1	5	cHS GU/cWS Double Platform creates Intercalation site
11	HL_72273.1	5	tRNA D-loop
12	HL_85534.1	5	LSU Helix 65 (H65) Hairpin Loop. T-loop like.
13	HL_78731.1	5	LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
14	HL_64543.1	4	SSU Helix 31 (h31) Hairpin Loop
15	HL_62881.1	4	RNase P Structured Hairpin Loop
16	HL_47784.1	4	SSU Central Pseudoknot (forms helix 2)
17	HL_98523.1	4	GNRA-like. Closed by tSH UC.
18	HL_77235.1	4	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
19	HL_29831.1	4	GNRA-like with bulged base.
20	HL_13707.2	3	cSH AA Platform containing Hairpin Loop
21	HL_58083.2	3
22	HL_54751.1	3
23	HL_42687.2	3
24	HL_46794.2	3
25	HL_78361.1	3
26	HL_98833.1	3
27	HL_42077.2	3	LSU Helix 28 (H28) Hairpin Loop
28	HL_41827.1	3
29	HL_23182.1	3
30	HL_08382.2	3
31	HL_19221.2	3
32	HL_74686.1	3	SSU Central Pseudoknot (forms helix 2)
33	HL_80492.2	3	tRNA D-loop
34	HL_32644.1	3	LSU Helix 69 (H69) Hairpin Loop
35	HL_25124.1	3	tSW GA closed tetraloops
36	HL_48254.1	3	LSU Helix 84 (H84) Hairpin Loop.
37	HL_84353.1	2
38	HL_75575.1	2
39	HL_33451.1	2
40	HL_76766.1	2
41	HL_44467.1	2
42	HL_99633.1	2
43	HL_68697.1	2
44	HL_16770.1	2
45	HL_94578.1	2
46	HL_26057.1	2
47	HL_57014.1	2
48	HL_53753.1	2
49	HL_81752.1	2
50	HL_86123.2	2	SSU Helix 42 (h42) Hairpin Loop. T-loop like.
51	HL_49210.1	2
52	HL_05361.1	2
53	HL_06312.1	2
54	HL_67692.1	2
55	HL_98577.1	2
56	HL_87554.1	2
57	HL_65924.1	2
58	HL_23290.1	2
59	HL_19399.1	2
60	HL_67367.1	2
61	HL_24711.1	2
62	HL_12595.1	2
63	HL_24473.3	2	tRNA D-loop
64	HL_42436.1	2	Kissing Hairpin from di-GMP-II riboswitch
65	HL_62967.1	2
66	HL_06122.1	2
67	HL_57904.1	2
68	HL_38130.2	2
69	HL_77555.1	2
70	HL_42553.1	2
71	HL_64371.2	2
72	HL_03791.1	2
73	HL_96915.1	2
74	HL_38897.1	1	S8 operon binding Hairpin Loop. T-loop like with purine stacking.
75	HL_25197.1	1
76	HL_48480.1	1
77	HL_94697.1	1	LSU Helix 84 (H84) Hairpin Loop. E.coli.
78	HL_63690.1	1
79	HL_84289.1	1
80	HL_27397.1	1
81	HL_56809.1	1
82	HL_63304.1	1
83	HL_68733.1	1	LSU Yeast Hairpin Loop
84	HL_66900.1	1
85	HL_55202.1	1	U2B"-U2A" binding hairpin loop
86	HL_33640.1	1
87	HL_30128.1	1
88	HL_99779.1	1
89	HL_97499.1	1
90	HL_35004.1	1
91	HL_05113.1	1
92	HL_34440.1	1
93	HL_27819.1	1
94	HL_00090.1	1
95	HL_55272.1	1
96	HL_47337.1	1
97	HL_90102.1	1	Kink-turn-like Hairpin Loop
