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

Loading the Sankey diagram...

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_31555.3	15	Tandem sheared with inserted, unpaired purine.
18	IL_92109.1	15	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
19	IL_94430.4	15	16S h32-h33-h34 3WJ
20	IL_49493.3	14	Sarcin-ricin Parent Motif - bacterial LSU H95 IL
21	IL_21304.2	11	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
22	IL_46648.2	11	23S H91 IL \| Single-Base Intercalation Site
23	IL_40090.3	11	16S h34 ILa : Part of larger motif
24	IL_43124.1	11	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
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_83451.2	7	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
32	IL_92321.3	7	Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
33	IL_73000.2	7	cHS-cWS
34	IL_54420.1	6
35	IL_25230.3	6	Bacterial 5S rRNA Loop E
36	IL_44067.3	6	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
37	IL_97057.3	6
38	IL_53635.3	6	LSU Helix 32 (H32) IL
39	IL_90133.2	6
40	IL_72158.3	6	LSU Helix 62 (H62) IL
41	IL_13069.3	6	LSU 3WJ H32-H33-H35A
42	IL_39585.1	6	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
43	IL_70237.3	6
44	IL_25300.1	5	16S h19 IL and 23S H41 IL
45	IL_45262.3	5
46	IL_86357.3	5	LSU Helix 61 IL2
47	IL_16207.1	5	Single sheared with bulged bases
48	IL_02359.3	5
49	IL_08926.2	5	23S H91 IL
50	IL_78732.3	5	Double S-turn motif
51	IL_77263.1	5	Kink-turn from U4
52	IL_92484.1	5
53	IL_82188.1	5	LSU H68 IL from H.m.
54	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
55	IL_79083.3	5
56	IL_42251.1	4
57	IL_38807.3	4
58	IL_34363.2	4	Kink-turn from 23S H42
59	IL_08559.1	4	LSU Helix 89 (H89) IL2
60	IL_28572.1	4	16S h18 kink-turn like motif
61	IL_21333.2	4	tSH-tHW-bulge
62	IL_16166.3	4	23S H91 IL
63	IL_31066.2	4	SSU Helix 44 (h44) extension
64	IL_39526.4	4
65	IL_47758.1	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
66	IL_01080.1	4
67	IL_98591.3	4
68	IL_93568.2	4	Triple Sheared (tSH-tHS-tHS) with wobble cWW.
69	IL_22732.1	4	tSH-inserted-tHS
70	IL_79955.2	3	SSU Helix (23) h23 IL1
71	IL_37053.1	3	Kink-turn from 23S H58
72	IL_92267.1	3	23S H73 ILa : Part of larger Motif
73	IL_34156.6	3	cWW AG or UU
74	IL_75447.1	3
75	IL_48918.2	3	Kink-turn variant
76	IL_62499.6	3
77	IL_43946.1	3
78	IL_82563.1	3	Thi-box riboswitch T-loop
79	IL_10647.1	3	tHS tHH bulge with S-turn
80	IL_95652.2	3	SSU Helix 27 (h27) IL Sarcin-Ricin motif
81	IL_30840.1	3
82	IL_80348.1	3	23S H91 IL
83	IL_52173.1	3
84	IL_58586.2	3
85	IL_34628.2	3	Kink-turn
86	IL_98421.3	3	SSU Helix 12 (h12) IL
87	IL_05723.1	3
88	IL_56077.1	3
89	IL_74876.2	3	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
90	IL_95150.3	3
91	IL_80494.2	3	LSU H58 IL2 H.m.
92	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.
