1.5 | 1.6

Changes in PDB files used for clustering

Release 1.5 has 203 PDB files, release 1.6 has 203 PDB files, 202 of them are identical.

1 equivalence classes changed representatives: 3NPB → 4KQY.

No new PDB files have been added.

Obsolete: 3NPB → 4KQY.

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 1.5 has 274 motif groups, release 1.6 has 272 motif groups, 254 of them are identical.

6 motif groups were updated, 14 groups are present only in release 1.5, 12 groups are only in release 1.6.

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_97217.7	243	1-3 bulged nucleotides, same chain \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
2	IL_47174.8	205	cWW AG or water inserted cWW Y-Y.
3	IL_39199.4	53	Hoogsteen-edge Platform, Single bulged base
4	IL_41766.4	49	Tandem cWW pairs (Not AU or GC)
5	IL_56465.3	46	Single, unpaired intercalated base, consensus A
6	IL_44540.4	43	Sugar-edge, 1-base platform, consensus tHS
7	IL_87904.5	31	Triple sheared (tSH-tHS-tHS) no inserted bases
8	IL_82444.1	29	cWH basepair with syn base \| cWW AG or water inserted cWW Y-Y. \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) \| 16S h34 ILa : Part of larger motif
9	IL_13959.4	26	Double Sheared (tSH-tHS)
10	IL_73276.4	21	C-loop
11	IL_28947.1	21	23S H91 IL \| cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
12	IL_93424.4	21	tSH-inserted-tHW
13	IL_55938.4	18	LSU Helix 89 (H89) IL2. cSH Platform.
14	IL_92027.3	17	16S h21 S8 binding site
15	IL_94430.5	16	16S h32-h33-h34 3WJ
16	IL_85647.3	16	Sarcin-ricin parent motif with 15 Nts
17	IL_24982.5	16	SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
18	IL_92109.2	15	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
19	IL_31555.4	13	Tandem sheared with inserted, unpaired purine.
20	IL_49493.4	13	Sarcin-ricin Parent Motif - bacterial LSU H95 IL
21	IL_58291.4	10	Recurrent Sub-motif found in junctions
22	IL_24546.4	10	23S H41 IL and 16S h18 IL : Has large bulge on one side
23	IL_90459.3	9	cWW AG or UU
24	IL_92114.3	9	GAAA loop receptor "platform" motif
25	IL_47444.3	9	SRP Loop E-like motif
26	IL_83451.3	7	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
27	IL_92321.4	7	Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
28	IL_73000.2	7	cHS-cWS
29	IL_08926.3	6	23S H91 IL
30	IL_25230.3	6	Bacterial 5S rRNA Loop E
31	IL_39585.1	6	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
32	IL_70237.3	6
33	IL_90133.3	6
34	IL_13069.3	6	LSU 3WJ H32-H33-H35A
35	IL_25380.1	6	LSU Helix 89 (H89) IL2
36	IL_53635.3	6	LSU Helix 32 (H32) IL
37	IL_72158.3	6	LSU Helix 62 (H62) IL
38	IL_77263.2	6	Kink-turn from U4
39	IL_97057.3	6
40	IL_79083.3	5
41	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
42	IL_25300.1	5	16S h19 IL and 23S H41 IL
43	IL_02359.3	5
44	IL_05684.1	5	tHS tHH bulge with S-turn \| Double S-turn motif
45	IL_44067.4	5	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
46	IL_86357.3	5	LSU Helix 61 IL2
47	IL_31066.3	4	SSU Helix 44 (h44) extension
48	IL_93568.2	4	Triple Sheared (tSH-tHS-tHS) with wobble cWW.
49	IL_28572.2	4	16S h18 kink-turn like motif
50	IL_39526.4	4
51	IL_47758.2	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
52	IL_22732.1	4	tSH-inserted-tHS
53	IL_42251.1	4
54	IL_82188.2	4	LSU H68 IL from H.m.
55	IL_31663.1	4	23S H73 ILa : Part of larger Motif
56	IL_39980.1	4
57	IL_01080.1	4
58	IL_38807.3	4
59	IL_95652.3	4	SSU Helix 27 (h27) IL Sarcin-Ricin motif
60	IL_09530.1	4	Double S-turn motif
61	IL_21333.2	4	tSH-tHW-bulge
62	IL_34363.2	4	Kink-turn from 23S H42
63	IL_45262.4	4
64	IL_98591.3	4
65	IL_06180.1	3	tHS tHH bulge with S-turn
66	IL_07300.2	3
67	IL_34628.2	3	Kink-turn
68	IL_52173.1	3
69	IL_89028.6	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.
70	IL_06211.1	3
71	IL_37053.1	3	Kink-turn from 23S H58
72	IL_62499.7	3
73	IL_74876.2	3	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
74	IL_87065.1	3	23S H91 IL \| Single-Base Intercalation Site
75	IL_48918.2	3	Kink-turn variant
76	IL_16166.4	3	23S H91 IL
77	IL_25271.2	3	SSU Helix 8 (h8) IL E.c. and Yeast
78	IL_75447.1	3
79	IL_79955.2	3	SSU Helix (23) h23 IL1
80	IL_43946.1	3
81	IL_58586.2	3
82	IL_82563.1	3	Thi-box riboswitch T-loop
83	IL_95150.4	3
