1.5 | 1.6

Changes in PDB files used for clustering

Release 1.5 has 204 PDB files, release 1.6 has 204 PDB files, 203 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_28947.1	21	23S H91 IL \| cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
11	IL_93424.4	21	tSH-inserted-tHW
12	IL_73276.4	21	C-loop
13	IL_55938.4	18	LSU Helix 89 (H89) IL2. cSH Platform.
14	IL_92027.3	17	16S h21 S8 binding site
15	IL_24982.5	16	SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
16	IL_94430.5	16	16S h32-h33-h34 3WJ
17	IL_85647.3	16	Sarcin-ricin parent motif with 15 Nts
18	IL_92109.2	15	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
19	IL_49493.4	13	Sarcin-ricin Parent Motif - bacterial LSU H95 IL
20	IL_31555.4	13	Tandem sheared with inserted, unpaired purine.
21	IL_24546.4	10	23S H41 IL and 16S h18 IL : Has large bulge on one side
22	IL_58291.4	10	Recurrent Sub-motif found in junctions
23	IL_47444.3	9	SRP Loop E-like motif
24	IL_90459.3	9	cWW AG or UU
25	IL_92114.3	9	GAAA loop receptor "platform" 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_97057.3	6
30	IL_08926.3	6	23S H91 IL
31	IL_25230.3	6	Bacterial 5S rRNA Loop E
32	IL_53635.3	6	LSU Helix 32 (H32) IL
33	IL_90133.3	6
34	IL_72158.3	6	LSU Helix 62 (H62) IL
35	IL_13069.3	6	LSU 3WJ H32-H33-H35A
36	IL_39585.1	6	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
37	IL_77263.2	6	Kink-turn from U4
38	IL_25380.1	6	LSU Helix 89 (H89) IL2
39	IL_70237.3	6
40	IL_86357.3	5	LSU Helix 61 IL2
41	IL_44067.4	5	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
42	IL_79083.3	5
43	IL_02359.3	5
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_05684.1	5	tHS tHH bulge with S-turn \| Double S-turn motif
47	IL_42251.1	4
48	IL_34363.2	4	Kink-turn from 23S H42
49	IL_21333.2	4	tSH-tHW-bulge
50	IL_95652.3	4	SSU Helix 27 (h27) IL Sarcin-Ricin motif
51	IL_39980.1	4
52	IL_98591.3	4
53	IL_09530.1	4	Double S-turn motif
54	IL_28572.2	4	16S h18 kink-turn like motif
55	IL_31066.3	4	SSU Helix 44 (h44) extension
56	IL_82188.2	4	LSU H68 IL from H.m.
57	IL_39526.4	4
58	IL_47758.2	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
59	IL_01080.1	4
60	IL_31663.1	4	23S H73 ILa : Part of larger Motif
61	IL_93568.2	4	Triple Sheared (tSH-tHS-tHS) with wobble cWW.
62	IL_22732.1	4	tSH-inserted-tHS
63	IL_38807.3	4
64	IL_45262.4	4
65	IL_79955.2	3	SSU Helix (23) h23 IL1
66	IL_95150.4	3
67	IL_16415.2	3	SSU Helix 23 (h23) Kink-turn T. thermophilus
68	IL_16166.4	3	23S H91 IL
69	IL_75447.1	3
70	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.
71	IL_34628.2	3	Kink-turn
72	IL_07300.2	3
73	IL_62499.7	3
74	IL_82563.1	3	Thi-box riboswitch T-loop
75	IL_87065.1	3	23S H91 IL \| Single-Base Intercalation Site
76	IL_74876.2	3	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
77	IL_48918.2	3	Kink-turn variant
78	IL_25271.2	3	SSU Helix 8 (h8) IL E.c. and Yeast
79	IL_52173.1	3
80	IL_58586.2	3
81	IL_05723.1	3
82	IL_80348.1	3	23S H91 IL
83	IL_80494.2	3	LSU H58 IL2 H.m.
84	IL_98421.4	3	SSU Helix 12 (h12) IL
85	IL_37053.1	3	Kink-turn from 23S H58
86	IL_06180.1	3	tHS tHH bulge with S-turn
87	IL_06211.1	3
88	IL_43946.1	3
89	IL_09520.2	3	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
90	IL_30840.2	3
91	IL_50521.1	2
92	IL_19898.1	2
93	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
94	IL_46034.1	2
95	IL_87548.1	2
96	IL_52940.1	2
97	IL_98566.1	2
98	IL_30381.1	2	tHS tHH bulge with S-turn
99	IL_67887.1	2
100	IL_21639.1	2
101	IL_37197.1	2
102	IL_96446.1	2
103	IL_11751.1	2
104	IL_65137.1	2	Kink-turn like motif in Group I Intron
105	IL_97833.1	2
106	IL_00998.1	2
107	IL_45794.1	2
108	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
109	IL_76095.3	2	Motif from Hairpin Ribozyme
110	IL_46435.1	2
111	IL_09587.1	2
112	IL_16330.1	2
113	IL_87507.1	2	tHS tHH bulge with S-turn
114	IL_80093.1	2
115	IL_97509.1	2	Double sheared with wobble cWW.
116	IL_40892.1	2
117	IL_33964.1	2
118	IL_31707.1	2	Vitamin B12 aptamer
119	IL_09348.5	2	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
120	IL_12211.1	2
121	IL_21495.1	2
122	IL_37406.1	2
123	IL_90735.1	2
124	IL_09882.1	2
125	IL_77076.1	2
126	IL_01054.1	2
127	IL_15840.2	2	Triple Sheared with unpaired, inserted A
128	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
