0.10 | 0.11

Changes in PDB files used for clustering

Release 0.10 has 196 PDB files, release 0.11 has 197 PDB files, 195 of them are identical.

No equivalence class representatives have been replaced.

2 new structures in release 0.11: 3ZD3, 4E59.

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 0.10 has 266 motif groups, release 0.11 has 266 motif groups, 252 of them are identical.

6 motif groups were updated, 8 groups are present only in release 0.10, 8 groups are only in release 0.11.

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_97217.4	235	1-3 bulged nucleotides, same chain
2	IL_39199.2	55	Hoogsteen-edge Platform, Single bulged base
3	IL_41766.2	49	Tandem cWW pairs (Not AU or GC)
4	IL_56465.2	45	Single, unpaired intercalated base, consensus A
5	IL_44540.2	43	Sugar-edge, 1-base platform, consensus tHS
6	IL_87904.3	31	Triple sheared (tSH-tHS-tHS) no inserted bases
7	IL_06390.1	25	cWH basepair with syn base
8	IL_13959.2	24	Double Sheared (tSH-tHS)
9	IL_93424.2	22	tSH-inserted-tHW
10	IL_65553.4	22	Kink-turn
11	IL_32390.2	21	16S h19 IL and 23S H41 IL
12	IL_73276.1	20	C-loop
13	IL_55938.2	19	LSU Helix 89 (H89) IL2. cSH Platform.
14	IL_92027.2	17	16S h21 S8 binding site
15	IL_06429.2	16	cWW-bulge-cWW
16	IL_85647.2	16	Sarcin-ricin parent motif with 15 Nts
17	IL_31555.3	15	Tandem sheared with inserted, unpaired purine.
18	IL_24982.3	15	SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
19	IL_94430.3	15	16S h32-h33-h34 3WJ
20	IL_49493.2	14	Sarcin-ricin Parent Motif - bacterial LSU H95 IL
21	IL_21304.1	11	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
22	IL_46648.1	11	23S H91 IL \| Single-Base Intercalation Site
23	IL_27618.2	11	23S H73 ILa : Part of larger Motif
24	IL_40090.2	11	16S h34 ILa : Part of larger motif
25	IL_24546.2	10	23S H41 IL and 16S h18 IL : Has large bulge on one side
26	IL_47444.3	9	SRP Loop E-like motif
27	IL_92114.3	9	GAAA loop receptor "platform" motif
28	IL_58291.2	9	Recurrent Sub-motif found in junctions
29	IL_90459.2	8	cWW AG or UU
30	IL_92321.2	8	Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
31	IL_02809.1	8	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
32	IL_86357.2	7	LSU Helix 61 IL2
33	IL_83451.2	7	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
34	IL_73000.2	7	cHS-cWS
35	IL_54420.1	6
36	IL_10007.1	6	Single sheared with bulged bases
37	IL_89088.1	6	16S h19 IL and 23S H41 IL
38	IL_08926.1	6	23S H91 IL
39	IL_25230.2	6	Bacterial 5S rRNA Loop E
40	IL_44067.2	6	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
41	IL_97057.2	6
42	IL_53635.2	6	LSU Helix 32 (H32) IL
43	IL_72158.2	6	LSU Helix 62 (H62) IL
44	IL_13069.2	6	LSU 3WJ H32-H33-H35A
45	IL_70237.3	6
46	IL_24022.2	6
47	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
48	IL_45262.2	5
49	IL_90133.1	5
50	IL_78732.3	5	Double S-turn motif
51	IL_02359.2	5
52	IL_77263.1	5	Kink-turn from U4
53	IL_01239.1	5
54	IL_92484.1	5
55	IL_82188.1	5	LSU H68 IL from H.m.
56	IL_79083.2	5
