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_65553.5	22	Kink-turn
11	IL_93424.3	22	tSH-inserted-tHW
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_85647.3	16	Sarcin-ricin parent motif with 15 Nts
16	IL_24982.4	16	SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
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_43124.1	11	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
22	IL_46648.2	11	23S H91 IL \| Single-Base Intercalation Site
23	IL_21304.2	11	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
24	IL_40090.3	11	16S h34 ILa : Part of larger motif
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_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_70237.3	6
35	IL_90133.2	6
36	IL_25230.3	6	Bacterial 5S rRNA Loop E
37	IL_53635.3	6	LSU Helix 32 (H32) IL
38	IL_13069.3	6	LSU 3WJ H32-H33-H35A
39	IL_44067.3	6	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
40	IL_54420.1	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_97057.3	6
44	IL_78732.3	5	Double S-turn motif
45	IL_86357.3	5	LSU Helix 61 IL2
46	IL_16207.1	5	Single sheared with bulged bases
47	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
48	IL_79083.3	5
49	IL_08926.2	5	23S H91 IL
50	IL_25300.1	5	16S h19 IL and 23S H41 IL
51	IL_82188.1	5	LSU H68 IL from H.m.
52	IL_45262.3	5
53	IL_77263.1	5	Kink-turn from U4
54	IL_92484.1	5
55	IL_02359.3	5
56	IL_93568.2	4	Triple Sheared (tSH-tHS-tHS) with wobble cWW.
57	IL_22732.1	4	tSH-inserted-tHS
58	IL_31066.2	4	SSU Helix 44 (h44) extension
59	IL_34363.2	4	Kink-turn from 23S H42
60	IL_16166.3	4	23S H91 IL
61	IL_28572.1	4	16S h18 kink-turn like motif
62	IL_38807.3	4
63	IL_08559.1	4	LSU Helix 89 (H89) IL2
64	IL_39526.4	4
65	IL_01080.1	4
66	IL_21333.2	4	tSH-tHW-bulge
67	IL_42251.1	4
68	IL_47758.1	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
69	IL_98591.3	4
70	IL_09520.2	3	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
71	IL_30840.1	3
72	IL_34156.6	3	cWW AG or UU
73	IL_48918.2	3	Kink-turn variant
74	IL_62499.6	3
75	IL_74876.2	3	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
76	IL_34628.2	3	Kink-turn
77	IL_43946.1	3
78	IL_58586.2	3
79	IL_75447.1	3
80	IL_05723.1	3
81	IL_56077.1	3
82	IL_92267.1	3	23S H73 ILa : Part of larger Motif
83	IL_10647.1	3	tHS tHH bulge with S-turn
84	IL_37053.1	3	Kink-turn from 23S H58
85	IL_52173.1	3
86	IL_79955.2	3	SSU Helix (23) h23 IL1
87	IL_95150.3	3
88	IL_82563.1	3	Thi-box riboswitch T-loop
89	IL_95652.2	3	SSU Helix 27 (h27) IL Sarcin-Ricin motif
90	IL_98421.3	3	SSU Helix 12 (h12) IL
91	IL_80348.1	3	23S H91 IL
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_80494.2	3	LSU H58 IL2 H.m.
