1.8 | 1.9

Changes in PDB files used for clustering

Release 1.8 has 206 PDB files, release 1.9 has 210 PDB files, 206 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_73276.5	22	C-loop
9	IL_65553.7	22	Kink-turn
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_24982.5	16	SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
14	IL_94430.5	16	16S h32-h33-h34 3WJ
15	IL_85647.3	16	Sarcin-ricin parent motif with 15 Nts
16	IL_92109.2	15	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
17	IL_49493.4	13	Sarcin-ricin Parent Motif - bacterial LSU H95 IL
18	IL_31555.4	13	Tandem sheared with inserted, unpaired purine.
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_02809.3	9	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
25	IL_47444.3	9	SRP Loop E-like motif
26	IL_90459.3	9	cWW AG or UU
27	IL_92114.3	9	GAAA loop receptor "platform" motif
28	IL_73000.2	7	cHS-cWS
29	IL_83451.3	7	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
30	IL_92321.4	7	Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
31	IL_70237.3	6
32	IL_39585.1	6	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
33	IL_77263.2	6	Kink-turn from U4
34	IL_97057.3	6
35	IL_53635.3	6	LSU Helix 32 (H32) IL
36	IL_13069.3	6	LSU 3WJ H32-H33-H35A
37	IL_90133.3	6
38	IL_72158.3	6	LSU Helix 62 (H62) IL
39	IL_08926.3	6	23S H91 IL
40	IL_25230.3	6	Bacterial 5S rRNA Loop E
41	IL_25380.1	6	LSU Helix 89 (H89) IL2
42	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
43	IL_05684.1	5	tHS tHH bulge with S-turn \| Double S-turn motif
44	IL_44067.4	5	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
45	IL_86357.3	5	LSU Helix 61 IL2
46	IL_79083.3	5
47	IL_02359.3	5
48	IL_31066.3	4	SSU Helix 44 (h44) extension
49	IL_01080.1	4
50	IL_38807.3	4
51	IL_31663.1	4	23S H73 ILa : Part of larger Motif
52	IL_42251.1	4
53	IL_34363.2	4	Kink-turn from 23S H42
54	IL_45262.4	4
55	IL_93568.2	4	Triple Sheared (tSH-tHS-tHS) with wobble cWW.
56	IL_22732.1	4	tSH-inserted-tHS
57	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)
58	IL_47758.2	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
59	IL_21333.2	4	tSH-tHW-bulge
60	IL_39980.1	4
61	IL_98591.3	4
62	IL_09530.1	4	Double S-turn motif
63	IL_28572.2	4	16S h18 kink-turn like motif
64	IL_95652.3	4	SSU Helix 27 (h27) IL Sarcin-Ricin motif
65	IL_82188.2	4	LSU H68 IL from H.m.
66	IL_39526.4	4
67	IL_52173.1	3
68	IL_80494.2	3	LSU H58 IL2 H.m.
69	IL_25271.2	3	SSU Helix 8 (h8) IL E.c. and Yeast
70	IL_98421.4	3	SSU Helix 12 (h12) IL
71	IL_37053.1	3	Kink-turn from 23S H58
72	IL_06180.1	3	tHS tHH bulge with S-turn
73	IL_30840.2	3
74	IL_79955.2	3	SSU Helix (23) h23 IL1
75	IL_16166.4	3	23S H91 IL
76	IL_43946.1	3
77	IL_75447.1	3
78	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.
79	IL_07300.2	3
80	IL_16415.2	3	SSU Helix 23 (h23) Kink-turn T. thermophilus
81	IL_82563.1	3	Thi-box riboswitch T-loop
82	IL_87065.1	3	23S H91 IL \| Single-Base Intercalation Site
83	IL_34628.2	3	Kink-turn
84	IL_62499.7	3
85	IL_35043.1	3	cWW AG or UU \| cWH basepair with syn base \| cWH basepair with syn base
86	IL_05723.1	3
87	IL_74876.2	3	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
88	IL_58586.2	3
89	IL_74214.1	2	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
90	IL_46435.1	2
91	IL_21495.1	2
92	IL_37406.1	2
93	IL_68880.1	2	cWW AG or UU \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
94	IL_90735.1	2
95	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
96	IL_77076.1	2
97	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
98	IL_39355.1	2	SSU Helix 12 (h12) IL \| LSU Eukaryal Helix 96 (H96) IL1
99	IL_90057.1	2
100	IL_12211.1	2
101	IL_15840.2	2	Triple Sheared with unpaired, inserted A
102	IL_23262.4	2
103	IL_69536.1	2	LSU Helix 96 (H96) IL2
104	IL_23414.1	2
105	IL_31707.1	2	Vitamin B12 aptamer
106	IL_50521.1	2
107	IL_09882.1	2
108	IL_98566.1	2
109	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
110	IL_96446.1	2
111	IL_87548.1	2
112	IL_19898.1	2
113	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)
114	IL_67887.1	2
115	IL_21639.1	2
116	IL_37197.1	2
117	IL_52940.1	2
118	IL_65137.1	2	Kink-turn like motif in Group I Intron
119	IL_00998.1	2
120	IL_45794.1	2
121	IL_87507.1	2	tHS tHH bulge with S-turn
122	IL_11751.1	2
123	IL_97833.1	2
124	IL_30381.1	2	tHS tHH bulge with S-turn
125	IL_16330.1	2
126	IL_33964.1	2
127	IL_76095.3	2	Motif from Hairpin Ribozyme
128	IL_80093.1	2
129	IL_09587.1	2
130	IL_97509.1	2	Double sheared with wobble cWW.
131	IL_40892.1	2
132	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
133	IL_40845.1	1
134	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
135	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.
