1.11 | 1.12

Changes in PDB files used for clustering

Release 1.11 has 229 PDB files, release 1.12 has 231 PDB files, 229 of them are identical.

No equivalence class representatives have been replaced.

2 new structures in release 1.12: 4C4W, 4OO8.

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 1.11 has 253 motif groups, release 1.12 has 253 motif groups, 249 of them are identical.

4 motif groups were updated, 0 groups are present only in release 1.11, 0 groups are only in release 1.12.

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_72498.12	66	T-loops with two bulged bases
2	HL_39895.6	35	UNCG Hairpin motifs
3	HL_18781.4	20	Double sheared (tSH) with U-turn
4	HL_91226.3	17	Kissing Hairpin motif
5	HL_97270.3	15	T-loops with 1 bulged base
6	HL_52574.3	14	LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
7	HL_74465.5	13	tRNA Anti-Codon loop
8	HL_49036.3	12	GNRA with one bulged base
9	HL_27271.2	12	LSU Helix 96 (H96) Hairpin Loop
10	HL_48039.2	11	MS2 virus RNA Hairpin
11	HL_17723.4	10	LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
12	HL_68081.3	10	LSU Helix 20 Hairpin loop
13	HL_46175.2	10	16S helix 23 and 24 hairpin loops
14	HL_56824.2	10	LSU Helix 60A. LSU Helix 63A.
15	HL_87844.2	9	LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
16	HL_80459.3	9
17	HL_33402.3	8	LSU Helix 13 (H13) Hairpin loop. GNRA-like.
18	HL_82294.3	8	SSU Helix 37 (h37) Hairpin loop.
19	HL_34027.2	8	5S Loop C - Upper part of Hairpin Loop.
20	HL_11547.2	8	LSU Helix 80 (H80) P-site Hairpin Loop.
21	HL_24544.2	8	LSU Helix 53 (H53) Hairpin Loop. T-loop like.
22	HL_42677.2	7
23	HL_01926.3	6	LSU Helix 71 (H71) Hairpin Loop.
24	HL_70420.2	6	LSU Helix 97 Hairpin loop
25	HL_57514.2	6	Two base, cross-stacked hairpin loop
26	HL_18156.2	6	LSU Helix 72 (H72) Hairpin Loop
27	HL_39872.2	6	LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
28	HL_34108.2	6	LSU Helix 37 (H37) Hairpin Loop.
29	HL_75579.2	6
30	HL_87136.2	6	LSU Helix 39A Hairpin loop
31	HL_41833.2	6	LSU Helix 81 (H81) Hairpin Loop
32	HL_11509.2	6	LSU Helix 6 (H6) Hairpin Loop.
33	HL_46489.2	6	LSU H89 Hairpin Loop
34	HL_39942.2	6	LSU Helix 91 (H91) Hairpin Loop
35	HL_85534.1	5	LSU Helix 65 (H65) Hairpin Loop. T-loop like.
36	HL_66174.1	5	cHS GU/cWS Double Platform creates Intercalation site
37	HL_95720.1	5	Double tSH (double sheared) with bulged base \| LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
38	HL_88311.2	5	LSU Helix 35 (H35) Hairpin Loop
39	HL_62228.3	5	LSU Helix 35A (H35A) Hairpin Loop
40	HL_78731.1	5	LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
41	HL_72273.1	5	tRNA D-loop
42	HL_72543.2	5	LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
43	HL_45018.3	5	Hairpin-Hairpin Interacting HL
44	HL_82538.1	5	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