57	IL_93568.1	4	Triple Sheared (tSH-tHS-tHS) with wobble cWW.
58	IL_38807.2	4
59	IL_21333.1	4	tSH-tHW-bulge
60	IL_31066.2	4	SSU Helix 44 (h44) extension
61	IL_28572.1	4	16S h18 kink-turn like motif
62	IL_98591.2	4
63	IL_39526.3	4
64	IL_47758.1	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
65	IL_10005.1	4
66	IL_22732.1	4	tSH-inserted-tHS
67	IL_62661.2	4	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
68	IL_95150.3	3
69	IL_37053.1	3	Kink-turn from 23S H58
70	IL_43946.1	3
71	IL_23262.3	3
72	IL_79955.2	3	SSU Helix (23) h23 IL1
73	IL_34363.1	3	Kink-turn from 23S H42
74	IL_36254.1	3
75	IL_75447.1	3
76	IL_30840.1	3
77	IL_53774.1	3	Single sheared with bulged bases
78	IL_34628.2	3	Kink-turn
79	IL_16166.2	3
80	IL_82563.1	3	Thi-box riboswitch T-loop
81	IL_95652.2	3	SSU Helix 27 (h27) IL Sarcin-Ricin motif
82	IL_52173.1	3
83	IL_71565.1	3
84	IL_58586.2	3
85	IL_09348.3	3	cWW-L-cWW-cWW
86	IL_98421.2	3	SSU Helix 12 (h12) IL
87	IL_80494.2	3	LSU H58 IL2 H.m.
88	IL_16252.2	3	23S H91 IL
89	IL_09882.1	2
90	IL_77076.1	2
91	IL_01054.1	2
92	IL_15840.2	2	Triple Sheared with unpaired, inserted A
93	IL_81441.1	2
94	IL_55287.1	2
95	IL_37197.1	2
96	IL_50521.1	2
97	IL_90057.1	2
98	IL_91132.1	2
99	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
100	IL_28942.1	2
101	IL_07300.1	2
102	IL_45794.1	2
103	IL_87548.1	2
104	IL_16415.1	2	SSU Helix 23 (h23) Kink-turn T. thermophilus
105	IL_52940.1	2
106	IL_65137.1	2	Kink-turn like motif in Group I Intron
107	IL_23414.1	2
108	IL_16330.1	2
109	IL_11751.1	2
110	IL_97833.1	2
111	IL_98566.1	2
112	IL_00998.1	2
113	IL_74876.1	2
114	IL_40892.1	2
115	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
116	IL_76095.3	2	Motif from Hairpin Ribozyme
117	IL_82831.2	2	Kink-turn from 16S H23
118	IL_41397.2	2	LSU Helix 96 (H96) IL2
119	IL_69901.1	2
120	IL_25174.1	2
121	IL_16377.1	2
122	IL_87336.1	2	LSU Eukaryal Helix 96 (H96) IL1
123	IL_46435.1	2
124	IL_25271.1	2	SSU Helix 8 (h8) IL E.c. and Yeast
125	IL_70280.1	2	Double sheared with wobble cWW.
126	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
127	IL_31707.1	2	Vitamin B12 aptamer
128	IL_80093.1	2
129	IL_21495.1	2
130	IL_37406.1	2
131	IL_89231.1	2	LSU H77
132	IL_54965.1	2	Leadzyme Motif. SSU Decoding site motif, extended.
133	IL_12211.1	2
134	IL_96446.1	2
135	IL_85805.1	1
136	IL_39324.1	1
137	IL_82650.1	1
138	IL_20775.1	1	tSH-inserted
139	IL_65788.1	1
140	IL_75688.1	1	Part of Helix 71 (H71) junction in 23S of D.r.
141	IL_78809.1	1
142	IL_67735.1	1
143	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
144	IL_23639.1	1	tWH-tHS-L-cWW
145	IL_90880.1	1
146	IL_15205.1	1
147	IL_91044.1	1
148	IL_27668.1	1
149	IL_83250.1	1	16S h40 3WJ T.th.
150	IL_57977.1	1
151	IL_76263.1	1
152	IL_25307.1	1
153	IL_26868.1	1
154	IL_89794.1	1
155	IL_05462.1	1
156	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
157	IL_11869.1	1
158	IL_54576.1	1
159	IL_13682.1	1
160	IL_76486.1	1	Sarcin-ricin motif with syn G
161	IL_37990.1	1
162	IL_17603.1	1
163	IL_85510.1	1
164	IL_06847.1	1	Group II Intron IL