84	IL_09520.2	3	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
85	IL_16415.2	3	SSU Helix 23 (h23) Kink-turn T. thermophilus
86	IL_80348.1	3	23S H91 IL
87	IL_98421.4	3	SSU Helix 12 (h12) IL
88	IL_05723.1	3
89	IL_80494.2	3	LSU H58 IL2 H.m.
90	IL_30840.2	3
91	IL_09882.1	2
92	IL_21495.1	2
93	IL_39355.1	2	SSU Helix 12 (h12) IL \| LSU Eukaryal Helix 96 (H96) IL1
94	IL_45794.1	2
95	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
96	IL_69536.1	2	LSU Helix 96 (H96) IL2
97	IL_19898.1	2
98	IL_21639.1	2
99	IL_46034.1	2
100	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
101	IL_00998.1	2
102	IL_11751.1	2
103	IL_15840.2	2	Triple Sheared with unpaired, inserted A
104	IL_37197.1	2
105	IL_87507.1	2	tHS tHH bulge with S-turn
106	IL_90057.1	2
107	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
108	IL_97509.1	2	Double sheared with wobble cWW.
109	IL_01054.1	2
110	IL_09348.5	2	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
111	IL_23262.4	2
112	IL_46435.1	2
113	IL_52940.1	2
114	IL_97833.1	2
115	IL_12211.1	2
116	IL_16330.1	2
117	IL_23414.1	2
118	IL_31707.1	2	Vitamin B12 aptamer
119	IL_37406.1	2
120	IL_65137.1	2	Kink-turn like motif in Group I Intron
121	IL_76095.3	2	Motif from Hairpin Ribozyme
122	IL_80093.1	2
123	IL_87548.1	2
124	IL_90735.1	2
125	IL_30381.1	2	tHS tHH bulge with S-turn
126	IL_33964.1	2
127	IL_40892.1	2
128	IL_50521.1	2
129	IL_67887.1	2
130	IL_77076.1	2
131	IL_96206.1	2
132	IL_98566.1	2
133	IL_09587.1	2
134	IL_02957.1	1
135	IL_18675.1	1	cWW-bulge-cWW
136	IL_25082.1	1
137	IL_26971.1	1
138	IL_47732.1	1
139	IL_54450.1	1
140	IL_61730.1	1
141	IL_77296.1	1
142	IL_80652.1	1
143	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
144	IL_91089.1	1
145	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
146	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
147	IL_03110.1	1
148	IL_11302.1	1
149	IL_15205.1	1
150	IL_25181.1	1
151	IL_31224.1	1	23S H91 IL
152	IL_41791.1	1
153	IL_52509.1	1
154	IL_54470.1	1	tHS tHH bulge with S-turn
155	IL_57977.1	1
156	IL_69799.1	1
157	IL_81398.1	1
158	IL_83856.1	1
159	IL_89794.1	1
160	IL_91904.1	1
161	IL_98924.1	1
162	IL_03282.1	1
163	IL_06306.1	1
164	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
165	IL_20530.1	1
166	IL_28644.1	1
167	IL_46306.1	1
168	IL_52610.1	1
169	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
170	IL_63952.1	1
171	IL_75415.1	1	Pseudo-knot forming internal loop
172	IL_83920.1	1
173	IL_03741.1	1
174	IL_06421.1	1	Single sheared with bulged bases
175	IL_11778.1	1
176	IL_20775.1	1	tSH-inserted
177	IL_37347.1	1
178	IL_43316.1	1
179	IL_55649.1	1
180	IL_58454.1	1
181	IL_64589.1	1
182	IL_85510.1	1
183	IL_87523.1	1
184	IL_94973.1	1	Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
185	IL_05221.1	1
186	IL_06468.1	1	16S h40 3WJ E.c.
187	IL_09491.1	1
188	IL_21077.1	1
189	IL_30067.1	1
190	IL_40527.1	1	Kink-turn
191	IL_46721.1	1
192	IL_49527.1	1
193	IL_52958.1	1
194	IL_71685.1	1	Sarcin-like with an intercalated basepair
195	IL_97842.1	1
196	IL_06471.1	1
197	IL_12507.1	1
198	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
199	IL_23639.1	1	tWH-tHS-L-cWW
200	IL_25307.1	1
201	IL_30354.1	1
202	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
203	IL_40845.1	1
204	IL_49976.1	1
205	IL_53323.1	1
206	IL_59529.1	1
207	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
208	IL_71942.1	1
209	IL_76486.1	1	Sarcin-ricin motif with syn G
210	IL_82601.1	1	Tandem cWW water-inserted CU pairs
211	IL_85805.1	1
212	IL_92280.1	1
213	IL_02835.1	1
214	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
215	IL_17603.1	1
216	IL_56513.1	1
217	IL_59934.1	1	SSU Helix 23 (h23) Kink-turn E. coli
218	IL_82650.1	1
219	IL_86059.1	1
220	IL_88119.1	1
221	IL_91044.1	1
222	IL_02897.1	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.
223	IL_06177.1	1	cWW AG or UU
224	IL_06847.1	1	Group II Intron IL
225	IL_13682.1	1
226	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
227	IL_21421.1	1
228	IL_26868.1	1
229	IL_39324.1	1
230	IL_41139.1	1
231	IL_47687.1	1
232	IL_50911.1	1	16S h34 ILa : Part of larger motif
233	IL_53988.1	1
234	IL_57364.1	1	LSU Helix 89 (H89) IL2
235	IL_60649.1	1	Kink-turn
236	IL_68767.1	1
237	IL_80505.1	1
238	IL_83250.1	1	16S h40 3WJ T.th.
239	IL_88367.1	1
240	IL_91078.1	1