45	HL_55718.1	4	UNCG-like. cWW Closing pair. \| UNCG-like. cWW Closing pair. \| LSU: Part of IL/3WJ between H55 and H56.
46	HL_47784.2	4	SSU Central Pseudoknot (forms helix 2)
47	HL_64543.2	4	SSU Helix 31 (h31) Hairpin Loop
48	HL_86115.1	4
49	HL_62881.1	4	RNase P Structured Hairpin Loop
50	HL_25124.2	4	tSW GA closed tetraloops
51	HL_61547.5	4	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
52	HL_29831.1	4	GNRA-like with bulged base.
53	HL_98523.2	4	GNRA-like. Closed by tSH UC.
54	HL_48116.2	4	GNRA-like with 5'-stacking of first unpaired base.
55	HL_11376.1	4	LSU Helix 8 (H8) Hairpin Loop
56	HL_90579.3	3	LSU Helix 69 (H69) Hairpin Loop
57	HL_19221.2	3
58	HL_13707.2	3	cSH AA Platform containing Hairpin Loop
59	HL_76036.3	3	LSU Helix 8 (H8) Hairpin Loop
60	HL_58083.2	3
61	HL_74686.1	3	SSU Central Pseudoknot (forms helix 2)
62	HL_48254.1	3	LSU Helix 84 (H84) Hairpin Loop.
63	HL_41827.1	3
64	HL_98833.3	3
65	HL_80492.2	3	tRNA D-loop
66	HL_27429.3	3
67	HL_06997.2	3
68	HL_33875.1	3	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
69	HL_42077.2	3	LSU Helix 28 (H28) Hairpin Loop
70	HL_23182.1	3
71	HL_19905.3	3	LSU: Part of IL/3WJ between H55 and H56.
72	HL_35619.2	3
73	HL_76766.4	3
74	HL_68697.2	3
75	HL_08382.2	3
76	HL_78361.1	3
77	HL_23290.1	2
78	HL_94578.1	2
79	HL_32644.2	2	LSU Helix 69 (H69) Hairpin Loop
80	HL_44467.1	2
81	HL_18587.1	2
82	HL_62967.1	2
83	HL_24711.1	2
84	HL_21675.3	2	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
85	HL_24473.3	2	tRNA D-loop
86	HL_65347.1	2	SSU Helix 43 (h43) Hairpin Loop E.coli \| 16S helix 23 and 24 hairpin loops
87	HL_19399.1	2
88	HL_63941.1	2
89	HL_54751.2	2
90	HL_91693.1	2
91	HL_42094.1	2
92	HL_98577.1	2
93	HL_21545.1	2	LSU Helix 96 (H96) Hairpin Loop
94	HL_99633.1	2
95	HL_74505.1	2
96	HL_17790.1	2	UNCG-like. cWW Closing pair.
97	HL_05361.1	2
98	HL_93771.1	2	tRNA T-loop distorted by RS binding
99	HL_38130.2	2
100	HL_26495.1	2
101	HL_19528.1	2
102	HL_87554.1	2
103	HL_86398.1	2
104	HL_96915.1	2
105	HL_66948.1	2	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
106	HL_06122.1	2
107	HL_65924.1	2
108	HL_86123.2	2	SSU Helix 42 (h42) Hairpin Loop. T-loop like.
109	HL_65249.1	2
110	HL_64371.2	2
111	HL_42436.1	2	Kissing Hairpin from di-GMP-II riboswitch
112	HL_23129.1	2
113	HL_91872.1	2
114	HL_84353.1	2
115	HL_42553.1	2
116	HL_60200.1	2
117	HL_16770.1	2
118	HL_49210.1	2
119	HL_33451.1	2
120	HL_50312.1	2
121	HL_74559.1	2	Two base, cross-stacked hairpin loop
122	HL_90542.1	2
123	HL_38898.1	1
124	HL_59610.1	1
125	HL_56775.1	1
126	HL_77692.1	1	tRNA D-loop
127	HL_93567.1	1
128	HL_99779.1	1
129	HL_19226.1	1
130	HL_95049.1	1	Two base, cross-stacked hairpin loop
131	HL_42969.1	1
132	HL_79902.1	1
133	HL_30731.1	1
134	HL_07915.1	1
135	HL_95716.1	1
136	HL_82243.1	1
137	HL_10116.1	1	Kink-turn-like Hairpin Loop
138	HL_98233.1	1
139	HL_30008.1	1
140	HL_17008.1	1	Nova-2 KH3 domain binding hairpin
141	HL_57923.1	1
