1.3 | 1.4

Changes in PDB files used for clustering

Release 1.3 has 201 PDB files, release 1.4 has 202 PDB files, 201 of them are identical.

No equivalence class representatives have been replaced.

1 new structures in release 1.4: 4KYY.

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

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Changes in motif groups

Release 1.3 has 271 motif groups, release 1.4 has 271 motif groups, 269 of them are identical.

2 motif groups were updated, 0 groups are present only in release 1.3, 0 groups are only in release 1.4.

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_39199.3	54	Hoogsteen-edge Platform, Single bulged base
3	IL_41766.3	49	Tandem cWW pairs (Not AU or GC)
4	IL_56465.3	46	Single, unpaired intercalated base, consensus A
5	IL_44540.3	43	Sugar-edge, 1-base platform, consensus tHS
6	IL_87904.4	31	Triple sheared (tSH-tHS-tHS) no inserted bases
7	IL_06390.3	26	cWH basepair with syn base
8	IL_13959.3	24	Double Sheared (tSH-tHS)
9	IL_93424.3	22	tSH-inserted-tHW
10	IL_65553.5	22	Kink-turn
11	IL_28947.1	21	23S H91 IL \| cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
12	IL_73276.3	21	C-loop
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_43124.1	11	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
22	IL_21304.2	11	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
23	IL_46648.2	11	23S H91 IL \| Single-Base Intercalation Site
24	IL_24546.3	10	23S H41 IL and 16S h18 IL : Has large bulge on one side
25	IL_02809.2	9	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
26	IL_92114.3	9	GAAA loop receptor "platform" motif
27	IL_58291.3	9	Recurrent Sub-motif found in junctions
28	IL_90459.3	9	cWW AG or UU
29	IL_47444.3	9	SRP Loop E-like motif
30	IL_83451.2	7	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
31	IL_92321.3	7	Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
32	IL_73000.2	7	cHS-cWS
33	IL_25230.3	6	Bacterial 5S rRNA Loop E
34	IL_39585.1	6	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
35	IL_44067.3	6	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
36	IL_97057.3	6
37	IL_53635.3	6	LSU Helix 32 (H32) IL
38	IL_90133.2	6
39	IL_72158.3	6	LSU Helix 62 (H62) IL
40	IL_54420.1	6
41	IL_70237.3	6
42	IL_13069.3	6	LSU 3WJ H32-H33-H35A
43	IL_25300.1	5	16S h19 IL and 23S H41 IL
44	IL_82188.1	5	LSU H68 IL from H.m.
45	IL_78732.3	5	Double S-turn motif
46	IL_02359.3	5
47	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
48	IL_77263.1	5	Kink-turn from U4
49	IL_45262.3	5
50	IL_86357.3	5	LSU Helix 61 IL2
51	IL_16207.1	5	Single sheared with bulged bases
52	IL_08926.2	5	23S H91 IL
53	IL_79083.3	5
54	IL_92484.1	5
55	IL_94403.1	4	LSU H77
56	IL_08559.1	4	LSU Helix 89 (H89) IL2
57	IL_39526.4	4
58	IL_28572.1	4	16S h18 kink-turn like motif
59	IL_31066.2	4	SSU Helix 44 (h44) extension
60	IL_21333.2	4	tSH-tHW-bulge
61	IL_42251.1	4
62	IL_38807.3	4
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_16166.3	4	23S H91 IL
66	IL_34363.2	4	Kink-turn from 23S H42
67	IL_22732.1	4	tSH-inserted-tHS
68	IL_93568.2	4	Triple Sheared (tSH-tHS-tHS) with wobble cWW.
69	IL_98591.3	4
70	IL_79955.2	3	SSU Helix (23) h23 IL1
71	IL_05723.1	3
72	IL_62499.6	3
73	IL_71565.3	3
74	IL_80494.2	3	LSU H58 IL2 H.m.
75	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.
76	IL_30840.1	3
77	IL_37053.1	3	Kink-turn from 23S H58
78	IL_92267.1	3	23S H73 ILa : Part of larger Motif
79	IL_48918.2	3	Kink-turn variant
80	IL_95652.2	3	SSU Helix 27 (h27) IL Sarcin-Ricin motif
81	IL_34156.6	3	cWW AG or UU
82	IL_10647.1	3	tHS tHH bulge with S-turn
83	IL_80348.1	3	23S H91 IL
84	IL_52173.1	3
85	IL_43946.1	3
86	IL_09520.2	3	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
87	IL_56077.1	3
88	IL_34628.2	3	Kink-turn
89	IL_98421.3	3	SSU Helix 12 (h12) IL
90	IL_74876.2	3	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
91	IL_95150.3	3
92	IL_75447.1	3
93	IL_58586.2	3
94	IL_82563.1	3	Thi-box riboswitch T-loop
95	IL_87548.1	2
96	IL_52940.1	2
97	IL_09348.5	2	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
98	IL_80093.1	2
99	IL_46435.1	2
100	IL_09587.1	2
101	IL_27892.1	2
102	IL_88180.1	2	cWW-bulge-cWW
103	IL_16415.1	2	SSU Helix 23 (h23) Kink-turn T. thermophilus
104	IL_65137.1	2	Kink-turn like motif in Group I Intron
105	IL_77076.1	2
106	IL_25271.1	2	SSU Helix 8 (h8) IL E.c. and Yeast
107	IL_55287.1	2
108	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
