1.1 | 1.2

Changes in PDB files used for clustering

Release 1.1 has 199 PDB files, release 1.2 has 200 PDB files, 199 of them are identical.

No equivalence class representatives have been replaced.

1 new structures in release 1.2: 4JRC.

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

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Changes in motif groups

Release 1.1 has 271 motif groups, release 1.2 has 271 motif groups, 268 of them are identical.

2 motif groups were updated, 1 groups are present only in release 1.1, 1 groups are only in release 1.2.

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_97217.6	239	1-3 bulged nucleotides, same chain \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
2	IL_47174.6	201	cWW AG or water inserted cWW Y-Y.
3	IL_39199.3	54	Hoogsteen-edge Platform, Single bulged base
4	IL_41766.3	49	Tandem cWW pairs (Not AU or GC)
5	IL_56465.3	46	Single, unpaired intercalated base, consensus A
6	IL_44540.3	43	Sugar-edge, 1-base platform, consensus tHS
7	IL_87904.4	31	Triple sheared (tSH-tHS-tHS) no inserted bases
8	IL_06390.3	26	cWH basepair with syn base
9	IL_13959.3	24	Double Sheared (tSH-tHS)
10	IL_93424.3	22	tSH-inserted-tHW
11	IL_65553.5	22	Kink-turn
12	IL_28947.1	21	23S H91 IL \| cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
13	IL_55938.3	18	LSU Helix 89 (H89) IL2. cSH Platform.
14	IL_92027.3	17	16S h21 S8 binding site
15	IL_24982.4	16	SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
16	IL_85647.3	16	Sarcin-ricin parent motif with 15 Nts
17	IL_94430.4	15	16S h32-h33-h34 3WJ
18	IL_31555.3	15	Tandem sheared with inserted, unpaired purine.
19	IL_92109.1	15	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
20	IL_49493.3	14	Sarcin-ricin Parent Motif - bacterial LSU H95 IL
21	IL_46648.2	11	23S H91 IL \| Single-Base Intercalation Site
22	IL_40090.3	11	16S h34 ILa : Part of larger motif
23	IL_43124.1	11	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
24	IL_21304.2	11	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
25	IL_24546.3	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_02809.2	9	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
28	IL_92114.3	9	GAAA loop receptor "platform" motif
29	IL_58291.3	9	Recurrent Sub-motif found in junctions
30	IL_90459.3	9	cWW AG or UU
31	IL_73000.2	7	cHS-cWS
32	IL_83451.2	7	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
33	IL_92321.3	7	Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
34	IL_13069.3	6	LSU 3WJ H32-H33-H35A
35	IL_39585.1	6	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
36	IL_70237.3	6
37	IL_54420.1	6
38	IL_25230.3	6	Bacterial 5S rRNA Loop E
39	IL_44067.3	6	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
40	IL_97057.3	6
41	IL_53635.3	6	LSU Helix 32 (H32) IL
42	IL_90133.2	6
43	IL_72158.3	6	LSU Helix 62 (H62) IL
44	IL_92484.1	5
45	IL_82188.1	5	LSU H68 IL from H.m.
46	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
47	IL_79083.3	5
48	IL_25300.1	5	16S h19 IL and 23S H41 IL
49	IL_45262.3	5
50	IL_86357.3	5	LSU Helix 61 IL2
51	IL_16207.1	5	Single sheared with bulged bases
52	IL_02359.3	5
53	IL_08926.2	5	23S H91 IL
54	IL_78732.3	5	Double S-turn motif
55	IL_77263.1	5	Kink-turn from U4
56	IL_47758.1	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
57	IL_01080.1	4
58	IL_98591.3	4
59	IL_93568.2	4	Triple Sheared (tSH-tHS-tHS) with wobble cWW.
60	IL_22732.1	4	tSH-inserted-tHS
61	IL_42251.1	4
62	IL_38807.3	4
63	IL_34363.2	4	Kink-turn from 23S H42
64	IL_08559.1	4	LSU Helix 89 (H89) IL2
65	IL_28572.1	4	16S h18 kink-turn like motif
66	IL_21333.2	4	tSH-tHW-bulge
67	IL_16166.3	4	23S H91 IL
68	IL_31066.2	4	SSU Helix 44 (h44) extension
69	IL_39526.4	4
70	IL_80348.1	3	23S H91 IL
71	IL_52173.1	3
72	IL_58586.2	3
73	IL_34628.2	3	Kink-turn
74	IL_98421.3	3	SSU Helix 12 (h12) IL
75	IL_05723.1	3
76	IL_56077.1	3
77	IL_74876.2	3	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
78	IL_95150.3	3
79	IL_80494.2	3	LSU H58 IL2 H.m.
80	IL_89028.5	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.
81	IL_09520.2	3	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
82	IL_79955.2	3	SSU Helix (23) h23 IL1
83	IL_37053.1	3	Kink-turn from 23S H58
84	IL_92267.1	3	23S H73 ILa : Part of larger Motif
85	IL_34156.6	3	cWW AG or UU
86	IL_75447.1	3
87	IL_48918.2	3	Kink-turn variant
88	IL_62499.6	3
89	IL_43946.1	3
90	IL_82563.1	3	Thi-box riboswitch T-loop
91	IL_10647.1	3	tHS tHH bulge with S-turn
92	IL_95652.2	3	SSU Helix 27 (h27) IL Sarcin-Ricin motif
93	IL_30840.1	3
94	IL_31707.1	2	Vitamin B12 aptamer
