1.1 | 1.2

Changes in PDB files used for clustering

Release 1.1 has 200 PDB files, release 1.2 has 201 PDB files, 200 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_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_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_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_46648.2	11	23S H91 IL \| Single-Base Intercalation Site
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_70237.3	6
35	IL_39585.1	6	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
36	IL_54420.1	6
37	IL_25230.3	6	Bacterial 5S rRNA Loop E
38	IL_44067.3	6	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
39	IL_97057.3	6
40	IL_53635.3	6	LSU Helix 32 (H32) IL
41	IL_90133.2	6
42	IL_72158.3	6	LSU Helix 62 (H62) IL
43	IL_13069.3	6	LSU 3WJ H32-H33-H35A
44	IL_82188.1	5	LSU H68 IL from H.m.
45	IL_78732.3	5	Double S-turn motif
46	IL_02359.3	5
47	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
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_77263.1	5	Kink-turn from U4
53	IL_08926.2	5	23S H91 IL
54	IL_79083.3	5
55	IL_92484.1	5
56	IL_93568.2	4	Triple Sheared (tSH-tHS-tHS) with wobble cWW.
57	IL_22732.1	4	tSH-inserted-tHS
58	IL_08559.1	4	LSU Helix 89 (H89) IL2
59	IL_39526.4	4
60	IL_42251.1	4
61	IL_38807.3	4
62	IL_28572.1	4	16S h18 kink-turn like motif
63	IL_21333.2	4	tSH-tHW-bulge
64	IL_16166.3	4	23S H91 IL
65	IL_34363.2	4	Kink-turn from 23S H42
66	IL_31066.2	4	SSU Helix 44 (h44) extension
67	IL_47758.1	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
68	IL_01080.1	4
69	IL_98591.3	4
70	IL_95150.3	3
71	IL_05723.1	3
72	IL_79955.2	3	SSU Helix (23) h23 IL1
73	IL_80494.2	3	LSU H58 IL2 H.m.
74	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.
