1.9 | 1.10

Changes in PDB files used for clustering

Release 1.9 has 209 PDB files, release 1.10 has 213 PDB files, 209 of them are identical.

No equivalence class representatives have been replaced.

4 new structures in release 1.10: 3WBM, 4M30, 4M4O, 4M6D.

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 1.9 has 271 motif groups, release 1.10 has 275 motif groups, 255 of them are identical.

6 motif groups were updated, 10 groups are present only in release 1.9, 14 groups are only in release 1.10.

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_39199.4	53	Hoogsteen-edge Platform, Single bulged base
2	IL_44540.4	43	Sugar-edge, 1-base platform, consensus tHS
3	IL_87904.5	31	Triple sheared (tSH-tHS-tHS) no inserted bases
4	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
5	IL_13959.4	26	Double Sheared (tSH-tHS)
6	IL_65553.7	22	Kink-turn
7	IL_73276.5	22	C-loop
8	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
9	IL_93424.4	21	tSH-inserted-tHW
10	IL_55938.4	18	LSU Helix 89 (H89) IL2. cSH Platform.
11	IL_92027.3	17	16S h21 S8 binding site
12	IL_85647.3	16	Sarcin-ricin parent motif with 15 Nts
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_92109.2	15	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
16	IL_49493.4	13	Sarcin-ricin Parent Motif - bacterial LSU H95 IL
17	IL_43124.2	11	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
18	IL_37104.2	11	Single sheared with bulged bases \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
19	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
20	IL_24546.4	10	23S H41 IL and 16S h18 IL : Has large bulge on one side
21	IL_58291.4	10	Recurrent Sub-motif found in junctions
22	IL_02809.3	9	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
23	IL_90459.3	9	cWW AG or UU
24	IL_92114.3	9	GAAA loop receptor "platform" motif
25	IL_47444.3	9	SRP Loop E-like motif
26	IL_92321.4	7	Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
27	IL_73000.2	7	cHS-cWS
28	IL_70237.3	6
29	IL_90133.3	6
30	IL_13069.3	6	LSU 3WJ H32-H33-H35A
31	IL_25380.1	6	LSU Helix 89 (H89) IL2
32	IL_72158.3	6	LSU Helix 62 (H62) IL
33	IL_53635.3	6	LSU Helix 32 (H32) IL
34	IL_77263.2	6	Kink-turn from U4
35	IL_25230.3	6	Bacterial 5S rRNA Loop E
36	IL_97057.3	6
37	IL_08926.3	6	23S H91 IL
38	IL_25300.2	6	16S h19 IL and 23S H41 IL
39	IL_39585.1	6	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
40	IL_02359.3	5
41	IL_05684.1	5	tHS tHH bulge with S-turn \| Double S-turn motif
42	IL_44067.4	5	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
43	IL_86357.3	5	LSU Helix 61 IL2
44	IL_79083.3	5
45	IL_39980.1	4
46	IL_48918.3	4	Kink-turn variant
47	IL_09530.1	4	Double S-turn motif
48	IL_34363.2	4	Kink-turn from 23S H42
49	IL_38807.3	4
50	IL_95652.3	4	SSU Helix 27 (h27) IL Sarcin-Ricin motif
51	IL_22732.1	4	tSH-inserted-tHS
52	IL_31066.3	4	SSU Helix 44 (h44) extension
53	IL_93568.2	4	Triple Sheared (tSH-tHS-tHS) with wobble cWW.
54	IL_98591.3	4
55	IL_28572.2	4	16S h18 kink-turn like motif
56	IL_45262.4	4
57	IL_94403.5	4	LSU H77
58	IL_31663.1	4	23S H73 ILa : Part of larger Motif
59	IL_39526.4	4
60	IL_01080.1	4
61	IL_21333.2	4	tSH-tHW-bulge
62	IL_42251.1	4
63	IL_47758.2	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
64	IL_82188.2	4	LSU H68 IL from H.m.
65	IL_79955.2	3	SSU Helix (23) h23 IL1
66	IL_58586.2	3
67	IL_82563.1	3	Thi-box riboswitch T-loop
68	IL_43946.1	3
69	IL_98421.4	3	SSU Helix 12 (h12) IL
70	IL_05723.1	3
71	IL_30840.2	3
72	IL_34628.2	3	Kink-turn
73	IL_80494.2	3	LSU H58 IL2 H.m.
74	IL_28003.1	3
75	IL_35043.1	3	cWW AG or UU \| cWH basepair with syn base \| cWH basepair with syn base
76	IL_96206.2	3
77	IL_06180.1	3	tHS tHH bulge with S-turn
78	IL_07300.2	3
79	IL_16166.4	3	23S H91 IL
80	IL_37053.1	3	Kink-turn from 23S H58
81	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.
82	IL_06211.2	3
83	IL_25271.2	3	SSU Helix 8 (h8) IL E.c. and Yeast
84	IL_52173.1	3
85	IL_62499.7	3
86	IL_87065.1	3	23S H91 IL \| Single-Base Intercalation Site
87	IL_16415.2	3	SSU Helix 23 (h23) Kink-turn T. thermophilus
88	IL_46034.2	3
89	IL_74876.2	3	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
90	IL_97833.1	2
91	IL_21495.1	2