95	IL_76095.3	2	Motif from Hairpin Ribozyme
96	IL_21495.1	2
97	IL_37406.1	2
98	IL_69536.1	2	LSU Helix 96 (H96) IL2
99	IL_28942.1	2
100	IL_40892.1	2
101	IL_09348.5	2	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
102	IL_80093.1	2
103	IL_01054.1	2
104	IL_15840.2	2	Triple Sheared with unpaired, inserted A
105	IL_23262.4	2
106	IL_49550.1	2	tHS tHH bulge with S-turn
107	IL_50521.1	2
108	IL_70280.1	2	Double sheared with wobble cWW.
109	IL_88180.1	2	cWW-bulge-cWW
110	IL_87548.1	2
111	IL_09882.1	2
112	IL_77076.1	2
113	IL_12211.1	2
114	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
115	IL_55287.1	2
116	IL_16415.1	2	SSU Helix 23 (h23) Kink-turn T. thermophilus
117	IL_52940.1	2
118	IL_90057.1	2
119	IL_33925.1	2
120	IL_00998.1	2
121	IL_16252.3	2	23S H91 IL
122	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
123	IL_11751.1	2
124	IL_65137.1	2	Kink-turn like motif in Group I Intron
125	IL_19898.1	2
126	IL_91273.1	2
127	IL_27892.1	2
128	IL_23414.1	2
129	IL_37197.1	2
130	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
131	IL_98566.1	2
132	IL_09587.1	2
133	IL_07300.1	2
134	IL_45794.1	2
135	IL_33964.1	2
136	IL_97833.1	2
137	IL_46435.1	2
138	IL_25271.1	2	SSU Helix 8 (h8) IL E.c. and Yeast
139	IL_09901.1	2	tHS tHH bulge with S-turn
140	IL_24358.1	2
141	IL_16330.1	2
142	IL_02835.1	1
143	IL_12507.1	1
144	IL_47687.1	1
145	IL_21221.1	1	SSU Helix 12 (h12) IL
146	IL_03741.1	1
147	IL_83856.1	1
148	IL_37347.1	1
149	IL_46306.1	1
150	IL_15674.1	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.
151	IL_15205.1	1
152	IL_60643.1	1
153	IL_52610.1	1
154	IL_92280.1	1
155	IL_03110.1	1
156	IL_80505.1	1
157	IL_55649.1	1
158	IL_52509.1	1
159	IL_02690.1	1
160	IL_91078.1	1
161	IL_81398.1	1
162	IL_05221.1	1
163	IL_06471.1	1
164	IL_91904.1	1
165	IL_56513.1	1
166	IL_91044.1	1
167	IL_47732.1	1
168	IL_85805.1	1
169	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
170	IL_41791.1	1
171	IL_43316.1	1
172	IL_82650.1	1
173	IL_26868.1	1
174	IL_89794.1	1
175	IL_95774.1	1	tHS tHH bulge with S-turn
176	IL_12486.1	1
177	IL_71942.1	1
178	IL_82113.1	1
179	IL_53323.1	1
180	IL_26971.1	1
181	IL_09491.1	1
182	IL_21421.1	1
183	IL_85510.1	1
184	IL_06847.1	1	Group II Intron IL
185	IL_30354.1	1
186	IL_83250.1	1	16S h40 3WJ T.th.
187	IL_57977.1	1
188	IL_39324.1	1
189	IL_25307.1	1
190	IL_11302.1	1
191	IL_53988.1	1
192	IL_28644.1	1
193	IL_11778.1	1
194	IL_37715.1	1
195	IL_54450.1	1
196	IL_41341.1	1	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
197	IL_25082.1	1
198	IL_98924.1	1
199	IL_59529.1	1
200	IL_02957.1	1
201	IL_28468.1	1	Single sheared with bulged bases
202	IL_88367.1	1
203	IL_60649.1	1	Kink-turn
204	IL_46721.1	1
205	IL_63952.1	1
206	IL_86059.1	1
207	IL_04550.1	1	tHS tHH bulge with S-turn
208	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
209	IL_05462.1	1
210	IL_20775.1	1	tSH-inserted
211	IL_13682.1	1
212	IL_31290.1	1
213	IL_13434.1	1
214	IL_71685.1	1	Sarcin-like with an intercalated basepair
215	IL_25181.1	1
216	IL_58454.1	1
217	IL_40527.1	1	Kink-turn
218	IL_77296.1	1
219	IL_59934.1	1	SSU Helix 23 (h23) Kink-turn E. coli
220	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
221	IL_61730.1	1
222	IL_67735.1	1
223	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
224	IL_23639.1	1	tWH-tHS-L-cWW
225	IL_64589.1	1
226	IL_41139.1	1
227	IL_03282.1	1
228	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
229	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
230	IL_83920.1	1
231	IL_52958.1	1
232	IL_80652.1	1
233	IL_65788.1	1
234	IL_78809.1	1
235	IL_75415.1	1	Pseudo-knot forming internal loop
236	IL_76486.1	1	Sarcin-ricin motif with syn G
237	IL_37990.1	1
238	IL_82601.1	1	Tandem cWW water-inserted CU pairs
239	IL_34868.1	1	LSU Eukaryal Helix 96 (H96) IL1
240	IL_94973.1	1	Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
241	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
242	IL_40845.1	1
243	IL_06468.1	1	16S h40 3WJ E.c.
244	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
245	IL_97073.1	1
246	IL_03931.1	1	16S h19 IL and 23S H41 IL
247	IL_54576.1	1
248	IL_06306.1	1
249	IL_97842.1	1
250	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
251	IL_17603.1	1
252	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
253	IL_91089.1	1
254	IL_30067.1	1

Updated motif groups

#	Motif id	Instances	Description
1	IL_73276.3	21	C-loop
2	IL_71565.3	3

Removed motif groups

#	Motif id	Instances	Description
1	IL_89231.1	2	LSU H77

Added motif groups

#	Motif id	Instances	Description
1	IL_94403.1	4	LSU H77