93	IL_09520.2	3	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
94	IL_87548.1	2
95	IL_09882.1	2
96	IL_77076.1	2
97	IL_12211.1	2
98	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
99	IL_55287.1	2
100	IL_16415.1	2	SSU Helix 23 (h23) Kink-turn T. thermophilus
101	IL_52940.1	2
102	IL_90057.1	2
103	IL_33925.1	2
104	IL_00998.1	2
105	IL_16252.3	2	23S H91 IL
106	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
107	IL_11751.1	2
108	IL_65137.1	2	Kink-turn like motif in Group I Intron
109	IL_19898.1	2
110	IL_91273.1	2
111	IL_27892.1	2
112	IL_23414.1	2
113	IL_37197.1	2
114	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
115	IL_98566.1	2
116	IL_09587.1	2
117	IL_07300.1	2
118	IL_45794.1	2
119	IL_33964.1	2
120	IL_97833.1	2
121	IL_46435.1	2
122	IL_25271.1	2	SSU Helix 8 (h8) IL E.c. and Yeast
123	IL_09901.1	2	tHS tHH bulge with S-turn
124	IL_24358.1	2
125	IL_16330.1	2
126	IL_31707.1	2	Vitamin B12 aptamer
127	IL_76095.3	2	Motif from Hairpin Ribozyme
128	IL_21495.1	2
129	IL_37406.1	2
130	IL_69536.1	2	LSU Helix 96 (H96) IL2
131	IL_28942.1	2
132	IL_40892.1	2
133	IL_09348.5	2	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
134	IL_80093.1	2
135	IL_01054.1	2
136	IL_15840.2	2	Triple Sheared with unpaired, inserted A
137	IL_23262.4	2
138	IL_49550.1	2	tHS tHH bulge with S-turn
139	IL_50521.1	2
140	IL_70280.1	2	Double sheared with wobble cWW.
141	IL_88180.1	2	cWW-bulge-cWW
142	IL_83250.1	1	16S h40 3WJ T.th.
143	IL_57977.1	1
144	IL_39324.1	1
145	IL_25307.1	1
146	IL_11302.1	1
147	IL_53988.1	1
148	IL_28644.1	1
149	IL_11778.1	1
150	IL_37715.1	1
151	IL_54450.1	1
152	IL_41341.1	1	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
153	IL_25082.1	1
154	IL_98924.1	1
155	IL_59529.1	1
156	IL_02957.1	1
157	IL_28468.1	1	Single sheared with bulged bases
158	IL_88367.1	1
159	IL_60649.1	1	Kink-turn
160	IL_46721.1	1
161	IL_63952.1	1
162	IL_86059.1	1
163	IL_04550.1	1	tHS tHH bulge with S-turn
164	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
165	IL_05462.1	1
166	IL_20775.1	1	tSH-inserted
167	IL_13682.1	1
168	IL_31290.1	1
169	IL_13434.1	1
170	IL_71685.1	1	Sarcin-like with an intercalated basepair
171	IL_25181.1	1
172	IL_58454.1	1
173	IL_40527.1	1	Kink-turn
174	IL_77296.1	1
175	IL_59934.1	1	SSU Helix 23 (h23) Kink-turn E. coli
176	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
177	IL_61730.1	1
178	IL_67735.1	1
179	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
180	IL_23639.1	1	tWH-tHS-L-cWW
181	IL_64589.1	1
182	IL_41139.1	1
183	IL_03282.1	1
184	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
185	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
186	IL_83920.1	1
187	IL_52958.1	1
188	IL_80652.1	1
189	IL_65788.1	1
190	IL_78809.1	1
191	IL_75415.1	1	Pseudo-knot forming internal loop
192	IL_76486.1	1	Sarcin-ricin motif with syn G
193	IL_37990.1	1
194	IL_82601.1	1	Tandem cWW water-inserted CU pairs
195	IL_34868.1	1	LSU Eukaryal Helix 96 (H96) IL1
196	IL_94973.1	1	Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
197	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
198	IL_40845.1	1
199	IL_06468.1	1	16S h40 3WJ E.c.
200	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
201	IL_97073.1	1
202	IL_03931.1	1	16S h19 IL and 23S H41 IL
203	IL_54576.1	1
204	IL_06306.1	1
205	IL_97842.1	1
206	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
207	IL_17603.1	1
208	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
209	IL_91089.1	1
210	IL_30067.1	1
211	IL_02835.1	1
212	IL_12507.1	1
213	IL_47687.1	1
214	IL_21221.1	1	SSU Helix 12 (h12) IL
215	IL_03741.1	1
216	IL_83856.1	1
217	IL_37347.1	1
218	IL_46306.1	1
219	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.
220	IL_15205.1	1
221	IL_60643.1	1
222	IL_52610.1	1
223	IL_92280.1	1
224	IL_03110.1	1
225	IL_80505.1	1
226	IL_55649.1	1
227	IL_52509.1	1
228	IL_02690.1	1
229	IL_91078.1	1
230	IL_81398.1	1
231	IL_05221.1	1
232	IL_06471.1	1
233	IL_91904.1	1
234	IL_56513.1	1
235	IL_91044.1	1
236	IL_47732.1	1
237	IL_85805.1	1
238	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
239	IL_41791.1	1
240	IL_43316.1	1
241	IL_82650.1	1
242	IL_26868.1	1
243	IL_89794.1	1
244	IL_95774.1	1	tHS tHH bulge with S-turn
245	IL_12486.1	1
246	IL_71942.1	1
247	IL_82113.1	1
248	IL_53323.1	1
249	IL_26971.1	1
250	IL_09491.1	1
251	IL_21421.1	1
252	IL_85510.1	1
253	IL_06847.1	1	Group II Intron IL
254	IL_30354.1	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