165	IL_91379.1	1
166	IL_11302.1	1
167	IL_53988.1	1
168	IL_80652.1	1
169	IL_02690.1	1
170	IL_06306.1	1
171	IL_97842.1	1
172	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
173	IL_56513.1	1
174	IL_88367.1	1
175	IL_60649.1	1	Kink-turn
176	IL_63952.1	1
177	IL_68827.1	1	Reverse Kink-Turn
178	IL_98688.1	1
179	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
180	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
181	IL_97073.1	1
182	IL_12486.1	1
183	IL_31241.1	1
184	IL_75415.1	1	Pseudo-knot forming internal loop
185	IL_83856.1	1
186	IL_37347.1	1
187	IL_46306.1	1
188	IL_21421.1	1
189	IL_40527.1	1	Kink-turn
190	IL_77296.1	1
191	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
192	IL_88865.1	1
193	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
194	IL_83920.1	1
195	IL_54450.1	1
196	IL_76256.1	1
197	IL_81398.1	1
198	IL_05221.1	1
199	IL_06471.1	1
200	IL_58454.1	1
201	IL_41139.1	1
202	IL_03282.1	1
203	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
204	IL_40845.1	1
205	IL_92280.1	1
206	IL_02835.1	1
207	IL_88403.1	1
208	IL_52958.1	1
209	IL_52509.1	1
210	IL_22579.1	1
211	IL_77014.1	1
212	IL_03741.1	1
213	IL_82113.1	1
214	IL_53323.1	1
215	IL_26971.1	1
216	IL_91904.1	1
217	IL_18755.1	1
218	IL_91089.1	1
219	IL_94973.1	1	Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
220	IL_03110.1	1
221	IL_43316.1	1
222	IL_12507.1	1
223	IL_06468.1	1	16S h40 3WJ E.c.
224	IL_37715.1	1
225	IL_55934.1	1	kink-turn-like
226	IL_27243.1	1
227	IL_71942.1	1
228	IL_91078.1	1
229	IL_25082.1	1
230	IL_98924.1	1
231	IL_59529.1	1
232	IL_02957.1	1
233	IL_82601.1	1	Tandem cWW water-inserted CU pairs
234	IL_23448.1	1
235	IL_57285.1	1
236	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
237	IL_41791.1	1
238	IL_86059.1	1
239	IL_80505.1	1
240	IL_61991.1	1
241	IL_47687.1	1
242	IL_31006.1	1	tSH-tHW-L-bif-cWW
243	IL_55649.1	1
244	IL_61730.1	1
245	IL_75328.1	1
246	IL_53423.1	1
247	IL_77195.1	1
248	IL_71685.1	1	Sarcin-like with an intercalated basepair
249	IL_25181.1	1
250	IL_47968.1	1
251	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
252	IL_60643.1	1

Updated motif groups

#	Motif id	Instances	Description
1	IL_47174.5	203	cWW AG or water inserted cWW Y-Y.
2	IL_40387.4	4	LSU Helix 89 (H89) IL2
3	IL_98556.3	4
4	IL_34156.4	3	cWW AG or UU
5	IL_62499.4	3
6	IL_89028.3	3	Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena

Removed motif groups

#	Motif id	Instances	Description
1	IL_86826.1	3	tHS tHH bulge with S-turn
2	IL_93782.1	2
3	IL_37737.1	2
4	IL_73816.1	2	tHS tHH bulge with S-turn
5	IL_06780.1	1
6	IL_17268.1	1
7	IL_62017.1	1	Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
8	IL_70550.1	1

Added motif groups

#	Motif id	Instances	Description
1	IL_91547.1	3	tHS tHH bulge with S-turn
2	IL_33965.1	2	tHS tHH bulge with S-turn
3	IL_58811.1	2
4	IL_96031.1	1	tHS tHH bulge with S-turn
5	IL_97961.1	1
6	IL_37150.1	1	tHS tHH bulge with S-turn
7	IL_41864.1	1	Part of H71 junction in 23S rRNA from T.th.
8	IL_87544.1	1