1.7 | 1.8

Changes in PDB files used for clustering

Release 1.7 has 204 PDB files, release 1.8 has 206 PDB files, 204 of them are identical.

No equivalence class representatives have been replaced.

2 new structures in release 1.8: 4L8H, 4MGN.

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 1.7 has 272 motif groups, release 1.8 has 272 motif groups, 266 of them are identical.

3 motif groups were updated, 3 groups are present only in release 1.7, 3 groups are only in release 1.8.

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_41766.4	49	Tandem cWW pairs (Not AU or GC)
4	IL_56465.3	46	Single, unpaired intercalated base, consensus A
5	IL_44540.4	43	Sugar-edge, 1-base platform, consensus tHS
6	IL_87904.5	31	Triple sheared (tSH-tHS-tHS) no inserted bases
7	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
8	IL_13959.4	26	Double Sheared (tSH-tHS)
9	IL_65553.7	22	Kink-turn
10	IL_93424.4	21	tSH-inserted-tHW
11	IL_28947.1	21	23S H91 IL \| cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
12	IL_55938.4	18	LSU Helix 89 (H89) IL2. cSH Platform.
13	IL_92027.3	17	16S h21 S8 binding site
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_85647.3	16	Sarcin-ricin parent motif with 15 Nts
17	IL_92109.2	15	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
18	IL_31555.4	13	Tandem sheared with inserted, unpaired purine.
19	IL_49493.4	13	Sarcin-ricin Parent Motif - bacterial LSU H95 IL
20	IL_46648.4	11	23S H91 IL \| Single-Base Intercalation Site
21	IL_37104.2	11	Single sheared with bulged bases \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
22	IL_43124.2	11	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
23	IL_24546.4	10	23S H41 IL and 16S h18 IL : Has large bulge on one side
24	IL_58291.4	10	Recurrent Sub-motif found in junctions
25	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
26	IL_47444.3	9	SRP Loop E-like motif
27	IL_92114.3	9	GAAA loop receptor "platform" motif
28	IL_02809.3	9	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
29	IL_90459.3	9	cWW AG or UU
30	IL_83451.3	7	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
31	IL_92321.4	7	Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
32	IL_73000.2	7	cHS-cWS
33	IL_25230.3	6	Bacterial 5S rRNA Loop E
34	IL_39585.1	6	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
35	IL_97057.3	6
36	IL_25380.1	6	LSU Helix 89 (H89) IL2
37	IL_77263.2	6	Kink-turn from U4
38	IL_53635.3	6	LSU Helix 32 (H32) IL
39	IL_13069.3	6	LSU 3WJ H32-H33-H35A
40	IL_90133.3	6
41	IL_72158.3	6	LSU Helix 62 (H62) IL
42	IL_08926.3	6	23S H91 IL
43	IL_70237.3	6
44	IL_25300.1	5	16S h19 IL and 23S H41 IL
45	IL_02359.3	5
46	IL_44067.4	5	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
47	IL_86357.3	5	LSU Helix 61 IL2
48	IL_05684.1	5	tHS tHH bulge with S-turn \| Double S-turn motif
49	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
50	IL_79083.3	5
51	IL_42251.1	4
52	IL_38807.3	4
53	IL_31663.1	4	23S H73 ILa : Part of larger Motif
54	IL_09530.1	4	Double S-turn motif
55	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)
56	IL_95652.3	4	SSU Helix 27 (h27) IL Sarcin-Ricin motif
57	IL_21333.2	4	tSH-tHW-bulge
58	IL_34363.2	4	Kink-turn from 23S H42
59	IL_45262.4	4