129	IL_39355.1	2	SSU Helix 12 (h12) IL \| LSU Eukaryal Helix 96 (H96) IL1
130	IL_90057.1	2
131	IL_96206.1	2
132	IL_23262.4	2
133	IL_69536.1	2	LSU Helix 96 (H96) IL2
134	IL_23414.1	2
135	IL_83250.1	1	16S h40 3WJ T.th.
136	IL_76263.1	1
137	IL_91379.1	1
138	IL_11302.1	1
139	IL_89794.1	1
140	IL_28644.1	1
141	IL_52509.1	1
142	IL_61730.1	1
143	IL_75415.1	1	Pseudo-knot forming internal loop
144	IL_88119.1	1
145	IL_98924.1	1
146	IL_25181.1	1
147	IL_09491.1	1
148	IL_58454.1	1
149	IL_88367.1	1
150	IL_49976.1	1
151	IL_57285.1	1
152	IL_30354.1	1
153	IL_68827.1	1	Reverse Kink-Turn
154	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
155	IL_53988.1	1
156	IL_71685.1	1	Sarcin-like with an intercalated basepair
157	IL_02957.1	1
158	IL_18675.1	1	cWW-bulge-cWW
159	IL_40527.1	1	Kink-turn
160	IL_23448.1	1
161	IL_46721.1	1
162	IL_63952.1	1
163	IL_88865.1	1
164	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
165	IL_83920.1	1
166	IL_59934.1	1	SSU Helix 23 (h23) Kink-turn E. coli
167	IL_11778.1	1
168	IL_03741.1	1
169	IL_06306.1	1
170	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
171	IL_23639.1	1	tWH-tHS-L-cWW
172	IL_57364.1	1	LSU Helix 89 (H89) IL2
173	IL_41139.1	1
174	IL_91044.1	1
175	IL_27668.1	1
176	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
177	IL_02835.1	1
178	IL_06421.1	1	Single sheared with bulged bases
179	IL_20775.1	1	tSH-inserted
180	IL_77014.1	1
181	IL_91078.1	1
182	IL_83856.1	1
183	IL_76486.1	1	Sarcin-ricin motif with syn G
184	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
185	IL_64589.1	1
186	IL_54470.1	1	tHS tHH bulge with S-turn
187	IL_06847.1	1	Group II Intron IL
188	IL_30067.1	1
189	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
190	IL_40845.1	1
191	IL_92280.1	1
192	IL_03110.1	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_06808.1	1	Double sheared (tSH-tSH) one bulged base.
198	IL_71942.1	1
199	IL_81398.1	1
200	IL_97842.1	1
201	IL_46306.1	1
202	IL_82601.1	1	Tandem cWW water-inserted CU pairs
203	IL_91089.1	1
204	IL_60649.1	1	Kink-turn
205	IL_52610.1	1
206	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
207	IL_41791.1	1
208	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.
209	IL_80505.1	1
210	IL_69799.1	1
211	IL_47687.1	1
212	IL_80652.1	1
213	IL_54450.1	1
214	IL_75328.1	1
215	IL_20530.1	1
216	IL_37347.1	1
217	IL_06471.1	1
218	IL_68767.1	1
219	IL_17603.1	1
220	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
221	IL_87523.1	1
222	IL_77296.1	1
223	IL_87394.1	1
224	IL_50911.1	1	16S h34 ILa : Part of larger motif
225	IL_39324.1	1
226	IL_06177.1	1	cWW AG or UU
227	IL_82650.1	1
228	IL_31006.1	1	tSH-tHW-L-bif-cWW
229	IL_55649.1	1
230	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
231	IL_13682.1	1
232	IL_31224.1	1	23S H91 IL
233	IL_05221.1	1
234	IL_26971.1	1
235	IL_56513.1	1
236	IL_15205.1	1
237	IL_21077.1	1
238	IL_03282.1	1
239	IL_42891.1	1
240	IL_85805.1	1
241	IL_57977.1	1
242	IL_86059.1	1
243	IL_25307.1	1
244	IL_26868.1	1
245	IL_27243.1	1
246	IL_25082.1	1
247	IL_53323.1	1
248	IL_59529.1	1
249	IL_91904.1	1
250	IL_21421.1	1
251	IL_85510.1	1
252	IL_49527.1	1
253	IL_94973.1	1	Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
254	IL_47732.1	1

Updated motif groups

#	Motif id	Instances	Description
1	IL_65553.7	22	Kink-turn
2	IL_37104.2	11	Single sheared with bulged bases \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
3	IL_43124.2	11	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
4	IL_46648.4	11	23S H91 IL \| Single-Base Intercalation Site
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_15768.1	4	cWW AG or UU \| cWH basepair with syn base
3	IL_71565.4	4
4	IL_55287.1	2
5	IL_12685.1	2	cWW AG or UU \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
6	IL_35595.1	2	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
7	IL_35994.1	2	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
8	IL_59018.1	1
9	IL_60643.1	1
10	IL_78809.1	1
11	IL_37990.1	1
12	IL_96182.1	1	cWH basepair with syn base
13	IL_99438.1	1
14	IL_54576.1	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_10365.1	1
9	IL_95980.1	1	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
10	IL_25314.1	1
11	IL_97095.1	1	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
12	IL_41153.1	1