1.8 | 1.9

Changes in PDB files used for clustering

Release 1.8 has 221 PDB files, release 1.9 has 225 PDB files, 220 of them are identical.

No equivalence class representatives have been replaced.

5 new structures in release 1.9: 4BW0, 4C7O, 4C9D, 4K27, 4LGT.

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 1.8 has 254 motif groups, release 1.9 has 253 motif groups, 243 of them are identical.

7 motif groups were updated, 4 groups are present only in release 1.8, 3 groups are only in release 1.9.

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_39895.6	35	UNCG Hairpin motifs
2	HL_18781.4	20	Double sheared (tSH) with U-turn
3	HL_91226.3	17	Kissing Hairpin motif
4	HL_97270.3	15	T-loops with 1 bulged base
5	HL_52574.3	14	LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
6	HL_49036.3	12	GNRA with one bulged base
7	HL_48039.2	11	MS2 virus RNA Hairpin
8	HL_75759.3	10	LSU: Part of IL/3WJ between H55 and H56. \| UNCG-like. cWW Closing pair. \| LSU: Part of IL/3WJ between H55 and H56.
9	HL_56824.2	10	LSU Helix 60A. LSU Helix 63A.
10	HL_46175.2	10	16S helix 23 and 24 hairpin loops
11	HL_27271.1	10	LSU Helix 96 (H96) Hairpin Loop
12	HL_17723.4	10	LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
13	HL_68081.3	10	LSU Helix 20 Hairpin loop
14	HL_87844.2	9	LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
15	HL_80459.3	9
16	HL_33402.3	8	LSU Helix 13 (H13) Hairpin loop. GNRA-like.
17	HL_15603.1	8	U1A protein-binding Hairpin Loop.
18	HL_11547.2	8	LSU Helix 80 (H80) P-site Hairpin Loop.
19	HL_82294.3	8	SSU Helix 37 (h37) Hairpin loop.
20	HL_34027.2	8	5S Loop C - Upper part of Hairpin Loop.
21	HL_24544.2	8	LSU Helix 53 (H53) Hairpin Loop. T-loop like.
22	HL_42677.2	7
23	HL_46489.2	6	LSU H89 Hairpin Loop
24	HL_39942.2	6	LSU Helix 91 (H91) Hairpin Loop
25	HL_57514.2	6	Two base, cross-stacked hairpin loop
26	HL_01926.3	6	LSU Helix 71 (H71) Hairpin Loop.
27	HL_70420.2	6	LSU Helix 97 Hairpin loop
28	HL_34108.2	6	LSU Helix 37 (H37) Hairpin Loop.
29	HL_18156.2	6	LSU Helix 72 (H72) Hairpin Loop
30	HL_39872.2	6	LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
31	HL_75579.2	6
32	HL_87136.2	6	LSU Helix 39A Hairpin loop
33	HL_41833.2	6	LSU Helix 81 (H81) Hairpin Loop
34	HL_11509.2	6	LSU Helix 6 (H6) Hairpin Loop.
35	HL_06643.2	5	tRNA D-loop. Sec tRNA
36	HL_72543.2	5	LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
37	HL_45018.3	5	Hairpin-Hairpin Interacting HL
38	HL_72273.1	5	tRNA D-loop
39	HL_88311.2	5	LSU Helix 35 (H35) Hairpin Loop
40	HL_85534.1	5	LSU Helix 65 (H65) Hairpin Loop. T-loop like.
41	HL_66174.1	5	cHS GU/cWS Double Platform creates Intercalation site
42	HL_95720.1	5	Double tSH (double sheared) with bulged base \| LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
43	HL_62228.3	5	LSU Helix 35A (H35A) Hairpin Loop
44	HL_78731.1	5	LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
45	HL_98523.2	4	GNRA-like. Closed by tSH UC.
