1.7 | 1.8

Changes in PDB files used for clustering

Release 1.7 has 203 PDB files, release 1.8 has 205 PDB files, 203 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_49493.4	13	Sarcin-ricin Parent Motif - bacterial LSU H95 IL
19	IL_31555.4	13	Tandem sheared with inserted, unpaired purine.
20	IL_43124.2	11	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
21	IL_46648.4	11	23S H91 IL \| Single-Base Intercalation Site
22	IL_37104.2	11	Single sheared with bulged bases \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
23	IL_58291.4	10	Recurrent Sub-motif found in junctions
24	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
25	IL_24546.4	10	23S H41 IL and 16S h18 IL : Has large bulge on one side
26	IL_02809.3	9	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
27	IL_47444.3	9	SRP Loop E-like motif
28	IL_90459.3	9	cWW AG or UU
29	IL_92114.3	9	GAAA loop receptor "platform" motif
30	IL_73000.2	7	cHS-cWS
31	IL_92321.4	7	Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
32	IL_83451.3	7	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
33	IL_08926.3	6	23S H91 IL
34	IL_25380.1	6	LSU Helix 89 (H89) IL2
35	IL_97057.3	6
36	IL_25230.3	6	Bacterial 5S rRNA Loop E
37	IL_70237.3	6
38	IL_13069.3	6	LSU 3WJ H32-H33-H35A
39	IL_53635.3	6	LSU Helix 32 (H32) IL
40	IL_90133.3	6
41	IL_39585.1	6	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
42	IL_72158.3	6	LSU Helix 62 (H62) IL
43	IL_77263.2	6	Kink-turn from U4
44	IL_86357.3	5	LSU Helix 61 IL2
45	IL_79083.3	5
46	IL_02359.3	5
47	IL_44067.4	5	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
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_25300.1	5	16S h19 IL and 23S H41 IL
51	IL_47758.2	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
52	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)
53	IL_34363.2	4	Kink-turn from 23S H42
54	IL_38807.3	4
55	IL_98591.3	4
56	IL_01080.1	4
57	IL_31066.3	4	SSU Helix 44 (h44) extension
58	IL_93568.2	4	Triple Sheared (tSH-tHS-tHS) with wobble cWW.
59	IL_22732.1	4	tSH-inserted-tHS
60	IL_28572.2	4	16S h18 kink-turn like motif
61	IL_82188.2	4	LSU H68 IL from H.m.
62	IL_09530.1	4	Double S-turn motif
63	IL_31663.1	4	23S H73 ILa : Part of larger Motif
64	IL_39526.4	4
65	IL_45262.4	4
66	IL_21333.2	4	tSH-tHW-bulge
67	IL_39980.1	4
68	IL_42251.1	4
69	IL_95652.3	4	SSU Helix 27 (h27) IL Sarcin-Ricin motif
70	IL_06211.1	3
71	IL_62499.7	3
72	IL_30840.2	3
73	IL_48918.2	3	Kink-turn variant
74	IL_74876.2	3	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
75	IL_34628.2	3	Kink-turn
76	IL_43946.1	3
77	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.
78	IL_16166.4	3	23S H91 IL
79	IL_35043.1	3	cWW AG or UU \| cWH basepair with syn base \| cWH basepair with syn base
80	IL_58586.2	3
81	IL_75447.1	3
82	IL_79955.2	3	SSU Helix (23) h23 IL1
83	IL_87065.1	3	23S H91 IL \| Single-Base Intercalation Site
84	IL_09520.2	3	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
85	IL_25271.2	3	SSU Helix 8 (h8) IL E.c. and Yeast
86	IL_37053.1	3	Kink-turn from 23S H58
87	IL_05723.1	3
88	IL_16415.2	3	SSU Helix 23 (h23) Kink-turn T. thermophilus
89	IL_80348.1	3	23S H91 IL
90	IL_82563.1	3	Thi-box riboswitch T-loop
91	IL_95150.4	3
92	IL_06180.1	3	tHS tHH bulge with S-turn
93	IL_07300.2	3
94	IL_52173.1	3
95	IL_80494.2	3	LSU H58 IL2 H.m.
96	IL_98421.4	3	SSU Helix 12 (h12) IL
97	IL_00998.1	2
98	IL_30381.1	2	tHS tHH bulge with S-turn
99	IL_33964.1	2
100	IL_37406.1	2
101	IL_68880.1	2	cWW AG or UU \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
102	IL_98566.1	2
103	IL_01054.1	2
104	IL_11751.1	2
105	IL_21495.1	2
106	IL_46435.1	2
107	IL_69536.1	2	LSU Helix 96 (H96) IL2
108	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
109	IL_96206.1	2
110	IL_09348.5	2	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
111	IL_15840.2	2	Triple Sheared with unpaired, inserted A
112	IL_19898.1	2
113	IL_21639.1	2
114	IL_40892.1	2