92	IL_33964.1	2
93	IL_37406.1	2
94	IL_46435.1	2
95	IL_52940.1	2
96	IL_65137.1	2	Kink-turn like motif in Group I Intron
97	IL_76095.3	2	Motif from Hairpin Ribozyme
98	IL_80093.1	2
99	IL_87548.1	2
100	IL_95150.5	2
101	IL_09587.1	2
102	IL_21639.1	2
103	IL_30381.1	2	tHS tHH bulge with S-turn
104	IL_80348.2	2	23S H91 IL
105	IL_90735.1	2
106	IL_09882.1	2
107	IL_22358.1	2
108	IL_40892.1	2
109	IL_77076.1	2
110	IL_98566.1	2
111	IL_15840.2	2	Triple Sheared with unpaired, inserted A
112	IL_47475.1	2	LSU H77 \| cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
113	IL_50521.1	2
114	IL_67887.1	2
115	IL_11751.1	2
116	IL_39355.1	2	SSU Helix 12 (h12) IL \| LSU Eukaryal Helix 96 (H96) IL1
117	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
118	IL_00998.1	2
119	IL_16330.1	2
120	IL_23262.4	2
121	IL_45794.1	2
122	IL_69536.1	2	LSU Helix 96 (H96) IL2
123	IL_74214.1	2	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
124	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
125	IL_12211.1	2
126	IL_23414.1	2
127	IL_31707.1	2	Vitamin B12 aptamer
128	IL_37197.1	2
129	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)
130	IL_87507.1	2	tHS tHH bulge with S-turn
131	IL_90057.1	2
132	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
133	IL_97509.1	2	Double sheared with wobble cWW.
134	IL_05221.1	1
135	IL_06421.1	1	Single sheared with bulged bases
136	IL_09491.1	1
137	IL_12507.1	1
138	IL_21421.1	1
139	IL_23639.1	1	tWH-tHS-L-cWW
140	IL_25307.1	1
141	IL_30067.1	1
142	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
143	IL_37347.1	1
144	IL_46306.1	1
145	IL_52610.1	1
146	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
147	IL_58454.1	1
148	IL_64589.1	1
149	IL_75415.1	1	Pseudo-knot forming internal loop
150	IL_85510.1	1
151	IL_87523.1	1
152	IL_94973.1	1	Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
153	IL_05513.1	1
154	IL_06468.1	1	16S h40 3WJ E.c.
155	IL_17603.1	1
156	IL_30354.1	1
157	IL_40527.1	1	Kink-turn
158	IL_43316.1	1
159	IL_55649.1	1
160	IL_71685.1	1	Sarcin-like with an intercalated basepair
161	IL_97842.1	1
162	IL_02835.1	1
163	IL_06471.1	1
164	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
165	IL_26868.1	1
166	IL_40845.1	1
167	IL_46721.1	1
168	IL_49527.1	1
169	IL_52958.1	1
170	IL_59529.1	1
171	IL_71942.1	1
172	IL_76486.1	1	Sarcin-ricin motif with syn G
173	IL_82601.1	1	Tandem cWW water-inserted CU pairs
174	IL_85805.1	1
175	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.
176	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
177	IL_15205.1	1
178	IL_18675.1	1	cWW-bulge-cWW
179	IL_25082.1	1
180	IL_26971.1	1
181	IL_49976.1	1
182	IL_53323.1	1
183	IL_56513.1	1
184	IL_59934.1	1	SSU Helix 23 (h23) Kink-turn E. coli
185	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
186	IL_82650.1	1
187	IL_86059.1	1
188	IL_88119.1	1
189	IL_91044.1	1
190	IL_95980.1	1	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
191	IL_02957.1	1
192	IL_06177.1	1	cWW AG or UU
193	IL_06847.1	1	Group II Intron IL
194	IL_11302.1	1
195	IL_20775.1	1	tSH-inserted
196	IL_25181.1	1
197	IL_39324.1	1
198	IL_41139.1	1
199	IL_57364.1	1	LSU Helix 89 (H89) IL2
200	IL_60649.1	1	Kink-turn
201	IL_80505.1	1
202	IL_83250.1	1	16S h40 3WJ T.th.
203	IL_88367.1	1
204	IL_91078.1	1
205	IL_03110.1	1
206	IL_21077.1	1
207	IL_22909.1	1
208	IL_31224.1	1	23S H91 IL
209	IL_41153.1	1
210	IL_47687.1	1
211	IL_50911.1	1	16S h34 ILa : Part of larger motif
212	IL_53988.1	1
213	IL_61730.1	1
214	IL_68767.1	1
215	IL_77296.1	1
216	IL_80652.1	1
217	IL_83856.1	1
218	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
219	IL_91089.1	1
220	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
221	IL_03282.1	1
222	IL_11778.1	1
223	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
224	IL_28644.1	1
225	IL_41791.1	1
226	IL_47732.1	1
227	IL_54450.1	1
228	IL_57977.1	1
229	IL_81398.1	1
230	IL_83920.1	1
231	IL_89794.1	1
232	IL_91904.1	1
233	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
234	IL_98924.1	1
235	IL_03741.1	1
236	IL_06306.1	1
237	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
238	IL_52509.1	1
239	IL_54470.1	1	tHS tHH bulge with S-turn
240	IL_63952.1	1
241	IL_69799.1	1

