1.8 | 1.9

Changes in PDB files used for clustering

Release 1.8 has 205 PDB files, release 1.9 has 209 PDB files, 205 of them are identical.

No equivalence class representatives have been replaced.

4 new structures in release 1.9: 4BW0, 4C7O, 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 272 motif groups, release 1.9 has 271 motif groups, 251 of them are identical.

14 motif groups were updated, 7 groups are present only in release 1.8, 6 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	IL_47174.8	205	cWW AG or water inserted cWW Y-Y.
2	IL_39199.4	53	Hoogsteen-edge Platform, Single bulged base
3	IL_56465.3	46	Single, unpaired intercalated base, consensus A
4	IL_44540.4	43	Sugar-edge, 1-base platform, consensus tHS
5	IL_87904.5	31	Triple sheared (tSH-tHS-tHS) no inserted bases
6	IL_82444.1	29	cWH basepair with syn base \| cWW AG or water inserted cWW Y-Y. \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) \| 16S h34 ILa : Part of larger motif
7	IL_13959.4	26	Double Sheared (tSH-tHS)
8	IL_65553.7	22	Kink-turn
9	IL_73276.5	22	C-loop
10	IL_93424.4	21	tSH-inserted-tHW
11	IL_55938.4	18	LSU Helix 89 (H89) IL2. cSH Platform.
12	IL_92027.3	17	16S h21 S8 binding site
13	IL_85647.3	16	Sarcin-ricin parent motif with 15 Nts
14	IL_24982.5	16	SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
15	IL_94430.5	16	16S h32-h33-h34 3WJ
16	IL_92109.2	15	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
17	IL_31555.4	13	Tandem sheared with inserted, unpaired purine.
18	IL_49493.4	13	Sarcin-ricin Parent Motif - bacterial LSU H95 IL
19	IL_43124.2	11	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
20	IL_37104.2	11	Single sheared with bulged bases \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
21	IL_17212.1	10	cWW AG or UU \| cWH basepair with syn base \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) \| 16S h34 ILa : Part of larger motif
22	IL_24546.4	10	23S H41 IL and 16S h18 IL : Has large bulge on one side
23	IL_58291.4	10	Recurrent Sub-motif found in junctions
24	IL_47444.3	9	SRP Loop E-like motif
25	IL_90459.3	9	cWW AG or UU
26	IL_92114.3	9	GAAA loop receptor "platform" motif
27	IL_02809.3	9	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
28	IL_92321.4	7	Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
29	IL_73000.2	7	cHS-cWS
30	IL_83451.3	7	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
31	IL_08926.3	6	23S H91 IL
32	IL_70237.3	6
33	IL_25380.1	6	LSU Helix 89 (H89) IL2
34	IL_53635.3	6	LSU Helix 32 (H32) IL
35	IL_90133.3	6
36	IL_13069.3	6	LSU 3WJ H32-H33-H35A
37	IL_72158.3	6	LSU Helix 62 (H62) IL
38	IL_97057.3	6
39	IL_77263.2	6	Kink-turn from U4
40	IL_25230.3	6	Bacterial 5S rRNA Loop E
41	IL_39585.1	6	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
42	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
43	IL_79083.3	5
44	IL_02359.3	5
45	IL_44067.4	5	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
46	IL_05684.1	5	tHS tHH bulge with S-turn \| Double S-turn motif
47	IL_86357.3	5	LSU Helix 61 IL2
48	IL_39980.1	4
49	IL_82188.2	4	LSU H68 IL from H.m.
50	IL_01080.1	4
51	IL_34363.2	4	Kink-turn from 23S H42
52	IL_38807.3	4
53	IL_95652.3	4	SSU Helix 27 (h27) IL Sarcin-Ricin motif
54	IL_09530.1	4	Double S-turn motif
55	IL_21333.2	4	tSH-tHW-bulge
56	IL_31066.3	4	SSU Helix 44 (h44) extension
57	IL_98591.3	4
58	IL_28572.2	4	16S h18 kink-turn like motif
59	IL_45262.4	4
60	IL_15709.1	4	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) \| 16S h34 ILa : Part of larger motif \| cWW AG or UU \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
61	IL_31663.1	4	23S H73 ILa : Part of larger Motif
62	IL_39526.4	4
63	IL_47758.2	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
64	IL_93568.2	4	Triple Sheared (tSH-tHS-tHS) with wobble cWW.
65	IL_22732.1	4	tSH-inserted-tHS
66	IL_42251.1	4
67	IL_06180.1	3	tHS tHH bulge with S-turn
68	IL_16166.4	3	23S H91 IL
69	IL_25271.2	3	SSU Helix 8 (h8) IL E.c. and Yeast
70	IL_58586.2	3
71	IL_74876.2	3	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
72	IL_87065.1	3	23S H91 IL \| Single-Base Intercalation Site
73	IL_98421.4	3	SSU Helix 12 (h12) IL
74	IL_16415.2	3	SSU Helix 23 (h23) Kink-turn T. thermophilus
75	IL_30840.2	3
76	IL_43946.1	3
77	IL_75447.1	3
78	IL_79955.2	3	SSU Helix (23) h23 IL1
79	IL_82563.1	3	Thi-box riboswitch T-loop
80	IL_34628.2	3	Kink-turn
81	IL_35043.1	3	cWW AG or UU \| cWH basepair with syn base \| cWH basepair with syn base
82	IL_52173.1	3
83	IL_80494.2	3	LSU H58 IL2 H.m.