60	IL_39526.4	4
61	IL_28572.2	4	16S h18 kink-turn like motif
62	IL_31066.3	4	SSU Helix 44 (h44) extension
63	IL_01080.1	4
64	IL_39980.1	4
65	IL_47758.2	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
66	IL_93568.2	4	Triple Sheared (tSH-tHS-tHS) with wobble cWW.
67	IL_22732.1	4	tSH-inserted-tHS
68	IL_98591.3	4
69	IL_82188.2	4	LSU H68 IL from H.m.
70	IL_16415.2	3	SSU Helix 23 (h23) Kink-turn T. thermophilus
71	IL_80494.2	3	LSU H58 IL2 H.m.
72	IL_82563.1	3	Thi-box riboswitch T-loop
73	IL_87065.1	3	23S H91 IL \| Single-Base Intercalation Site
74	IL_34628.2	3	Kink-turn
75	IL_30840.2	3
76	IL_62499.7	3
77	IL_37053.1	3	Kink-turn from 23S H58
78	IL_25271.2	3	SSU Helix 8 (h8) IL E.c. and Yeast
79	IL_74876.2	3	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
80	IL_35043.1	3	cWW AG or UU \| cWH basepair with syn base \| cWH basepair with syn base
81	IL_16166.4	3	23S H91 IL
82	IL_07300.2	3
83	IL_52173.1	3
84	IL_80348.1	3	23S H91 IL
85	IL_58586.2	3
86	IL_43946.1	3
87	IL_09520.2	3	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
88	IL_48918.2	3	Kink-turn variant
89	IL_98421.4	3	SSU Helix 12 (h12) IL
90	IL_05723.1	3
91	IL_06211.1	3
92	IL_79955.2	3	SSU Helix (23) h23 IL1
93	IL_95150.4	3
94	IL_75447.1	3
95	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.
96	IL_06180.1	3	tHS tHH bulge with S-turn
97	IL_87548.1	2
98	IL_52940.1	2
99	IL_90057.1	2
100	IL_00998.1	2
101	IL_11751.1	2
102	IL_65137.1	2	Kink-turn like motif in Group I Intron
103	IL_19898.1	2
104	IL_96206.1	2
105	IL_46435.1	2
106	IL_09587.1	2
107	IL_67887.1	2
108	IL_39355.1	2	SSU Helix 12 (h12) IL \| LSU Eukaryal Helix 96 (H96) IL1
109	IL_46034.1	2
110	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
111	IL_97833.1	2
112	IL_98566.1	2
113	IL_12211.1	2
114	IL_21495.1	2
115	IL_37406.1	2
116	IL_21639.1	2
117	IL_76095.3	2	Motif from Hairpin Ribozyme
118	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)
119	IL_01054.1	2
120	IL_15840.2	2	Triple Sheared with unpaired, inserted A
121	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
122	IL_97509.1	2	Double sheared with wobble cWW.
123	IL_37197.1	2
124	IL_96446.1	2
125	IL_31707.1	2	Vitamin B12 aptamer
126	IL_23262.4	2
127	IL_69536.1	2	LSU Helix 96 (H96) IL2
128	IL_80433.1	2
129	IL_45794.1	2
130	IL_09348.5	2	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
131	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
132	IL_68880.1	2	cWW AG or UU \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
133	IL_16330.1	2
134	IL_87507.1	2	tHS tHH bulge with S-turn
135	IL_50521.1	2
136	IL_09882.1	2
137	IL_77076.1	2
138	IL_80093.1	2
139	IL_30381.1	2	tHS tHH bulge with S-turn
140	IL_23414.1	2
141	IL_90735.1	2
142	IL_40892.1	2
143	IL_33964.1	2
144	IL_57977.1	1
145	IL_39324.1	1
146	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.
147	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
148	IL_83920.1	1
149	IL_59934.1	1	SSU Helix 23 (h23) Kink-turn E. coli
150	IL_11778.1	1
151	IL_75415.1	1	Pseudo-knot forming internal loop
152	IL_31224.1	1	23S H91 IL
153	IL_05221.1	1
154	IL_06471.1	1
155	IL_68767.1	1
156	IL_17603.1	1
157	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
158	IL_87523.1	1
159	IL_77296.1	1
160	IL_87394.1	1