75	IL_30840.1	3
76	IL_37053.1	3	Kink-turn from 23S H58
77	IL_92267.1	3	23S H73 ILa : Part of larger Motif
78	IL_48918.2	3	Kink-turn variant
79	IL_62499.6	3
80	IL_34156.6	3	cWW AG or UU
81	IL_10647.1	3	tHS tHH bulge with S-turn
82	IL_95652.2	3	SSU Helix 27 (h27) IL Sarcin-Ricin motif
83	IL_43946.1	3
84	IL_09520.2	3	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
85	IL_56077.1	3
86	IL_34628.2	3	Kink-turn
87	IL_74876.2	3	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
88	IL_80348.1	3	23S H91 IL
89	IL_52173.1	3
90	IL_75447.1	3
91	IL_98421.3	3	SSU Helix 12 (h12) IL
92	IL_58586.2	3
93	IL_82563.1	3	Thi-box riboswitch T-loop
94	IL_50521.1	2
95	IL_09348.5	2	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
96	IL_80093.1	2
97	IL_46435.1	2
98	IL_09587.1	2
99	IL_27892.1	2
100	IL_88180.1	2	cWW-bulge-cWW
101	IL_87548.1	2
102	IL_09882.1	2
103	IL_77076.1	2
104	IL_25271.1	2	SSU Helix 8 (h8) IL E.c. and Yeast
105	IL_55287.1	2
106	IL_16415.1	2	SSU Helix 23 (h23) Kink-turn T. thermophilus
107	IL_52940.1	2
108	IL_90057.1	2
109	IL_12211.1	2
110	IL_21495.1	2
111	IL_09901.1	2	tHS tHH bulge with S-turn
112	IL_11751.1	2
113	IL_65137.1	2	Kink-turn like motif in Group I Intron
114	IL_19898.1	2
115	IL_33925.1	2
116	IL_01054.1	2
117	IL_15840.2	2	Triple Sheared with unpaired, inserted A
118	IL_37406.1	2
119	IL_69536.1	2	LSU Helix 96 (H96) IL2
120	IL_28942.1	2
121	IL_23414.1	2
122	IL_37197.1	2
123	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
124	IL_23262.4	2
125	IL_07300.1	2
126	IL_45794.1	2
127	IL_33964.1	2
128	IL_97833.1	2
129	IL_98566.1	2
130	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
131	IL_70280.1	2	Double sheared with wobble cWW.
132	IL_24358.1	2
133	IL_16330.1	2
134	IL_31707.1	2	Vitamin B12 aptamer
135	IL_76095.3	2	Motif from Hairpin Ribozyme
136	IL_40892.1	2
137	IL_91273.1	2
138	IL_00998.1	2
139	IL_16252.3	2	23S H91 IL
140	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
141	IL_49550.1	2	tHS tHH bulge with S-turn
142	IL_96446.1	2
143	IL_85805.1	1
144	IL_03110.1	1
145	IL_83920.1	1
146	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
147	IL_27243.1	1
148	IL_75328.1	1
149	IL_82113.1	1
150	IL_53323.1	1
151	IL_26971.1	1
152	IL_09491.1	1
153	IL_21421.1	1
154	IL_85510.1	1
155	IL_91044.1	1
156	IL_27668.1	1
157	IL_83250.1	1	16S h40 3WJ T.th.
158	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
159	IL_41791.1	1
160	IL_43316.1	1
161	IL_12507.1	1
162	IL_06468.1	1	16S h40 3WJ E.c.
163	IL_52958.1	1
164	IL_80652.1	1
165	IL_65788.1	1
166	IL_61730.1	1
167	IL_41341.1	1	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
168	IL_25082.1	1
169	IL_98924.1	1
170	IL_59529.1	1
171	IL_02957.1	1
172	IL_28468.1	1	Single sheared with bulged bases
173	IL_88367.1	1
174	IL_06847.1	1	Group II Intron IL
175	IL_30067.1	1
176	IL_63952.1	1
177	IL_57977.1	1
178	IL_39324.1	1
179	IL_80505.1	1
180	IL_47687.1	1
181	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
182	IL_97073.1	1
183	IL_03931.1	1	16S h19 IL and 23S H41 IL
184	IL_78809.1	1
185	IL_13682.1	1
186	IL_31290.1	1
187	IL_13434.1	1
188	IL_71685.1	1	Sarcin-like with an intercalated basepair
189	IL_25181.1	1
190	IL_58454.1	1
191	IL_40527.1	1	Kink-turn
192	IL_60649.1	1	Kink-turn
193	IL_52610.1	1
194	IL_86059.1	1
195	IL_82650.1	1
196	IL_31006.1	1	tSH-tHW-L-bif-cWW
197	IL_21221.1	1	SSU Helix 12 (h12) IL
198	IL_54576.1	1
199	IL_67735.1	1
200	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
201	IL_23639.1	1	tWH-tHS-L-cWW
202	IL_64589.1	1
203	IL_41139.1	1
204	IL_77296.1	1
205	IL_87394.1	1
206	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
207	IL_25307.1	1
208	IL_26868.1	1
209	IL_55649.1	1
210	IL_52509.1	1
211	IL_02690.1	1
212	IL_75415.1	1	Pseudo-knot forming internal loop
213	IL_76486.1	1	Sarcin-ricin motif with syn G
214	IL_37990.1	1
215	IL_82601.1	1	Tandem cWW water-inserted CU pairs
216	IL_34868.1	1	LSU Eukaryal Helix 96 (H96) IL1
217	IL_03282.1	1
218	IL_42891.1	1
219	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
220	IL_40845.1	1
221	IL_88865.1	1
222	IL_76263.1	1
223	IL_91379.1	1
224	IL_11302.1	1
225	IL_89794.1	1
226	IL_95774.1	1	tHS tHH bulge with S-turn
227	IL_12486.1	1
228	IL_06306.1	1
229	IL_97842.1	1
230	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
231	IL_17603.1	1
232	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
233	IL_91089.1	1
234	IL_94973.1	1	Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
235	IL_47732.1	1
236	IL_68827.1	1	Reverse Kink-Turn
237	IL_04550.1	1	tHS tHH bulge with S-turn
238	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
239	IL_53988.1	1
240	IL_28644.1	1
241	IL_11778.1	1
242	IL_37715.1	1
243	IL_54450.1	1
244	IL_77014.1	1
245	IL_03741.1	1
246	IL_83856.1	1
247	IL_37347.1	1
248	IL_46306.1	1
249	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.
250	IL_15205.1	1
251	IL_23448.1	1
252	IL_57285.1	1
253	IL_30354.1	1
254	IL_92280.1	1
255	IL_02835.1	1
256	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
257	IL_59934.1	1	SSU Helix 23 (h23) Kink-turn E. coli
258	IL_05462.1	1
259	IL_20775.1	1	tSH-inserted
260	IL_71942.1	1
261	IL_91078.1	1
262	IL_81398.1	1
263	IL_05221.1	1
264	IL_06471.1	1
265	IL_91904.1	1
266	IL_56513.1	1
267	IL_60643.1	1
268	IL_46721.1	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