115	IL_52940.1	2
116	IL_12211.1	2
117	IL_65137.1	2	Kink-turn like motif in Group I Intron
118	IL_16330.1	2
119	IL_23262.4	2
120	IL_39355.1	2	SSU Helix 12 (h12) IL \| LSU Eukaryal Helix 96 (H96) IL1
121	IL_76095.3	2	Motif from Hairpin Ribozyme
122	IL_80093.1	2
123	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)
124	IL_87507.1	2	tHS tHH bulge with S-turn
125	IL_90057.1	2
126	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
127	IL_97509.1	2	Double sheared with wobble cWW.
128	IL_23414.1	2
129	IL_50521.1	2
130	IL_97833.1	2
131	IL_09587.1	2
132	IL_31707.1	2	Vitamin B12 aptamer
133	IL_37197.1	2
134	IL_45794.1	2
135	IL_67887.1	2
136	IL_77076.1	2
137	IL_80433.1	2
138	IL_87548.1	2
139	IL_09882.1	2
140	IL_46034.1	2
141	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
142	IL_90735.1	2
143	IL_03110.1	1
144	IL_11302.1	1
145	IL_15205.1	1
146	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
147	IL_21421.1	1
148	IL_40527.1	1	Kink-turn
149	IL_46306.1	1
150	IL_52509.1	1
151	IL_54470.1	1	tHS tHH bulge with S-turn
152	IL_57977.1	1
153	IL_77296.1	1
154	IL_80505.1	1
155	IL_83250.1	1	16S h40 3WJ T.th.
156	IL_86059.1	1
157	IL_88119.1	1
158	IL_91044.1	1
159	IL_95980.1	1	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
160	IL_03282.1	1
161	IL_06306.1	1
162	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
163	IL_18675.1	1	cWW-bulge-cWW
164	IL_25082.1	1
165	IL_26868.1	1
166	IL_40845.1	1
167	IL_43316.1	1
168	IL_52610.1	1
169	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
170	IL_63952.1	1
171	IL_80652.1	1
172	IL_88367.1	1
173	IL_91078.1	1
174	IL_03741.1	1
175	IL_06421.1	1	Single sheared with bulged bases
176	IL_11778.1	1
177	IL_25181.1	1
178	IL_26971.1	1
179	IL_55649.1	1
180	IL_58454.1	1
181	IL_64589.1	1
182	IL_69799.1	1
183	IL_75415.1	1	Pseudo-knot forming internal loop
184	IL_81398.1	1
185	IL_83856.1	1
186	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
187	IL_91089.1	1
188	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
189	IL_05221.1	1
190	IL_06468.1	1	16S h40 3WJ E.c.
191	IL_09491.1	1
192	IL_20530.1	1
193	IL_31224.1	1	23S H91 IL
194	IL_39324.1	1
195	IL_41139.1	1
196	IL_46721.1	1
197	IL_49527.1	1
198	IL_52958.1	1
199	IL_83920.1	1
200	IL_89794.1	1
201	IL_91904.1	1
202	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
203	IL_98924.1	1
204	IL_06471.1	1
205	IL_12507.1	1
206	IL_20775.1	1	tSH-inserted
207	IL_28644.1	1
208	IL_41153.1	1
209	IL_49976.1	1
210	IL_53323.1	1
211	IL_59529.1	1
212	IL_02835.1	1
213	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
214	IL_21077.1	1
215	IL_56513.1	1
216	IL_59934.1	1	SSU Helix 23 (h23) Kink-turn E. coli
217	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
218	IL_71685.1	1	Sarcin-like with an intercalated basepair
219	IL_76486.1	1	Sarcin-ricin motif with syn G
220	IL_85510.1	1
221	IL_87523.1	1
222	IL_94973.1	1	Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
223	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.
224	IL_06177.1	1	cWW AG or UU
225	IL_06847.1	1	Group II Intron IL
226	IL_13682.1	1
227	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
228	IL_23639.1	1	tWH-tHS-L-cWW
229	IL_25307.1	1
230	IL_30067.1	1
231	IL_41791.1	1
232	IL_47687.1	1
233	IL_50911.1	1	16S h34 ILa : Part of larger motif
234	IL_53988.1	1
235	IL_57364.1	1	LSU Helix 89 (H89) IL2
236	IL_60649.1	1	Kink-turn
237	IL_71942.1	1
238	IL_82601.1	1	Tandem cWW water-inserted CU pairs
239	IL_97842.1	1
240	IL_02957.1	1
241	IL_17603.1	1
242	IL_25314.1	1
243	IL_30354.1	1
244	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
245	IL_37347.1	1
246	IL_47732.1	1
247	IL_54450.1	1
248	IL_61730.1	1
249	IL_68767.1	1
250	IL_82650.1	1
251	IL_85805.1	1
252	IL_92280.1	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_10365.1	1
3	IL_97095.1	1	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW

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