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_92109.1	15	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
18	IL_94430.4	15	16S h32-h33-h34 3WJ
19	IL_31555.3	15	Tandem sheared with inserted, unpaired purine.
20	IL_49493.3	14	Sarcin-ricin Parent Motif - bacterial LSU H95 IL
21	IL_40090.3	11	16S h34 ILa : Part of larger motif
22	IL_43124.1	11	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
23	IL_46648.2	11	23S H91 IL \| Single-Base Intercalation Site
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_58291.3	9	Recurrent Sub-motif found in junctions
27	IL_02809.2	9	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
28	IL_90459.3	9	cWW AG or UU
29	IL_92114.3	9	GAAA loop receptor "platform" motif
30	IL_47444.3	9	SRP Loop E-like motif
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_39585.1	6	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
35	IL_72158.3	6	LSU Helix 62 (H62) IL
36	IL_97057.3	6
37	IL_70237.3	6
38	IL_90133.2	6
39	IL_25230.3	6	Bacterial 5S rRNA Loop E
40	IL_53635.3	6	LSU Helix 32 (H32) IL
41	IL_13069.3	6	LSU 3WJ H32-H33-H35A
42	IL_44067.3	6	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
43	IL_54420.1	6
44	IL_77263.1	5	Kink-turn from U4
45	IL_92484.1	5
46	IL_02359.3	5
47	IL_78732.3	5	Double S-turn motif
48	IL_86357.3	5	LSU Helix 61 IL2
49	IL_16207.1	5	Single sheared with bulged bases
50	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
51	IL_79083.3	5
52	IL_08926.2	5	23S H91 IL
53	IL_25300.1	5	16S h19 IL and 23S H41 IL
54	IL_82188.1	5	LSU H68 IL from H.m.
55	IL_45262.3	5
56	IL_01080.1	4
57	IL_21333.2	4	tSH-tHW-bulge
58	IL_42251.1	4
59	IL_47758.1	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
60	IL_98591.3	4
61	IL_93568.2	4	Triple Sheared (tSH-tHS-tHS) with wobble cWW.
62	IL_22732.1	4	tSH-inserted-tHS
63	IL_31066.2	4	SSU Helix 44 (h44) extension
64	IL_34363.2	4	Kink-turn from 23S H42
65	IL_16166.3	4	23S H91 IL
66	IL_28572.1	4	16S h18 kink-turn like motif
67	IL_38807.3	4
68	IL_08559.1	4	LSU Helix 89 (H89) IL2
69	IL_39526.4	4
70	IL_80348.1	3	23S H91 IL
71	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.
