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_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_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_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_70237.3	6
43	IL_39585.1	6	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
44	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
45	IL_25300.1	5	16S h19 IL and 23S H41 IL
46	IL_45262.3	5
47	IL_86357.3	5	LSU Helix 61 IL2
48	IL_16207.1	5	Single sheared with bulged bases
49	IL_77263.1	5	Kink-turn from U4
50	IL_08926.2	5	23S H91 IL
51	IL_79083.3	5
52	IL_92484.1	5
53	IL_82188.1	5	LSU H68 IL from H.m.
54	IL_78732.3	5	Double S-turn motif
55	IL_02359.3	5
56	IL_39526.4	4
57	IL_42251.1	4
58	IL_38807.3	4
59	IL_28572.1	4	16S h18 kink-turn like motif
60	IL_21333.2	4	tSH-tHW-bulge
61	IL_16166.3	4	23S H91 IL
62	IL_34363.2	4	Kink-turn from 23S H42
63	IL_31066.2	4	SSU Helix 44 (h44) extension
64	IL_47758.1	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
65	IL_01080.1	4
66	IL_98591.3	4
67	IL_93568.2	4	Triple Sheared (tSH-tHS-tHS) with wobble cWW.
68	IL_22732.1	4	tSH-inserted-tHS
69	IL_08559.1	4	LSU Helix 89 (H89) IL2
70	IL_79955.2	3	SSU Helix (23) h23 IL1
71	IL_80494.2	3	LSU H58 IL2 H.m.
72	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.