98	HL_71607.1	1
99	HL_10116.1	1	Kink-turn-like Hairpin Loop
100	HL_38898.1	1
101	HL_17468.1	1
102	HL_35865.1	1
103	HL_93567.1	1
104	HL_57923.1	1
105	HL_30366.1	1	LSU Helix 10 (H10) Hairpin E.coli
106	HL_37962.1	1
107	HL_45358.1	1	Double hairpin loop based on GGA triple
108	HL_42969.1	1
109	HL_79902.1	1
110	HL_30731.1	1
111	HL_12706.1	1
112	HL_67761.1	1
113	HL_53015.1	1
114	HL_78420.1	1
115	HL_95716.1	1
116	HL_82243.1	1
117	HL_49492.1	1	Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
118	HL_17008.1	1	Nova-2 KH3 domain binding hairpin
119	HL_38138.1	1
120	HL_12984.1	1
121	HL_94145.1	1	SSU Helix 43 (h43) Hairpin Loop E.coli
122	HL_45411.1	1
123	HL_59604.1	1
124	HL_57217.1	1	cHS platform Intercalation Site
125	HL_20914.1	1
126	HL_68435.1	1
127	HL_84888.1	1	T-loop like but without tWH UA
128	HL_57843.1	1
129	HL_68579.1	1
130	HL_70912.1	1
131	HL_13786.1	1
132	HL_13105.1	1
133	HL_25175.1	1
134	HL_97971.1	1
135	HL_69403.1	1	GNRA-like
136	HL_17537.1	1
137	HL_81661.1	1	tRNA D-loop
138	HL_07315.1	1
139	HL_19226.1	1
140	HL_58223.1	1
141	HL_19132.1	1
142	HL_91613.1	1
143	HL_62970.1	1
144	HL_80746.1	1
145	HL_78228.1	1
146	HL_35200.1	1
147	HL_82288.1	1
148	HL_85018.1	1
149	HL_83053.1	1	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
150	HL_56775.1	1
151	HL_52393.1	1	Double tSH (double sheared) with bulged base
152	HL_85044.1	1	LSU Helix 10 (H10) Hairpin E.coli
153	HL_53789.1	1
154	HL_25195.1	1
155	HL_20806.1	1
156	HL_26579.1	1
157	HL_58601.1	1
158	HL_88960.1	1
159	HL_29084.1	1
160	HL_85753.1	1
161	HL_62880.1	1
162	HL_04194.1	1
163	HL_75850.1	1
164	HL_39486.1	1
165	HL_36842.1	1
166	HL_19452.1	1	tRNA D-loop
167	HL_33524.1	1	tRNA T-loop distorted by RS binding
168	HL_60203.1	1
169	HL_00721.1	1
170	HL_44522.1	1
171	HL_66877.1	1	cSH GU/cWS double platform, intercalation site
172	HL_67000.1	1
173	HL_96192.1	1
174	HL_33277.1	1
175	HL_99207.1	1	Tetrahymena LSU hairpin poorly modeled
176	HL_98233.1	1
177	HL_59610.1	1
178	HL_55543.1	1
179	HL_65802.1	1
180	HL_24707.1	1
181	HL_78507.1	1
182	HL_87223.1	1
183	HL_65071.1	1
184	HL_39422.1	1
185	HL_66880.1	1
186	HL_44390.1	1
187	HL_10378.1	1	Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
188	HL_50059.1	1	LSU Helix 35 (H35) Hairpin Loop from Yeast
189	HL_66467.1	1
190	HL_97784.1	1

