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_94430.4	15	16S h32-h33-h34 3WJ
18	IL_31555.3	15	Tandem sheared with inserted, unpaired purine.
19	IL_92109.1	15	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
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_90459.3	9	cWW AG or UU
28	IL_47444.3	9	SRP Loop E-like motif
29	IL_02809.2	9	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
30	IL_92114.3	9	GAAA loop receptor "platform" 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_53635.3	6	LSU Helix 32 (H32) IL
35	IL_90133.2	6
36	IL_72158.3	6	LSU Helix 62 (H62) IL
37	IL_13069.3	6	LSU 3WJ H32-H33-H35A
38	IL_70237.3	6
39	IL_39585.1	6	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
40	IL_54420.1	6
41	IL_25230.3	6	Bacterial 5S rRNA Loop E
42	IL_44067.3	6	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
43	IL_97057.3	6
44	IL_92484.1	5
45	IL_82188.1	5	LSU H68 IL from H.m.
46	IL_78732.3	5	Double S-turn motif
47	IL_02359.3	5
48	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
49	IL_25300.1	5	16S h19 IL and 23S H41 IL
50	IL_45262.3	5
51	IL_86357.3	5	LSU Helix 61 IL2
52	IL_16207.1	5	Single sheared with bulged bases
53	IL_77263.1	5	Kink-turn from U4
54	IL_08926.2	5	23S H91 IL
55	IL_79083.3	5
56	IL_47758.1	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
57	IL_01080.1	4
58	IL_98591.3	4
59	IL_93568.2	4	Triple Sheared (tSH-tHS-tHS) with wobble cWW.
60	IL_22732.1	4	tSH-inserted-tHS
61	IL_08559.1	4	LSU Helix 89 (H89) IL2
62	IL_39526.4	4
63	IL_42251.1	4
64	IL_38807.3	4
65	IL_28572.1	4	16S h18 kink-turn like motif
66	IL_21333.2	4	tSH-tHW-bulge
67	IL_16166.3	4	23S H91 IL
68	IL_34363.2	4	Kink-turn from 23S H42
69	IL_31066.2	4	SSU Helix 44 (h44) extension
70	IL_80348.1	3	23S H91 IL
71	IL_52173.1	3
72	IL_75447.1	3
73	IL_98421.3	3	SSU Helix 12 (h12) IL
74	IL_58586.2	3
75	IL_82563.1	3	Thi-box riboswitch T-loop
76	IL_95150.3	3
77	IL_05723.1	3
78	IL_79955.2	3	SSU Helix (23) h23 IL1
79	IL_80494.2	3	LSU H58 IL2 H.m.
80	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.