46	HL_48116.2	4	GNRA-like with 5'-stacking of first unpaired base.
47	HL_29831.1	4	GNRA-like with bulged base.
48	HL_11376.1	4	LSU Helix 8 (H8) Hairpin Loop
49	HL_55718.1	4	UNCG-like. cWW Closing pair. \| UNCG-like. cWW Closing pair. \| LSU: Part of IL/3WJ between H55 and H56.
50	HL_47784.2	4	SSU Central Pseudoknot (forms helix 2)
51	HL_64543.2	4	SSU Helix 31 (h31) Hairpin Loop
52	HL_62881.1	4	RNase P Structured Hairpin Loop
53	HL_42077.2	3	LSU Helix 28 (H28) Hairpin Loop
54	HL_19905.3	3	LSU: Part of IL/3WJ between H55 and H56.
55	HL_78361.1	3
56	HL_90579.3	3	LSU Helix 69 (H69) Hairpin Loop
57	HL_33875.1	3	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
58	HL_08382.2	3
59	HL_19221.2	3
60	HL_76036.3	3	LSU Helix 8 (H8) Hairpin Loop
61	HL_48254.1	3	LSU Helix 84 (H84) Hairpin Loop.
62	HL_06997.2	3
63	HL_13707.2	3	cSH AA Platform containing Hairpin Loop
64	HL_42687.4	3
65	HL_58083.2	3
66	HL_74686.1	3	SSU Central Pseudoknot (forms helix 2)
67	HL_68697.2	3
68	HL_98833.3	3
69	HL_27429.3	3
70	HL_41827.1	3
71	HL_23182.1	3
72	HL_80492.2	3	tRNA D-loop
73	HL_06122.1	2
74	HL_65924.1	2
75	HL_86123.2	2	SSU Helix 42 (h42) Hairpin Loop. T-loop like.
76	HL_33451.1	2
77	HL_50312.1	2
78	HL_44467.1	2
79	HL_18587.1	2
80	HL_62967.1	2
81	HL_84353.1	2
82	HL_49210.1	2
83	HL_94578.1	2
84	HL_32644.2	2	LSU Helix 69 (H69) Hairpin Loop
85	HL_16770.1	2
86	HL_23290.1	2
87	HL_19399.1	2
88	HL_99633.1	2
89	HL_24711.1	2
90	HL_24473.3	2	tRNA D-loop
91	HL_65347.1	2	SSU Helix 43 (h43) Hairpin Loop E.coli \| 16S helix 23 and 24 hairpin loops
92	HL_21545.1	2	LSU Helix 96 (H96) Hairpin Loop
93	HL_66948.1	2	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
94	HL_91693.1	2
95	HL_42094.1	2
96	HL_05361.1	2
97	HL_98577.1	2
98	HL_86398.1	2
99	HL_96915.1	2
100	HL_54751.2	2
101	HL_17790.1	2	UNCG-like. cWW Closing pair.
102	HL_19528.1	2
103	HL_87554.1	2
104	HL_91872.1	2
105	HL_63941.1	2
106	HL_74505.1	2
107	HL_38130.2	2
108	HL_26495.1	2
109	HL_64371.2	2
110	HL_42436.1	2	Kissing Hairpin from di-GMP-II riboswitch
111	HL_23129.1	2
112	HL_60200.1	2
113	HL_90542.1	2
114	HL_93771.1	2	tRNA T-loop distorted by RS binding
115	HL_65249.1	2
116	HL_42553.1	2
117	HL_76766.3	2
118	HL_74559.1	2	Two base, cross-stacked hairpin loop
119	HL_38138.1	1
120	HL_33640.1	1
121	HL_48480.1	1
122	HL_20806.1	1
123	HL_52540.1	1
124	HL_34440.1	1
125	HL_56809.1	1
126	HL_97971.1	1
127	HL_69403.1	1	GNRA-like
128	HL_46570.1	1
129	HL_73465.1	1
130	HL_96994.1	1
131	HL_30128.1	1
132	HL_99779.1	1
133	HL_19226.1	1
134	HL_95049.1	1	Two base, cross-stacked hairpin loop
135	HL_05113.1	1
136	HL_79902.1	1
137	HL_30731.1	1
138	HL_07915.1	1
139	HL_00090.1	1
140	HL_10378.1	1	Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
141	HL_50059.1	1	LSU Helix 35 (H35) Hairpin Loop from Yeast
142	HL_78228.1	1
143	HL_35200.1	1
144	HL_82288.1	1
145	HL_83865.1	1
146	HL_01418.1	1
147	HL_24108.1	1
148	HL_55202.1	1	U2B"-U2A" binding hairpin loop
149	HL_56775.1	1
150	HL_77692.1	1	tRNA D-loop
151	HL_93567.1	1
152	HL_57923.1	1