142	HL_78507.1	1
143	HL_45358.1	1	Double hairpin loop based on GGA triple
144	HL_84888.1	1	T-loop like but without tWH UA
145	HL_57843.1	1
146	HL_68579.1	1
147	HL_27819.1	1
148	HL_00090.1	1
149	HL_10378.1	1	Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
150	HL_50059.1	1	LSU Helix 35 (H35) Hairpin Loop from Yeast
151	HL_78228.1	1
152	HL_97971.1	1
153	HL_69403.1	1	GNRA-like
154	HL_46570.1	1
155	HL_73465.1	1
156	HL_42345.1	1
157	HL_52116.1	1
158	HL_85044.1	1	LSU Helix 10 (H10) Hairpin E.coli
159	HL_45411.1	1
160	HL_94697.1	1	LSU Helix 84 (H84) Hairpin Loop. E.coli.
161	HL_60203.1	1
162	HL_68435.1	1
163	HL_19132.1	1
164	HL_12706.1	1
165	HL_67761.1	1
166	HL_63304.1	1
167	HL_75850.1	1
168	HL_35200.1	1
169	HL_82288.1	1
170	HL_83865.1	1
171	HL_79038.1	1	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
172	HL_96994.1	1
173	HL_73972.1	1
174	HL_53789.1	1
175	HL_30366.1	1	LSU Helix 10 (H10) Hairpin E.coli
176	HL_76585.1	1
177	HL_87223.1	1
178	HL_58223.1	1
179	HL_58601.1	1
180	HL_88960.1	1
181	HL_91613.1	1
182	HL_70912.1	1
183	HL_13786.1	1
184	HL_55272.1	1
185	HL_47337.1	1
186	HL_39486.1	1
187	HL_36842.1	1
188	HL_23195.1	1
189	HL_01418.1	1
190	HL_24108.1	1
191	HL_38897.1	1	S8 operon binding Hairpin Loop. T-loop like with purine stacking.
192	HL_24707.1	1
193	HL_25195.1	1
194	HL_59604.1	1
195	HL_97499.1	1
196	HL_00721.1	1
197	HL_26579.1	1
198	HL_66877.1	1	cSH GU/cWS double platform, intercalation site
199	HL_53015.1	1
200	HL_78420.1	1
201	HL_33277.1	1
202	HL_49492.1	1	Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
203	HL_20028.1	1
204	HL_59182.1	1
205	HL_84768.1	1
206	HL_65802.1	1
207	HL_35865.1	1
208	HL_25197.1	1
209	HL_37962.1	1
210	HL_65071.1	1
211	HL_44522.1	1
212	HL_66880.1	1
213	HL_03785.1	1	LSU Helix 8 (H8) Hairpin Loop
214	HL_25175.1	1
215	HL_68733.1	1	LSU Yeast Hairpin Loop
216	HL_66467.1	1
217	HL_99207.1	1	Tetrahymena LSU hairpin poorly modeled
218	HL_17537.1	1
219	HL_59225.1	1
220	HL_55202.1	1	U2B"-U2A" binding hairpin loop
221	HL_38138.1	1
222	HL_33640.1	1
223	HL_28676.1	1
224	HL_57217.1	1	cHS platform Intercalation Site
225	HL_39422.1	1
226	HL_84289.1	1
227	HL_27397.1	1
228	HL_44390.1	1
229	HL_67000.1	1
230	HL_62970.1	1
231	HL_76679.1	1
232	HL_90102.1	1	Kink-turn-like Hairpin Loop
233	HL_97784.1	1
234	HL_85018.1	1
235	HL_99584.1	1
236	HL_29196.1	1
237	HL_30128.1	1
238	HL_48480.1	1
239	HL_20806.1	1
240	HL_52540.1	1
241	HL_05113.1	1
242	HL_34440.1	1
243	HL_56809.1	1
244	HL_93263.1	1
245	HL_62880.1	1
246	HL_04194.1	1
247	HL_93530.1	1
248	HL_19452.1	1	tRNA D-loop
249	HL_08203.1	1

Updated motif groups

#	Motif id	Instances	Description
1	HL_67042.11	231	GNRA Hairpin motifs
2	HL_75759.4	11
3	HL_15603.2	9	U1A protein-binding Hairpin Loop.
4	HL_06643.3	6	tRNA D-loop. Sec tRNA

Removed motif groups

#	Motif id	Instances	Description

Added motif groups

#	Motif id	Instances	Description