94	IL_12211.1	2
95	IL_21495.1	2
96	IL_27892.1	2
97	IL_46435.1	2
98	IL_55287.1	2
99	IL_69536.1	2	LSU Helix 96 (H96) IL2
100	IL_90057.1	2
101	IL_09587.1	2
102	IL_15840.2	2	Triple Sheared with unpaired, inserted A
103	IL_19898.1	2
104	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
105	IL_07300.1	2
106	IL_09882.1	2
107	IL_23262.4	2
108	IL_40892.1	2
109	IL_49550.1	2	tHS tHH bulge with S-turn
110	IL_70280.1	2	Double sheared with wobble cWW.
111	IL_87548.1	2
112	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
113	IL_09901.1	2	tHS tHH bulge with S-turn
114	IL_23414.1	2
115	IL_25271.1	2	SSU Helix 8 (h8) IL E.c. and Yeast
116	IL_50521.1	2
117	IL_65137.1	2	Kink-turn like motif in Group I Intron
118	IL_76095.3	2	Motif from Hairpin Ribozyme
119	IL_97833.1	2
120	IL_00998.1	2
121	IL_16252.3	2	23S H91 IL
122	IL_28942.1	2
123	IL_31707.1	2	Vitamin B12 aptamer
124	IL_88180.1	2	cWW-bulge-cWW
125	IL_01054.1	2
126	IL_16330.1	2
127	IL_24358.1	2
128	IL_37197.1	2
129	IL_77076.1	2
130	IL_80093.1	2
131	IL_09348.5	2	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
132	IL_11751.1	2
133	IL_16415.1	2	SSU Helix 23 (h23) Kink-turn T. thermophilus
134	IL_33925.1	2
135	IL_45794.1	2
136	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
137	IL_91273.1	2
138	IL_98566.1	2
139	IL_33964.1	2
140	IL_37406.1	2
141	IL_52940.1	2
142	IL_02690.1	1
143	IL_04550.1	1	tHS tHH bulge with S-turn
144	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
145	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.
146	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
147	IL_25082.1	1
148	IL_37715.1	1
149	IL_40527.1	1	Kink-turn
150	IL_52958.1	1
151	IL_80505.1	1
152	IL_83250.1	1	16S h40 3WJ T.th.
153	IL_97073.1	1
154	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
155	IL_05221.1	1
156	IL_06847.1	1	Group II Intron IL
157	IL_12486.1	1
158	IL_25181.1	1
159	IL_28468.1	1	Single sheared with bulged bases
160	IL_37990.1	1
161	IL_40845.1	1
162	IL_43316.1	1
163	IL_53323.1	1
164	IL_55649.1	1
165	IL_58454.1	1
166	IL_63952.1	1
167	IL_75415.1	1	Pseudo-knot forming internal loop
168	IL_80652.1	1
169	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
170	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
171	IL_98924.1	1
172	IL_02835.1	1
173	IL_05462.1	1
174	IL_12507.1	1
175	IL_20775.1	1	tSH-inserted
176	IL_31290.1	1
177	IL_46721.1	1
178	IL_64589.1	1
179	IL_78809.1	1
180	IL_81398.1	1
181	IL_83856.1	1
182	IL_02957.1	1
183	IL_21221.1	1	SSU Helix 12 (h12) IL
184	IL_28644.1	1
185	IL_34868.1	1	LSU Eukaryal Helix 96 (H96) IL1
186	IL_41139.1	1
187	IL_53988.1	1
188	IL_59529.1	1
189	IL_82113.1	1
190	IL_83920.1	1
191	IL_91044.1	1
192	IL_94973.1	1	Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
193	IL_03110.1	1
194	IL_06306.1	1
195	IL_13434.1	1
196	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
197	IL_23639.1	1	tWH-tHS-L-cWW
198	IL_39324.1	1
199	IL_41341.1	1	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
200	IL_59934.1	1	SSU Helix 23 (h23) Kink-turn E. coli
201	IL_71685.1	1	Sarcin-like with an intercalated basepair
202	IL_76486.1	1	Sarcin-ricin motif with syn G
203	IL_85510.1	1
204	IL_91078.1	1
205	IL_92280.1	1
206	IL_97842.1	1
207	IL_03282.1	1
208	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
209	IL_11302.1	1
210	IL_13682.1	1
211	IL_25307.1	1
212	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
213	IL_47687.1	1
214	IL_52509.1	1
215	IL_54450.1	1
216	IL_56513.1	1
217	IL_60643.1	1
218	IL_65788.1	1
219	IL_71942.1	1
220	IL_88367.1	1
221	IL_91089.1	1
222	IL_03741.1	1
223	IL_06468.1	1	16S h40 3WJ E.c.
224	IL_26868.1	1
225	IL_30067.1	1
226	IL_37347.1	1
227	IL_41791.1	1
228	IL_47732.1	1
229	IL_52610.1	1
230	IL_54576.1	1
231	IL_60649.1	1	Kink-turn
232	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
233	IL_82601.1	1	Tandem cWW water-inserted CU pairs
234	IL_85805.1	1
235	IL_95774.1	1	tHS tHH bulge with S-turn
236	IL_03931.1	1	16S h19 IL and 23S H41 IL
237	IL_06471.1	1
238	IL_09491.1	1
239	IL_11778.1	1
240	IL_15205.1	1
241	IL_17603.1	1
242	IL_21421.1	1
243	IL_26971.1	1
244	IL_30354.1	1
245	IL_46306.1	1
246	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
247	IL_57977.1	1
248	IL_61730.1	1
249	IL_67735.1	1
250	IL_77296.1	1
251	IL_82650.1	1
252	IL_86059.1	1
253	IL_89794.1	1
254	IL_91904.1	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