81	IL_30840.1	3
82	IL_37053.1	3	Kink-turn from 23S H58
83	IL_92267.1	3	23S H73 ILa : Part of larger Motif
84	IL_48918.2	3	Kink-turn variant
85	IL_62499.6	3
86	IL_34156.6	3	cWW AG or UU
87	IL_10647.1	3	tHS tHH bulge with S-turn
88	IL_95652.2	3	SSU Helix 27 (h27) IL Sarcin-Ricin motif
89	IL_43946.1	3
90	IL_09520.2	3	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
91	IL_56077.1	3
92	IL_34628.2	3	Kink-turn
93	IL_74876.2	3	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
94	IL_31707.1	2	Vitamin B12 aptamer
95	IL_76095.3	2	Motif from Hairpin Ribozyme
96	IL_40892.1	2
97	IL_91273.1	2
98	IL_00998.1	2
99	IL_16252.3	2	23S H91 IL
100	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
101	IL_49550.1	2	tHS tHH bulge with S-turn
102	IL_96446.1	2
103	IL_50521.1	2
104	IL_09348.5	2	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
105	IL_80093.1	2
106	IL_46435.1	2
107	IL_09587.1	2
108	IL_27892.1	2
109	IL_88180.1	2	cWW-bulge-cWW
110	IL_87548.1	2
111	IL_09882.1	2
112	IL_77076.1	2
113	IL_25271.1	2	SSU Helix 8 (h8) IL E.c. and Yeast
114	IL_55287.1	2
115	IL_16415.1	2	SSU Helix 23 (h23) Kink-turn T. thermophilus
116	IL_52940.1	2
117	IL_90057.1	2
118	IL_12211.1	2
119	IL_21495.1	2
120	IL_09901.1	2	tHS tHH bulge with S-turn
121	IL_11751.1	2
122	IL_65137.1	2	Kink-turn like motif in Group I Intron
123	IL_19898.1	2
124	IL_33925.1	2
125	IL_01054.1	2
126	IL_15840.2	2	Triple Sheared with unpaired, inserted A
127	IL_37406.1	2
128	IL_69536.1	2	LSU Helix 96 (H96) IL2
129	IL_28942.1	2
130	IL_23414.1	2
131	IL_37197.1	2
132	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
133	IL_23262.4	2
134	IL_07300.1	2
135	IL_45794.1	2
136	IL_33964.1	2
137	IL_97833.1	2
138	IL_98566.1	2
139	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
140	IL_70280.1	2	Double sheared with wobble cWW.
141	IL_24358.1	2
142	IL_16330.1	2
143	IL_68827.1	1	Reverse Kink-Turn
144	IL_04550.1	1	tHS tHH bulge with S-turn
145	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
146	IL_53988.1	1
147	IL_28644.1	1
148	IL_11778.1	1
149	IL_37715.1	1
150	IL_54450.1	1
151	IL_77014.1	1
152	IL_03741.1	1
153	IL_83856.1	1
154	IL_37347.1	1
155	IL_46306.1	1
156	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.
157	IL_15205.1	1
158	IL_23448.1	1
159	IL_57285.1	1
160	IL_30354.1	1
161	IL_92280.1	1
162	IL_02835.1	1
163	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
164	IL_59934.1	1	SSU Helix 23 (h23) Kink-turn E. coli
165	IL_05462.1	1
166	IL_20775.1	1	tSH-inserted
167	IL_71942.1	1
168	IL_91078.1	1
169	IL_81398.1	1
170	IL_05221.1	1
171	IL_06471.1	1
172	IL_91904.1	1
173	IL_56513.1	1
174	IL_60643.1	1
175	IL_46721.1	1
176	IL_85805.1	1
177	IL_03110.1	1
178	IL_83920.1	1
179	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
180	IL_27243.1	1
181	IL_75328.1	1
182	IL_82113.1	1
183	IL_53323.1	1
184	IL_26971.1	1
185	IL_09491.1	1
186	IL_21421.1	1
187	IL_85510.1	1
188	IL_91044.1	1
189	IL_27668.1	1
190	IL_83250.1	1	16S h40 3WJ T.th.
191	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
192	IL_41791.1	1
193	IL_43316.1	1
194	IL_12507.1	1
195	IL_06468.1	1	16S h40 3WJ E.c.
196	IL_52958.1	1
197	IL_80652.1	1
198	IL_65788.1	1
199	IL_61730.1	1
200	IL_41341.1	1	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
201	IL_25082.1	1
202	IL_98924.1	1
203	IL_59529.1	1
204	IL_02957.1	1
205	IL_28468.1	1	Single sheared with bulged bases
206	IL_88367.1	1
207	IL_06847.1	1	Group II Intron IL
208	IL_30067.1	1
209	IL_63952.1	1
210	IL_57977.1	1
211	IL_39324.1	1
212	IL_80505.1	1
213	IL_47687.1	1
214	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
215	IL_97073.1	1
216	IL_03931.1	1	16S h19 IL and 23S H41 IL
217	IL_78809.1	1
218	IL_13682.1	1
219	IL_31290.1	1
220	IL_13434.1	1
221	IL_71685.1	1	Sarcin-like with an intercalated basepair
222	IL_25181.1	1
223	IL_58454.1	1
224	IL_40527.1	1	Kink-turn
225	IL_60649.1	1	Kink-turn
226	IL_52610.1	1
227	IL_86059.1	1
228	IL_82650.1	1
229	IL_31006.1	1	tSH-tHW-L-bif-cWW
230	IL_21221.1	1	SSU Helix 12 (h12) IL
231	IL_54576.1	1
232	IL_67735.1	1
233	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
234	IL_23639.1	1	tWH-tHS-L-cWW
235	IL_64589.1	1
236	IL_41139.1	1
237	IL_77296.1	1
238	IL_87394.1	1
239	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
240	IL_25307.1	1
241	IL_26868.1	1
242	IL_55649.1	1
243	IL_52509.1	1
244	IL_02690.1	1
245	IL_75415.1	1	Pseudo-knot forming internal loop
246	IL_76486.1	1	Sarcin-ricin motif with syn G
247	IL_37990.1	1
248	IL_82601.1	1	Tandem cWW water-inserted CU pairs
249	IL_34868.1	1	LSU Eukaryal Helix 96 (H96) IL1
250	IL_03282.1	1
251	IL_42891.1	1
252	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
253	IL_40845.1	1
254	IL_88865.1	1
255	IL_76263.1	1
256	IL_91379.1	1
257	IL_11302.1	1
258	IL_89794.1	1
259	IL_95774.1	1	tHS tHH bulge with S-turn
260	IL_12486.1	1
261	IL_06306.1	1
262	IL_97842.1	1
263	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
264	IL_17603.1	1
265	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
266	IL_91089.1	1
267	IL_94973.1	1	Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
268	IL_47732.1	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