Updated motif groups

#	Motif id	Instances	Description
1	IL_65553.7	22	Kink-turn
2	IL_43124.2	11	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
3	IL_46648.4	11	23S H91 IL \| Single-Base Intercalation Site
4	IL_37104.2	11	Single sheared with bulged bases \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
5	IL_02809.3	9	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
6	IL_94403.3	4	LSU H77

Removed motif groups

#	Motif id	Instances	Description
1	IL_40090.5	10	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) \| 16S h34 ILa : Part of larger motif
2	IL_71565.4	4
3	IL_15768.1	4	cWW AG or UU \| cWH basepair with syn base
4	IL_35595.1	2	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
5	IL_35994.1	2	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
6	IL_55287.1	2
7	IL_12685.1	2	cWW AG or UU \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
8	IL_78809.1	1
9	IL_37990.1	1
10	IL_96182.1	1	cWH basepair with syn base
11	IL_99438.1	1
12	IL_54576.1	1
13	IL_59018.1	1
14	IL_60643.1	1

Added motif groups

#	Motif id	Instances	Description
1	IL_17212.1	10	cWW AG or UU \| cWH basepair with syn base \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) \| 16S h34 ILa : Part of larger motif
2	IL_15709.1	4	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) \| 16S h34 ILa : Part of larger motif \| cWW AG or UU \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
3	IL_33484.1	3	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
4	IL_35043.1	3	cWW AG or UU \| cWH basepair with syn base \| cWH basepair with syn base
5	IL_68880.1	2	cWW AG or UU \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
6	IL_80433.1	2
7	IL_85015.1	2	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases \| Single sheared with bulged bases \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
8	IL_95980.1	1	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
9	IL_25314.1	1
10	IL_97095.1	1	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
11	IL_41153.1	1
12	IL_10365.1	1