161	IL_63952.1	1
162	IL_06421.1	1	Single sheared with bulged bases
163	IL_20775.1	1	tSH-inserted
164	IL_25082.1	1
165	IL_53323.1	1
166	IL_26971.1	1
167	IL_56513.1	1
168	IL_15205.1	1
169	IL_21077.1	1
170	IL_03282.1	1
171	IL_42891.1	1
172	IL_86059.1	1
173	IL_43316.1	1
174	IL_12507.1	1
175	IL_06468.1	1	16S h40 3WJ E.c.
176	IL_52958.1	1
177	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
178	IL_77014.1	1
179	IL_03741.1	1
180	IL_88119.1	1
181	IL_98924.1	1
182	IL_59529.1	1
183	IL_91904.1	1
184	IL_21421.1	1
185	IL_85510.1	1
186	IL_49527.1	1
187	IL_94973.1	1	Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
188	IL_47732.1	1
189	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
190	IL_40845.1	1
191	IL_88865.1	1
192	IL_80505.1	1
193	IL_69799.1	1
194	IL_47687.1	1
195	IL_80652.1	1
196	IL_54450.1	1
197	IL_71942.1	1
198	IL_91078.1	1
199	IL_71685.1	1	Sarcin-like with an intercalated basepair
200	IL_25181.1	1
201	IL_09491.1	1
202	IL_58454.1	1
203	IL_88367.1	1
204	IL_49976.1	1
205	IL_57285.1	1
206	IL_30354.1	1
207	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
208	IL_06177.1	1	cWW AG or UU
209	IL_82650.1	1
210	IL_31006.1	1	tSH-tHW-L-bif-cWW
211	IL_55649.1	1
212	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
213	IL_75328.1	1
214	IL_06306.1	1
215	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
216	IL_23639.1	1	tWH-tHS-L-cWW
217	IL_02957.1	1
218	IL_18675.1	1	cWW-bulge-cWW
219	IL_40527.1	1	Kink-turn
220	IL_23448.1	1
221	IL_46721.1	1
222	IL_50911.1	1	16S h34 ILa : Part of larger motif
223	IL_92280.1	1
224	IL_25307.1	1
225	IL_26868.1	1
226	IL_27243.1	1
227	IL_25314.1	1
228	IL_20530.1	1
229	IL_83856.1	1
230	IL_76486.1	1	Sarcin-ricin motif with syn G
231	IL_57364.1	1	LSU Helix 89 (H89) IL2
232	IL_41139.1	1
233	IL_91044.1	1
234	IL_27668.1	1
235	IL_41153.1	1
236	IL_85805.1	1
237	IL_03110.1	1
238	IL_02835.1	1
239	IL_76263.1	1
240	IL_91379.1	1
241	IL_11302.1	1
242	IL_89794.1	1
243	IL_28644.1	1
244	IL_52509.1	1
245	IL_95980.1	1	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
246	IL_13682.1	1
247	IL_81398.1	1
248	IL_97842.1	1
249	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
250	IL_64589.1	1
251	IL_54470.1	1	tHS tHH bulge with S-turn
252	IL_06847.1	1	Group II Intron IL
253	IL_30067.1	1
254	IL_83250.1	1	16S h40 3WJ T.th.
255	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
256	IL_41791.1	1
257	IL_68827.1	1	Reverse Kink-Turn
258	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
259	IL_53988.1	1
260	IL_61730.1	1
261	IL_37347.1	1
262	IL_46306.1	1
263	IL_82601.1	1	Tandem cWW water-inserted CU pairs
264	IL_91089.1	1
265	IL_60649.1	1	Kink-turn
266	IL_52610.1	1

Updated motif groups

#	Motif id	Instances	Description
1	IL_97217.8	244	1-3 bulged nucleotides, same chain \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
2	IL_73276.5	22	C-loop
3	IL_94403.4	3	LSU H77

Removed motif groups

#	Motif id	Instances	Description
1	IL_33484.1	3	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
2	IL_97095.1	1	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
3	IL_10365.1	1

Added 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_74214.1	2	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
3	IL_05513.1	1