109	IL_11751.1	2
110	IL_19898.1	2
111	IL_90057.1	2
112	IL_12211.1	2
113	IL_21495.1	2
114	IL_09901.1	2	tHS tHH bulge with S-turn
115	IL_33925.1	2
116	IL_01054.1	2
117	IL_15840.2	2	Triple Sheared with unpaired, inserted A
118	IL_37406.1	2
119	IL_69536.1	2	LSU Helix 96 (H96) IL2
120	IL_28942.1	2
121	IL_23414.1	2
122	IL_37197.1	2
123	IL_31707.1	2	Vitamin B12 aptamer
124	IL_97833.1	2
125	IL_23262.4	2
126	IL_07300.1	2
127	IL_45794.1	2
128	IL_33964.1	2
129	IL_76095.3	2	Motif from Hairpin Ribozyme
130	IL_98566.1	2
131	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
132	IL_70280.1	2	Double sheared with wobble cWW.
133	IL_24358.1	2
134	IL_16330.1	2
135	IL_40892.1	2
136	IL_50521.1	2
137	IL_09882.1	2
138	IL_91273.1	2
139	IL_00998.1	2
140	IL_16252.3	2	23S H91 IL
141	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
142	IL_49550.1	2	tHS tHH bulge with S-turn
143	IL_96446.1	2
144	IL_03110.1	1
145	IL_83920.1	1
146	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
147	IL_27243.1	1
148	IL_75328.1	1
149	IL_82113.1	1
150	IL_53323.1	1
151	IL_26971.1	1
152	IL_09491.1	1
153	IL_21421.1	1
154	IL_85510.1	1
155	IL_91044.1	1
156	IL_27668.1	1
157	IL_63952.1	1
158	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
159	IL_41791.1	1
160	IL_43316.1	1
161	IL_12507.1	1
162	IL_06468.1	1	16S h40 3WJ E.c.
163	IL_52958.1	1
164	IL_80652.1	1
165	IL_65788.1	1
166	IL_61730.1	1
167	IL_41341.1	1	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
168	IL_25082.1	1
169	IL_98924.1	1
170	IL_59529.1	1
171	IL_02957.1	1
172	IL_28468.1	1	Single sheared with bulged bases
173	IL_88367.1	1
174	IL_06847.1	1	Group II Intron IL
175	IL_30067.1	1
176	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
177	IL_57977.1	1
178	IL_39324.1	1
179	IL_80505.1	1
180	IL_47687.1	1
181	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
182	IL_97073.1	1
183	IL_03931.1	1	16S h19 IL and 23S H41 IL
184	IL_78809.1	1
185	IL_13682.1	1
186	IL_31290.1	1
187	IL_13434.1	1
188	IL_71685.1	1	Sarcin-like with an intercalated basepair
189	IL_25181.1	1
190	IL_58454.1	1
191	IL_40527.1	1	Kink-turn
192	IL_60649.1	1	Kink-turn
193	IL_52610.1	1
194	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
195	IL_86059.1	1
196	IL_82650.1	1
197	IL_31006.1	1	tSH-tHW-L-bif-cWW
198	IL_21221.1	1	SSU Helix 12 (h12) IL
199	IL_54576.1	1
200	IL_67735.1	1
201	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
202	IL_23639.1	1	tWH-tHS-L-cWW
203	IL_64589.1	1
204	IL_41139.1	1
205	IL_77296.1	1
206	IL_87394.1	1
207	IL_40845.1	1
208	IL_25307.1	1
209	IL_26868.1	1
210	IL_55649.1	1
211	IL_52509.1	1
212	IL_02690.1	1
213	IL_75415.1	1	Pseudo-knot forming internal loop
214	IL_76486.1	1	Sarcin-ricin motif with syn G
215	IL_37990.1	1
216	IL_82601.1	1	Tandem cWW water-inserted CU pairs
217	IL_34868.1	1	LSU Eukaryal Helix 96 (H96) IL1
218	IL_03282.1	1
219	IL_42891.1	1
220	IL_88865.1	1
221	IL_76263.1	1
222	IL_91379.1	1
223	IL_11302.1	1
224	IL_89794.1	1
225	IL_95774.1	1	tHS tHH bulge with S-turn
226	IL_12486.1	1
227	IL_06306.1	1
228	IL_97842.1	1
229	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
230	IL_17603.1	1
231	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
232	IL_91089.1	1
233	IL_94973.1	1	Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
234	IL_47732.1	1
235	IL_85805.1	1
236	IL_92280.1	1
237	IL_68827.1	1	Reverse Kink-Turn
238	IL_04550.1	1	tHS tHH bulge with S-turn
239	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
240	IL_53988.1	1
241	IL_28644.1	1
242	IL_11778.1	1
243	IL_37715.1	1
244	IL_54450.1	1
245	IL_77014.1	1
246	IL_03741.1	1
247	IL_83856.1	1
248	IL_37347.1	1
249	IL_46306.1	1
250	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.
251	IL_15205.1	1
252	IL_23448.1	1
253	IL_57285.1	1
254	IL_30354.1	1
255	IL_83250.1	1	16S h40 3WJ T.th.
256	IL_02835.1	1
257	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
258	IL_59934.1	1	SSU Helix 23 (h23) Kink-turn E. coli
259	IL_05462.1	1
260	IL_20775.1	1	tSH-inserted
261	IL_71942.1	1
262	IL_91078.1	1
263	IL_81398.1	1
264	IL_05221.1	1
265	IL_06471.1	1
266	IL_91904.1	1
267	IL_56513.1	1
268	IL_60643.1	1
269	IL_46721.1	1

Updated motif groups

#	Motif id	Instances	Description
1	IL_47174.7	203	cWW AG or water inserted cWW Y-Y.
2	IL_40090.4	12	16S h34 ILa : Part of larger motif

Removed motif groups

#	Motif id	Instances	Description

Added motif groups

#	Motif id	Instances	Description