136	IL_06468.1	1	16S h40 3WJ E.c.
137	IL_80652.1	1
138	IL_54450.1	1
139	IL_71942.1	1
140	IL_37347.1	1
141	IL_06471.1	1
142	IL_68767.1	1
143	IL_56513.1	1
144	IL_15205.1	1
145	IL_21077.1	1
146	IL_03282.1	1
147	IL_42891.1	1
148	IL_57977.1	1
149	IL_39324.1	1
150	IL_43316.1	1
151	IL_12507.1	1
152	IL_47687.1	1
153	IL_31006.1	1	tSH-tHW-L-bif-cWW
154	IL_55649.1	1
155	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
156	IL_75328.1	1
157	IL_31224.1	1	23S H91 IL
158	IL_05221.1	1
159	IL_26971.1	1
160	IL_21421.1	1
161	IL_85510.1	1
162	IL_49527.1	1
163	IL_94973.1	1	Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
164	IL_47732.1	1
165	IL_50911.1	1	16S h34 ILa : Part of larger motif
166	IL_86059.1	1
167	IL_80505.1	1
168	IL_69799.1	1
169	IL_27243.1	1
170	IL_25082.1	1
171	IL_53323.1	1
172	IL_59529.1	1
173	IL_91904.1	1
174	IL_58454.1	1
175	IL_88367.1	1
176	IL_49976.1	1
177	IL_57285.1	1
178	IL_30354.1	1
179	IL_85805.1	1
180	IL_06177.1	1	cWW AG or UU
181	IL_82650.1	1
182	IL_26868.1	1
183	IL_89794.1	1
184	IL_28644.1	1
185	IL_52509.1	1
186	IL_95980.1	1	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
187	IL_75415.1	1	Pseudo-knot forming internal loop
188	IL_88119.1	1
189	IL_98924.1	1
190	IL_25181.1	1
191	IL_09491.1	1
192	IL_18675.1	1	cWW-bulge-cWW
193	IL_40527.1	1	Kink-turn
194	IL_23448.1	1
195	IL_46721.1	1
196	IL_83250.1	1	16S h40 3WJ T.th.
197	IL_25307.1	1
198	IL_11302.1	1
199	IL_53988.1	1
200	IL_61730.1	1
201	IL_71685.1	1	Sarcin-like with an intercalated basepair
202	IL_02957.1	1
203	IL_57364.1	1	LSU Helix 89 (H89) IL2
204	IL_41139.1	1
205	IL_91044.1	1
206	IL_27668.1	1
207	IL_41153.1	1
208	IL_63952.1	1
209	IL_88865.1	1
210	IL_76263.1	1
211	IL_91379.1	1
212	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
213	IL_11778.1	1
214	IL_03741.1	1
215	IL_06306.1	1
216	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
217	IL_23639.1	1	tWH-tHS-L-cWW
218	IL_64589.1	1
219	IL_54470.1	1	tHS tHH bulge with S-turn
220	IL_06847.1	1	Group II Intron IL
221	IL_30067.1	1
222	IL_05513.1	1
223	IL_02835.1	1
224	IL_68827.1	1	Reverse Kink-Turn
225	IL_59934.1	1	SSU Helix 23 (h23) Kink-turn E. coli
226	IL_06421.1	1	Single sheared with bulged bases
227	IL_20775.1	1	tSH-inserted
228	IL_91078.1	1
229	IL_83856.1	1
230	IL_76486.1	1	Sarcin-ricin motif with syn G
231	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
232	IL_82601.1	1	Tandem cWW water-inserted CU pairs
233	IL_91089.1	1
234	IL_60649.1	1	Kink-turn
235	IL_52610.1	1
236	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
237	IL_03110.1	1
238	IL_41791.1	1
239	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
240	IL_83920.1	1
241	IL_52958.1	1
242	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
243	IL_77014.1	1
244	IL_81398.1	1
245	IL_97842.1	1
246	IL_46306.1	1
247	IL_17603.1	1
248	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
249	IL_87523.1	1
250	IL_77296.1	1
251	IL_87394.1	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_06211.2	3
9	IL_09348.6	3	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
10	IL_96206.2	3
11	IL_46034.2	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_01054.1	2
3	IL_80433.1	2
4	IL_13682.1	1
5	IL_20530.1	1
6	IL_25314.1	1
7	IL_92280.1	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_22909.1	1
6	IL_90086.1	1