84	IL_37053.1	3	Kink-turn from 23S H58
85	IL_62499.7	3
86	IL_05723.1	3
87	IL_07300.2	3
88	IL_89028.6	3	Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena \| Part of H71 junction in 23S rRNA from T.th.
89	IL_23262.4	2
90	IL_46435.1	2
91	IL_65137.1	2	Kink-turn like motif in Group I Intron
92	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
93	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
94	IL_00998.1	2
95	IL_12211.1	2
96	IL_16330.1	2
97	IL_23414.1	2
98	IL_30381.1	2	tHS tHH bulge with S-turn
99	IL_33964.1	2
100	IL_37406.1	2
101	IL_85015.1	2	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases \| Single sheared with bulged bases \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
102	IL_87507.1	2	tHS tHH bulge with S-turn
103	IL_90057.1	2
104	IL_50521.1	2
105	IL_98566.1	2
106	IL_40892.1	2
107	IL_67887.1	2
108	IL_76095.3	2	Motif from Hairpin Ribozyme
109	IL_80093.1	2
110	IL_87548.1	2
111	IL_09587.1	2
112	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
113	IL_90735.1	2
114	IL_09882.1	2
115	IL_21495.1	2
116	IL_39355.1	2	SSU Helix 12 (h12) IL \| LSU Eukaryal Helix 96 (H96) IL1
117	IL_68880.1	2	cWW AG or UU \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
118	IL_77076.1	2
119	IL_21639.1	2
120	IL_45794.1	2
121	IL_69536.1	2	LSU Helix 96 (H96) IL2
122	IL_97509.1	2	Double sheared with wobble cWW.
123	IL_11751.1	2
124	IL_15840.2	2	Triple Sheared with unpaired, inserted A
125	IL_19898.1	2
126	IL_31707.1	2	Vitamin B12 aptamer
127	IL_37197.1	2
128	IL_52940.1	2
129	IL_74214.1	2	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
130	IL_97833.1	2
131	IL_03110.1	1
132	IL_11778.1	1
133	IL_20775.1	1	tSH-inserted
134	IL_30354.1	1
135	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
136	IL_37347.1	1
137	IL_49527.1	1
138	IL_52958.1	1
139	IL_83920.1	1
140	IL_89794.1	1
141	IL_91904.1	1
142	IL_97842.1	1
143	IL_03282.1	1
144	IL_06306.1	1
145	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
146	IL_21077.1	1
147	IL_25307.1	1
148	IL_40527.1	1	Kink-turn
149	IL_43316.1	1
150	IL_46721.1	1
151	IL_49976.1	1
152	IL_53323.1	1
153	IL_59529.1	1
154	IL_75415.1	1	Pseudo-knot forming internal loop
155	IL_94973.1	1	Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
156	IL_03741.1	1
157	IL_06421.1	1	Single sheared with bulged bases
158	IL_09491.1	1
159	IL_12507.1	1
160	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
161	IL_23639.1	1	tWH-tHS-L-cWW
162	IL_40845.1	1
163	IL_56513.1	1
164	IL_59934.1	1	SSU Helix 23 (h23) Kink-turn E. coli
165	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
166	IL_71685.1	1	Sarcin-like with an intercalated basepair
167	IL_85510.1	1
168	IL_87523.1	1
169	IL_05221.1	1
170	IL_06468.1	1	16S h40 3WJ E.c.
171	IL_26868.1	1
172	IL_50911.1	1	16S h34 ILa : Part of larger motif
173	IL_53988.1	1
174	IL_57364.1	1	LSU Helix 89 (H89) IL2
175	IL_60649.1	1	Kink-turn
176	IL_71942.1	1
177	IL_82601.1	1	Tandem cWW water-inserted CU pairs
178	IL_95980.1	1	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
179	IL_05513.1	1
180	IL_06471.1	1
181	IL_17603.1	1
182	IL_21421.1	1
183	IL_26971.1	1
184	IL_31224.1	1	23S H91 IL
185	IL_39324.1	1
186	IL_41139.1	1
187	IL_47687.1	1
188	IL_54450.1	1
189	IL_61730.1	1
190	IL_68767.1	1
191	IL_76486.1	1	Sarcin-ricin motif with syn G
192	IL_82650.1	1
193	IL_85805.1	1
194	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
195	IL_02835.1	1
196	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
197	IL_15205.1	1
198	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
199	IL_25082.1	1
200	IL_41153.1	1
201	IL_47732.1	1
202	IL_52509.1	1
203	IL_54470.1	1	tHS tHH bulge with S-turn
204	IL_57977.1	1
205	IL_80505.1	1
206	IL_83250.1	1	16S h40 3WJ T.th.
207	IL_86059.1	1
208	IL_88119.1	1
209	IL_91044.1	1
210	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
211	IL_98924.1	1
212	IL_02897.1	1	Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena \| Part of H71 junction in 23S rRNA from T.th.
213	IL_06847.1	1	Group II Intron IL
214	IL_11302.1	1
215	IL_18675.1	1	cWW-bulge-cWW
216	IL_25181.1	1
217	IL_28644.1	1
218	IL_41791.1	1
219	IL_52610.1	1
220	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
221	IL_63952.1	1
222	IL_80652.1	1
223	IL_88367.1	1
224	IL_91078.1	1
225	IL_02957.1	1
226	IL_06177.1	1	cWW AG or UU
227	IL_30067.1	1
228	IL_46306.1	1
229	IL_55649.1	1
230	IL_58454.1	1
231	IL_64589.1	1
232	IL_69799.1	1
233	IL_77296.1	1
234	IL_81398.1	1
235	IL_83856.1	1
236	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
237	IL_91089.1	1