72	IL_80494.2	3	LSU H58 IL2 H.m.
73	IL_09520.2	3	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
74	IL_30840.1	3
75	IL_34156.6	3	cWW AG or UU
76	IL_48918.2	3	Kink-turn variant
77	IL_62499.6	3
78	IL_74876.2	3	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
79	IL_34628.2	3	Kink-turn
80	IL_43946.1	3
81	IL_58586.2	3
82	IL_75447.1	3
83	IL_05723.1	3
84	IL_56077.1	3
85	IL_92267.1	3	23S H73 ILa : Part of larger Motif
86	IL_10647.1	3	tHS tHH bulge with S-turn
87	IL_37053.1	3	Kink-turn from 23S H58
88	IL_52173.1	3
89	IL_79955.2	3	SSU Helix (23) h23 IL1
90	IL_95150.3	3
91	IL_82563.1	3	Thi-box riboswitch T-loop
92	IL_95652.2	3	SSU Helix 27 (h27) IL Sarcin-Ricin motif
93	IL_98421.3	3	SSU Helix 12 (h12) IL
94	IL_09348.5	2	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
95	IL_11751.1	2
96	IL_16415.1	2	SSU Helix 23 (h23) Kink-turn T. thermophilus
97	IL_33925.1	2
98	IL_45794.1	2
99	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
100	IL_91273.1	2
101	IL_98566.1	2
102	IL_33964.1	2
103	IL_37406.1	2
104	IL_52940.1	2
105	IL_12211.1	2
106	IL_21495.1	2
107	IL_27892.1	2
108	IL_46435.1	2
109	IL_55287.1	2
110	IL_69536.1	2	LSU Helix 96 (H96) IL2
111	IL_90057.1	2
112	IL_09587.1	2
113	IL_15840.2	2	Triple Sheared with unpaired, inserted A
114	IL_19898.1	2
115	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
116	IL_07300.1	2
117	IL_09882.1	2
118	IL_23262.4	2
119	IL_40892.1	2
120	IL_49550.1	2	tHS tHH bulge with S-turn
121	IL_70280.1	2	Double sheared with wobble cWW.
122	IL_87548.1	2
123	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
124	IL_09901.1	2	tHS tHH bulge with S-turn
125	IL_23414.1	2
126	IL_25271.1	2	SSU Helix 8 (h8) IL E.c. and Yeast
127	IL_50521.1	2
128	IL_65137.1	2	Kink-turn like motif in Group I Intron
129	IL_76095.3	2	Motif from Hairpin Ribozyme
130	IL_97833.1	2
131	IL_00998.1	2
132	IL_16252.3	2	23S H91 IL
133	IL_28942.1	2
134	IL_31707.1	2	Vitamin B12 aptamer
135	IL_88180.1	2	cWW-bulge-cWW
136	IL_01054.1	2
137	IL_16330.1	2
138	IL_24358.1	2
139	IL_37197.1	2
140	IL_77076.1	2
141	IL_80093.1	2
142	IL_03741.1	1
143	IL_06468.1	1	16S h40 3WJ E.c.
144	IL_26868.1	1
145	IL_30067.1	1
146	IL_37347.1	1
147	IL_41791.1	1
148	IL_47732.1	1
149	IL_52610.1	1
150	IL_54576.1	1
151	IL_60649.1	1	Kink-turn
152	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
153	IL_82601.1	1	Tandem cWW water-inserted CU pairs
154	IL_85805.1	1
155	IL_95774.1	1	tHS tHH bulge with S-turn
156	IL_03931.1	1	16S h19 IL and 23S H41 IL
157	IL_06471.1	1
158	IL_09491.1	1
159	IL_11778.1	1
160	IL_15205.1	1
161	IL_17603.1	1
162	IL_21421.1	1
163	IL_26971.1	1
164	IL_30354.1	1
165	IL_46306.1	1
166	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
167	IL_57977.1	1
168	IL_61730.1	1
169	IL_67735.1	1
170	IL_77296.1	1
171	IL_82650.1	1
172	IL_86059.1	1
173	IL_89794.1	1
174	IL_91904.1	1
175	IL_02690.1	1
176	IL_04550.1	1	tHS tHH bulge with S-turn
177	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
178	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.
179	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
180	IL_25082.1	1
181	IL_37715.1	1
182	IL_40527.1	1	Kink-turn
183	IL_52958.1	1
184	IL_80505.1	1
185	IL_83250.1	1	16S h40 3WJ T.th.
186	IL_97073.1	1
187	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
188	IL_05221.1	1
189	IL_06847.1	1	Group II Intron IL
190	IL_12486.1	1
191	IL_25181.1	1
192	IL_28468.1	1	Single sheared with bulged bases
193	IL_37990.1	1
194	IL_40845.1	1
195	IL_43316.1	1
196	IL_53323.1	1
197	IL_55649.1	1
198	IL_58454.1	1
199	IL_63952.1	1
200	IL_75415.1	1	Pseudo-knot forming internal loop
201	IL_80652.1	1
202	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
203	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
204	IL_98924.1	1
205	IL_02835.1	1
206	IL_05462.1	1
207	IL_12507.1	1
208	IL_20775.1	1	tSH-inserted
209	IL_31290.1	1
210	IL_46721.1	1
211	IL_64589.1	1
212	IL_78809.1	1
213	IL_81398.1	1
214	IL_83856.1	1
215	IL_02957.1	1
216	IL_21221.1	1	SSU Helix 12 (h12) IL
217	IL_28644.1	1
218	IL_34868.1	1	LSU Eukaryal Helix 96 (H96) IL1
219	IL_41139.1	1
220	IL_53988.1	1
221	IL_59529.1	1
222	IL_82113.1	1
223	IL_83920.1	1
224	IL_91044.1	1
225	IL_94973.1	1	Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
226	IL_03110.1	1
227	IL_06306.1	1
228	IL_13434.1	1
229	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
230	IL_23639.1	1	tWH-tHS-L-cWW
231	IL_39324.1	1
232	IL_41341.1	1	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
233	IL_59934.1	1	SSU Helix 23 (h23) Kink-turn E. coli
234	IL_71685.1	1	Sarcin-like with an intercalated basepair
235	IL_76486.1	1	Sarcin-ricin motif with syn G
236	IL_85510.1	1
237	IL_91078.1	1
238	IL_92280.1	1
239	IL_97842.1	1
240	IL_03282.1	1
241	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
242	IL_11302.1	1
243	IL_13682.1	1
244	IL_25307.1	1
245	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
246	IL_47687.1	1
247	IL_52509.1	1
248	IL_54450.1	1
249	IL_56513.1	1
250	IL_60643.1	1
251	IL_65788.1	1
252	IL_71942.1	1
253	IL_88367.1	1
254	IL_91089.1	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