73	IL_30840.1	3
74	IL_37053.1	3	Kink-turn from 23S H58
75	IL_92267.1	3	23S H73 ILa : Part of larger Motif
76	IL_48918.2	3	Kink-turn variant
77	IL_62499.6	3
78	IL_34156.6	3	cWW AG or UU
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_43946.1	3
82	IL_09520.2	3	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
83	IL_56077.1	3
84	IL_34628.2	3	Kink-turn
85	IL_74876.2	3	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
86	IL_80348.1	3	23S H91 IL
87	IL_52173.1	3
88	IL_75447.1	3
89	IL_98421.3	3	SSU Helix 12 (h12) IL
90	IL_58586.2	3
91	IL_82563.1	3	Thi-box riboswitch T-loop
92	IL_95150.3	3
93	IL_05723.1	3
94	IL_87548.1	2
95	IL_09882.1	2
96	IL_77076.1	2
97	IL_25271.1	2	SSU Helix 8 (h8) IL E.c. and Yeast
98	IL_55287.1	2
99	IL_16415.1	2	SSU Helix 23 (h23) Kink-turn T. thermophilus
100	IL_52940.1	2
101	IL_90057.1	2
102	IL_12211.1	2
103	IL_21495.1	2
104	IL_09901.1	2	tHS tHH bulge with S-turn
105	IL_11751.1	2
106	IL_65137.1	2	Kink-turn like motif in Group I Intron
107	IL_19898.1	2
108	IL_33925.1	2
109	IL_01054.1	2
110	IL_15840.2	2	Triple Sheared with unpaired, inserted A
111	IL_37406.1	2
112	IL_69536.1	2	LSU Helix 96 (H96) IL2
113	IL_28942.1	2
114	IL_23414.1	2
115	IL_37197.1	2
116	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
117	IL_23262.4	2
118	IL_07300.1	2
119	IL_45794.1	2
120	IL_33964.1	2
121	IL_97833.1	2
122	IL_98566.1	2
123	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
124	IL_70280.1	2	Double sheared with wobble cWW.
125	IL_24358.1	2
126	IL_16330.1	2
127	IL_31707.1	2	Vitamin B12 aptamer
128	IL_76095.3	2	Motif from Hairpin Ribozyme
129	IL_40892.1	2
130	IL_91273.1	2
131	IL_00998.1	2
132	IL_16252.3	2	23S H91 IL
133	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
134	IL_49550.1	2	tHS tHH bulge with S-turn
135	IL_96446.1	2
136	IL_50521.1	2
137	IL_09348.5	2	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
138	IL_80093.1	2
139	IL_46435.1	2
140	IL_09587.1	2
141	IL_27892.1	2
142	IL_88180.1	2	cWW-bulge-cWW
143	IL_83250.1	1	16S h40 3WJ T.th.
144	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
145	IL_41791.1	1
146	IL_43316.1	1
147	IL_12507.1	1
148	IL_06468.1	1	16S h40 3WJ E.c.
149	IL_52958.1	1
150	IL_80652.1	1
151	IL_65788.1	1
152	IL_61730.1	1
153	IL_41341.1	1	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
154	IL_25082.1	1
155	IL_98924.1	1
156	IL_59529.1	1
157	IL_02957.1	1
158	IL_28468.1	1	Single sheared with bulged bases
159	IL_88367.1	1
160	IL_06847.1	1	Group II Intron IL
161	IL_30067.1	1
162	IL_63952.1	1
163	IL_57977.1	1
164	IL_39324.1	1
165	IL_80505.1	1
166	IL_47687.1	1
167	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
168	IL_97073.1	1
169	IL_03931.1	1	16S h19 IL and 23S H41 IL
170	IL_78809.1	1
171	IL_13682.1	1
172	IL_31290.1	1
173	IL_13434.1	1
174	IL_71685.1	1	Sarcin-like with an intercalated basepair
175	IL_25181.1	1
176	IL_58454.1	1
177	IL_40527.1	1	Kink-turn
178	IL_60649.1	1	Kink-turn
179	IL_52610.1	1
180	IL_86059.1	1
181	IL_82650.1	1
182	IL_31006.1	1	tSH-tHW-L-bif-cWW
183	IL_21221.1	1	SSU Helix 12 (h12) IL
184	IL_54576.1	1
185	IL_67735.1	1
186	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
187	IL_23639.1	1	tWH-tHS-L-cWW
188	IL_64589.1	1
189	IL_41139.1	1
190	IL_77296.1	1
191	IL_87394.1	1
192	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
193	IL_25307.1	1
194	IL_26868.1	1
195	IL_55649.1	1
196	IL_52509.1	1
197	IL_02690.1	1
198	IL_75415.1	1	Pseudo-knot forming internal loop
199	IL_76486.1	1	Sarcin-ricin motif with syn G
200	IL_37990.1	1
201	IL_82601.1	1	Tandem cWW water-inserted CU pairs
202	IL_34868.1	1	LSU Eukaryal Helix 96 (H96) IL1
203	IL_03282.1	1
204	IL_42891.1	1
205	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
206	IL_40845.1	1
207	IL_88865.1	1
208	IL_76263.1	1
209	IL_91379.1	1
210	IL_11302.1	1
211	IL_89794.1	1
212	IL_95774.1	1	tHS tHH bulge with S-turn
213	IL_12486.1	1
214	IL_06306.1	1
215	IL_97842.1	1
216	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
217	IL_17603.1	1
218	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
219	IL_91089.1	1
220	IL_94973.1	1	Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
221	IL_47732.1	1
222	IL_68827.1	1	Reverse Kink-Turn
223	IL_04550.1	1	tHS tHH bulge with S-turn
224	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
225	IL_53988.1	1
226	IL_28644.1	1
227	IL_11778.1	1
228	IL_37715.1	1
229	IL_54450.1	1
230	IL_77014.1	1
231	IL_03741.1	1
232	IL_83856.1	1
233	IL_37347.1	1
234	IL_46306.1	1
235	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.
236	IL_15205.1	1
237	IL_23448.1	1
238	IL_57285.1	1
239	IL_30354.1	1
240	IL_92280.1	1
241	IL_02835.1	1
242	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
243	IL_59934.1	1	SSU Helix 23 (h23) Kink-turn E. coli
244	IL_05462.1	1
245	IL_20775.1	1	tSH-inserted
246	IL_71942.1	1
247	IL_91078.1	1
248	IL_81398.1	1
249	IL_05221.1	1
250	IL_06471.1	1
251	IL_91904.1	1
252	IL_56513.1	1
253	IL_60643.1	1
254	IL_46721.1	1
255	IL_85805.1	1
256	IL_03110.1	1
257	IL_83920.1	1
258	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
259	IL_27243.1	1
260	IL_75328.1	1
261	IL_82113.1	1
262	IL_53323.1	1
263	IL_26971.1	1
264	IL_09491.1	1
265	IL_21421.1	1
266	IL_85510.1	1
267	IL_91044.1	1
268	IL_27668.1	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