Updated motif groups

#	Motif id	Instances	Description
1	IL_97217.9	247	1-3 bulged nucleotides, same chain \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
2	IL_41766.5	52	Tandem cWW pairs (Not AU or GC)
3	IL_28947.2	22	23S H91 IL \| cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW \| LSU H77 \| cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
4	IL_46648.5	12	23S H91 IL \| Single-Base Intercalation Site
5	IL_25300.2	6	16S h19 IL and 23S H41 IL
6	IL_48918.3	4	Kink-turn variant
7	IL_94403.5	4	LSU H77
8	IL_46034.2	3
9	IL_06211.2	3
10	IL_09348.6	3	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
11	IL_96206.2	3
12	IL_80348.2	2	23S H91 IL
13	IL_09520.3	2	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
14	IL_95150.5	2

Removed motif groups

#	Motif id	Instances	Description
1	IL_39674.1	4	LSU H77 \| cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
2	IL_80433.1	2
3	IL_01054.1	2
4	IL_92280.1	1
5	IL_13682.1	1
6	IL_20530.1	1
7	IL_25314.1	1

Added motif groups

#	Motif id	Instances	Description
1	IL_28003.1	3
2	IL_22358.1	2
3	IL_47475.1	2	LSU H77 \| cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
4	IL_51403.1	2
5	IL_90086.1	1
6	IL_22909.1	1