Updated motif groups

#	Motif id	Instances	Description
1	IL_97217.10	248	1-3 bulged nucleotides, same chain \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
2	IL_47174.9	208	cWW AG or water inserted cWW Y-Y.
3	IL_41766.6	54	Tandem cWW pairs (Not AU or GC)
4	IL_56465.4	47	Single, unpaired intercalated base, consensus A
5	IL_31555.5	13	Tandem sheared with inserted, unpaired purine.
6	IL_46648.6	13	23S H91 IL \| Single-Base Intercalation Site

Removed motif groups

#	Motif id	Instances	Description
1	IL_83451.3	7	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
2	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
3	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)
4	IL_09348.6	3	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
5	IL_75447.1	3
6	IL_09520.3	2	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
7	IL_19898.1	2
8	IL_51403.1	2
9	IL_68880.1	2	cWW AG or UU \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
10	IL_90086.1	1

Added motif groups

#	Motif id	Instances	Description
1	IL_46301.1	7	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW \| Leadzyme Motif. LSU H101 IL2. SSU Decoding site. \| Tandem sheared with inserted, unpaired purine. \| cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
2	IL_70173.1	6	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)
3	IL_97296.1	4	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW \| Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
4	IL_54966.1	4	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
5	IL_31473.1	2
6	IL_70401.1	2
7	IL_33842.1	2
8	IL_95884.1	2
9	IL_43877.1	2	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) \| cWW AG or UU \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
10	IL_69106.1	2	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
11	IL_27503.1	1
12	IL_91956.1	1
13	IL_34076.1	1
14	IL_99397.1	1	cWW AG or UU \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)