153	HL_78507.1	1
154	HL_45358.1	1	Double hairpin loop based on GGA triple
155	HL_42969.1	1
156	HL_57843.1	1
157	HL_68579.1	1
158	HL_27819.1	1
159	HL_67761.1	1
160	HL_63304.1	1
161	HL_75850.1	1
162	HL_39486.1	1
163	HL_36842.1	1
164	HL_23195.1	1
165	HL_20028.1	1
166	HL_59182.1	1
167	HL_59610.1	1
168	HL_45411.1	1
169	HL_94697.1	1	LSU Helix 84 (H84) Hairpin Loop. E.coli.
170	HL_60203.1	1
171	HL_68435.1	1
172	HL_84888.1	1	T-loop like but without tWH UA
173	HL_19132.1	1
174	HL_12706.1	1
175	HL_13786.1	1
176	HL_55272.1	1
177	HL_47337.1	1
178	HL_33277.1	1
179	HL_49492.1	1	Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
180	HL_59225.1	1
181	HL_38898.1	1
182	HL_52116.1	1
183	HL_85044.1	1	LSU Helix 10 (H10) Hairpin E.coli
184	HL_30366.1	1	LSU Helix 10 (H10) Hairpin E.coli
185	HL_76585.1	1
186	HL_87223.1	1
187	HL_58223.1	1
188	HL_88960.1	1
189	HL_91613.1	1
190	HL_70912.1	1
191	HL_53015.1	1
192	HL_78420.1	1
193	HL_66467.1	1
194	HL_99207.1	1	Tetrahymena LSU hairpin poorly modeled
195	HL_17537.1	1
196	HL_99584.1	1
197	HL_29196.1	1
198	HL_17008.1	1	Nova-2 KH3 domain binding hairpin
199	HL_73972.1	1
200	HL_53789.1	1
201	HL_25195.1	1
202	HL_59604.1	1
203	HL_97499.1	1
204	HL_00721.1	1
205	HL_26579.1	1
206	HL_58601.1	1
207	HL_66877.1	1	cSH GU/cWS double platform, intercalation site
208	HL_03785.1	1	LSU Helix 8 (H8) Hairpin Loop
209	HL_25175.1	1
210	HL_68733.1	1	LSU Yeast Hairpin Loop
211	HL_97784.1	1
212	HL_85018.1	1
213	HL_08203.1	1
214	HL_38897.1	1	S8 operon binding Hairpin Loop. T-loop like with purine stacking.
215	HL_24707.1	1
216	HL_37962.1	1
217	HL_65071.1	1
218	HL_44522.1	1
219	HL_66880.1	1
220	HL_62970.1	1
221	HL_76679.1	1
222	HL_90102.1	1	Kink-turn-like Hairpin Loop
223	HL_93530.1	1
224	HL_19452.1	1	tRNA D-loop
225	HL_30008.1	1
226	HL_84768.1	1
227	HL_65802.1	1
228	HL_35865.1	1
229	HL_25197.1	1
230	HL_28676.1	1
231	HL_57217.1	1	cHS platform Intercalation Site
232	HL_39422.1	1
233	HL_84289.1	1
234	HL_27397.1	1
235	HL_44390.1	1
236	HL_67000.1	1
237	HL_62880.1	1
238	HL_04194.1	1
239	HL_95716.1	1
240	HL_82243.1	1
241	HL_10116.1	1	Kink-turn-like Hairpin Loop
242	HL_98233.1	1
243	HL_42345.1	1

Updated motif groups

#	Motif id	Instances	Description
1	HL_67042.10	229	GNRA Hairpin motifs
2	HL_72498.11	65	T-loops with two bulged bases
3	HL_74465.4	12	tRNA Anti-Codon loop
4	HL_61547.5	4	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
5	HL_25124.2	4	tSW GA closed tetraloops
6	HL_35619.2	3
7	HL_21675.3	2	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking

Removed motif groups

#	Motif id	Instances	Description
1	HL_23971.1	4	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
2	HL_03791.1	2
3	HL_93633.1	1
4	HL_98234.1	1	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking

Added motif groups

#	Motif id	Instances	Description
1	HL_82538.1	5	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
2	HL_93263.1	1
3	HL_79038.1	1	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking