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_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_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_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_02809.2	9	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
27	IL_92114.3	9	GAAA loop receptor "platform" motif
28	IL_58291.3	9	Recurrent Sub-motif found in junctions
29	IL_90459.3	9	cWW AG or UU
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_44067.3	6	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
35	IL_97057.3	6
36	IL_53635.3	6	LSU Helix 32 (H32) IL
37	IL_90133.2	6
38	IL_72158.3	6	LSU Helix 62 (H62) IL
39	IL_13069.3	6	LSU 3WJ H32-H33-H35A
40	IL_70237.3	6
41	IL_39585.1	6	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
42	IL_54420.1	6
43	IL_25230.3	6	Bacterial 5S rRNA Loop E
44	IL_45262.3	5
45	IL_86357.3	5	LSU Helix 61 IL2
46	IL_16207.1	5	Single sheared with bulged bases
47	IL_77263.1	5	Kink-turn from U4
48	IL_08926.2	5	23S H91 IL
49	IL_79083.3	5
50	IL_92484.1	5
51	IL_82188.1	5	LSU H68 IL from H.m.
52	IL_78732.3	5	Double S-turn motif
53	IL_02359.3	5
54	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
55	IL_25300.1	5	16S h19 IL and 23S H41 IL
56	IL_42251.1	4
57	IL_38807.3	4
58	IL_28572.1	4	16S h18 kink-turn like motif
59	IL_21333.2	4	tSH-tHW-bulge
60	IL_16166.3	4	23S H91 IL
61	IL_34363.2	4	Kink-turn from 23S H42
62	IL_31066.2	4	SSU Helix 44 (h44) extension
63	IL_47758.1	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
64	IL_01080.1	4
65	IL_98591.3	4
66	IL_93568.2	4	Triple Sheared (tSH-tHS-tHS) with wobble cWW.
67	IL_22732.1	4	tSH-inserted-tHS
68	IL_08559.1	4	LSU Helix 89 (H89) IL2
69	IL_39526.4	4
70	IL_62499.6	3
71	IL_34156.6	3	cWW AG or UU
72	IL_10647.1	3	tHS tHH bulge with S-turn
73	IL_95652.2	3	SSU Helix 27 (h27) IL Sarcin-Ricin motif
74	IL_43946.1	3
75	IL_09520.2	3	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
76	IL_56077.1	3
77	IL_34628.2	3	Kink-turn
78	IL_74876.2	3	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
79	IL_80348.1	3	23S H91 IL
80	IL_52173.1	3
81	IL_75447.1	3
82	IL_98421.3	3	SSU Helix 12 (h12) IL
83	IL_58586.2	3
84	IL_82563.1	3	Thi-box riboswitch T-loop
85	IL_95150.3	3
86	IL_05723.1	3
87	IL_79955.2	3	SSU Helix (23) h23 IL1
88	IL_80494.2	3	LSU H58 IL2 H.m.
89	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.