Updated motif groups

#	Motif id	Instances	Description
1	HL_67042.5	224	GNRA Hairpin motifs
2	HL_72498.6	63	T-loops with two bulged bases
3	HL_39895.4	34	UNCG Hairpin motifs
4	HL_18781.2	20	Double sheared (tSH) with U-turn
5	HL_91226.3	17	Kissing Hairpin motif
6	HL_52574.2	15	LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
7	HL_97270.2	15	T-loops with 1 bulged base
8	HL_49036.2	11	GNRA with one bulged base
9	HL_17723.3	10	LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
10	HL_56824.2	10	LSU Helix 60A. LSU Helix 63A.
11	HL_75759.2	10	UNCG-like. cWW Closing pair. \| LSU: Part of IL/3WJ between H55 and H56.
12	HL_80459.2	10
13	HL_68081.3	10	LSU Helix 20 Hairpin loop
14	HL_28436.3	9	LSU Helix 96 (H96) Hairpin Loop
15	HL_87844.2	9	LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
16	HL_11547.2	8	LSU Helix 80 (H80) P-site Hairpin Loop.
17	HL_34027.2	8	5S Loop C - Upper part of Hairpin Loop.
18	HL_33402.2	7	LSU Helix 13 (H13) Hairpin loop. GNRA-like.
19	HL_34108.2	6	LSU Helix 37 (H37) Hairpin Loop.
20	HL_18156.2	6	LSU Helix 72 (H72) Hairpin Loop
21	HL_39872.2	6	LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
22	HL_75579.2	6
23	HL_39942.2	6	LSU Helix 91 (H91) Hairpin Loop
24	HL_01926.3	6	LSU Helix 71 (H71) Hairpin Loop.
25	HL_41833.2	6	LSU Helix 81 (H81) Hairpin Loop
26	HL_11509.2	6	LSU Helix 6 (H6) Hairpin Loop.
27	HL_46489.2	6	LSU H89 Hairpin Loop
28	HL_70420.2	6	LSU Helix 97 Hairpin loop
29	HL_87136.2	6	LSU Helix 39A Hairpin loop
30	HL_72543.2	5	LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
31	HL_88311.2	5	LSU Helix 35 (H35) Hairpin Loop
32	HL_12811.2	5	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
33	HL_61547.3	4
34	HL_62228.2	4	LSU Helix 35A (H35A) Hairpin Loop
35	HL_48116.2	4	GNRA-like with 5'-stacking of first unpaired base.
36	HL_90579.2	3
37	HL_19905.2	3	LSU: Part of IL/3WJ between H55 and H56.
38	HL_76036.3	3	LSU Helix 8 (H8) Hairpin Loop
39	HL_27429.3	3
40	HL_82253.2	3

Removed motif groups

#	Motif id	Instances	Description
1	HL_95423.2	5	UNCG-like. cWW Closing pair.
2	HL_73023.1	3	Two base, cross-stacked hairpin loop
3	HL_63823.1	2
4	HL_22614.1	2
5	HL_76105.1	2
6	HL_81555.1	2
7	HL_49267.1	2
8	HL_05510.1	2
9	HL_05797.1	2
10	HL_15771.1	1
11	HL_18011.1	1
12	HL_00238.1	1
13	HL_23522.1	1
14	HL_02479.1	1
15	HL_81780.1	1
16	HL_03431.1	1
17	HL_58786.1	1
18	HL_85138.1	1	LSU Helix 8 (H8) Hairpin Loop
19	HL_61061.1	1
20	HL_90365.1	1	5S rRNA Loop C from D.radiodurans
21	HL_63411.1	1
22	HL_93206.1	1

Added motif groups

#	Motif id	Instances	Description
1	HL_57514.1	5	Two base, cross-stacked hairpin loop
2	HL_18798.1	4	UNCG-like. cWW Closing pair.
3	HL_97512.1	2	LSU Helix 8 (H8) Hairpin Loop
4	HL_26495.1	2
5	HL_58687.1	2
6	HL_60200.1	2
7	HL_45440.1	2
8	HL_50312.1	2
9	HL_20028.1	1
10	HL_52109.1	1
11	HL_96994.1	1
12	HL_24108.1	1
13	HL_99584.1	1
14	HL_01418.1	1
15	HL_30008.1	1
16	HL_07915.1	1
17	HL_31969.1	1
18	HL_73465.1	1
19	HL_08203.1	1
20	HL_42345.1	1
21	HL_81295.1	1	UNCG-like. cWW Closing pair.
22	HL_16118.1	1
23	HL_93530.1	1
24	HL_95049.1	1	Two base, cross-stacked hairpin loop