90	IL_30840.1	3
91	IL_37053.1	3	Kink-turn from 23S H58
92	IL_92267.1	3	23S H73 ILa : Part of larger Motif
93	IL_48918.2	3	Kink-turn variant
94	IL_11751.1	2
95	IL_65137.1	2	Kink-turn like motif in Group I Intron
96	IL_19898.1	2
97	IL_33925.1	2
98	IL_01054.1	2
99	IL_15840.2	2	Triple Sheared with unpaired, inserted A
100	IL_37406.1	2
101	IL_69536.1	2	LSU Helix 96 (H96) IL2
102	IL_28942.1	2
103	IL_23414.1	2
104	IL_37197.1	2
105	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
106	IL_23262.4	2
107	IL_07300.1	2
108	IL_45794.1	2
109	IL_33964.1	2
110	IL_97833.1	2
111	IL_98566.1	2
112	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
113	IL_70280.1	2	Double sheared with wobble cWW.
114	IL_24358.1	2
115	IL_16330.1	2
116	IL_31707.1	2	Vitamin B12 aptamer
117	IL_76095.3	2	Motif from Hairpin Ribozyme
118	IL_40892.1	2
119	IL_91273.1	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_49550.1	2	tHS tHH bulge with S-turn
124	IL_96446.1	2
125	IL_50521.1	2
126	IL_09348.5	2	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
127	IL_80093.1	2
128	IL_46435.1	2
129	IL_09587.1	2
130	IL_27892.1	2
131	IL_88180.1	2	cWW-bulge-cWW
132	IL_87548.1	2
133	IL_09882.1	2
134	IL_77076.1	2
135	IL_25271.1	2	SSU Helix 8 (h8) IL E.c. and Yeast
136	IL_55287.1	2
137	IL_16415.1	2	SSU Helix 23 (h23) Kink-turn T. thermophilus
138	IL_52940.1	2
139	IL_90057.1	2
140	IL_12211.1	2
141	IL_21495.1	2
142	IL_09901.1	2	tHS tHH bulge with S-turn
143	IL_86059.1	1
144	IL_82650.1	1
145	IL_31006.1	1	tSH-tHW-L-bif-cWW
146	IL_21221.1	1	SSU Helix 12 (h12) IL
147	IL_54576.1	1
148	IL_67735.1	1
149	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
150	IL_23639.1	1	tWH-tHS-L-cWW
151	IL_64589.1	1
152	IL_41139.1	1
153	IL_77296.1	1
154	IL_87394.1	1
155	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
156	IL_25307.1	1
157	IL_26868.1	1
158	IL_55649.1	1
159	IL_52509.1	1
160	IL_02690.1	1
161	IL_75415.1	1	Pseudo-knot forming internal loop
162	IL_76486.1	1	Sarcin-ricin motif with syn G
163	IL_37990.1	1
164	IL_82601.1	1	Tandem cWW water-inserted CU pairs
165	IL_34868.1	1	LSU Eukaryal Helix 96 (H96) IL1
166	IL_03282.1	1
167	IL_42891.1	1
168	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
169	IL_40845.1	1
170	IL_88865.1	1
171	IL_76263.1	1
172	IL_91379.1	1
173	IL_11302.1	1
174	IL_89794.1	1
175	IL_95774.1	1	tHS tHH bulge with S-turn
176	IL_12486.1	1
177	IL_06306.1	1
178	IL_97842.1	1
179	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
180	IL_17603.1	1
181	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
182	IL_91089.1	1
183	IL_94973.1	1	Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
184	IL_47732.1	1
185	IL_68827.1	1	Reverse Kink-Turn
186	IL_04550.1	1	tHS tHH bulge with S-turn
187	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
188	IL_53988.1	1
189	IL_28644.1	1
190	IL_11778.1	1
191	IL_37715.1	1
192	IL_54450.1	1
193	IL_77014.1	1
194	IL_03741.1	1
195	IL_83856.1	1
196	IL_37347.1	1
197	IL_46306.1	1
198	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.
199	IL_15205.1	1
200	IL_23448.1	1
201	IL_57285.1	1
202	IL_30354.1	1
203	IL_92280.1	1
204	IL_02835.1	1
205	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
206	IL_59934.1	1	SSU Helix 23 (h23) Kink-turn E. coli
207	IL_05462.1	1
208	IL_20775.1	1	tSH-inserted
209	IL_71942.1	1
210	IL_91078.1	1
211	IL_81398.1	1
212	IL_05221.1	1
213	IL_06471.1	1
214	IL_91904.1	1
215	IL_56513.1	1
216	IL_60643.1	1
217	IL_46721.1	1
218	IL_85805.1	1
219	IL_03110.1	1
220	IL_83920.1	1
221	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
222	IL_27243.1	1
223	IL_75328.1	1
224	IL_82113.1	1
225	IL_53323.1	1
226	IL_26971.1	1
227	IL_09491.1	1
228	IL_21421.1	1
229	IL_85510.1	1
230	IL_91044.1	1
231	IL_27668.1	1
232	IL_83250.1	1	16S h40 3WJ T.th.
233	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
234	IL_41791.1	1
235	IL_43316.1	1
236	IL_12507.1	1
237	IL_06468.1	1	16S h40 3WJ E.c.
238	IL_52958.1	1
239	IL_80652.1	1
240	IL_65788.1	1
241	IL_61730.1	1
242	IL_41341.1	1	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
243	IL_25082.1	1
244	IL_98924.1	1
245	IL_59529.1	1
246	IL_02957.1	1
247	IL_28468.1	1	Single sheared with bulged bases
248	IL_88367.1	1
249	IL_06847.1	1	Group II Intron IL
250	IL_30067.1	1
251	IL_63952.1	1
252	IL_57977.1	1
253	IL_39324.1	1
254	IL_80505.1	1
255	IL_47687.1	1
256	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
257	IL_97073.1	1
258	IL_03931.1	1	16S h19 IL and 23S H41 IL
259	IL_78809.1	1
260	IL_13682.1	1
261	IL_31290.1	1
262	IL_13434.1	1
263	IL_71685.1	1	Sarcin-like with an intercalated basepair
264	IL_25181.1	1
265	IL_58454.1	1
266	IL_40527.1	1	Kink-turn
267	IL_60649.1	1	Kink-turn
268	IL_52610.1	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