1.4 | 1.5

Changes in PDB files used for clustering

Release 1.4 has 202 PDB files, release 1.5 has 204 PDB files, 201 of them are identical.

1 equivalence classes changed representatives: 2XZM → 4BPP.

2 new structures in release 1.5: 4K31, 4LCK.

Obsolete: 2XZM → 4V5O.

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 1.4 has 271 motif groups, release 1.5 has 274 motif groups, 189 of them are identical.

43 motif groups were updated, 39 groups are present only in release 1.4, 42 groups are only in release 1.5.

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_56465.3	46	Single, unpaired intercalated base, consensus A
2	IL_28947.1	21	23S H91 IL \| cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
3	IL_92027.3	17	16S h21 S8 binding site
4	IL_85647.3	16	Sarcin-ricin parent motif with 15 Nts
5	IL_43124.1	11	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
6	IL_02809.2	9	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
7	IL_92114.3	9	GAAA loop receptor "platform" motif
8	IL_47444.3	9	SRP Loop E-like motif
9	IL_90459.3	9	cWW AG or UU
10	IL_73000.2	7	cHS-cWS
11	IL_53635.3	6	LSU Helix 32 (H32) IL
12	IL_39585.1	6	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
13	IL_13069.3	6	LSU 3WJ H32-H33-H35A
14	IL_25230.3	6	Bacterial 5S rRNA Loop E
15	IL_70237.3	6
16	IL_72158.3	6	LSU Helix 62 (H62) IL
17	IL_97057.3	6
18	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
19	IL_86357.3	5	LSU Helix 61 IL2
20	IL_02359.3	5
21	IL_79083.3	5
22	IL_25300.1	5	16S h19 IL and 23S H41 IL
23	IL_42251.1	4
24	IL_38807.3	4
25	IL_39526.4	4
26	IL_01080.1	4
27	IL_34363.2	4	Kink-turn from 23S H42
28	IL_98591.3	4
29	IL_93568.2	4	Triple Sheared (tSH-tHS-tHS) with wobble cWW.
30	IL_22732.1	4	tSH-inserted-tHS
31	IL_21333.2	4	tSH-tHW-bulge
32	IL_09520.2	3	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
33	IL_80348.1	3	23S H91 IL
34	IL_52173.1	3
35	IL_80494.2	3	LSU H58 IL2 H.m.
36	IL_05723.1	3
37	IL_37053.1	3	Kink-turn from 23S H58
38	IL_75447.1	3
39	IL_43946.1	3
40	IL_82563.1	3	Thi-box riboswitch T-loop
41	IL_48918.2	3	Kink-turn variant
42	IL_34628.2	3	Kink-turn
43	IL_79955.2	3	SSU Helix (23) h23 IL1
44	IL_58586.2	3
45	IL_74876.2	3	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
46	IL_11751.1	2
47	IL_97833.1	2
48	IL_09348.5	2	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
49	IL_80093.1	2
50	IL_40892.1	2
51	IL_76095.3	2	Motif from Hairpin Ribozyme
52	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
53	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
54	IL_50521.1	2
55	IL_12211.1	2
56	IL_00998.1	2
57	IL_69536.1	2	LSU Helix 96 (H96) IL2
58	IL_87548.1	2
59	IL_55287.1	2
60	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
61	IL_52940.1	2
62	IL_09882.1	2
63	IL_77076.1	2
64	IL_09587.1	2
65	IL_96446.1	2
66	IL_31707.1	2	Vitamin B12 aptamer
67	IL_90057.1	2
68	IL_21495.1	2
69	IL_37406.1	2
70	IL_23414.1	2
71	IL_37197.1	2
72	IL_33964.1	2
73	IL_19898.1	2
74	IL_98566.1	2
75	IL_45794.1	2
76	IL_65137.1	2	Kink-turn like motif in Group I Intron
77	IL_46435.1	2
78	IL_01054.1	2
79	IL_15840.2	2	Triple Sheared with unpaired, inserted A
80	IL_23262.4	2
81	IL_16330.1	2
82	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
83	IL_12507.1	1
84	IL_26868.1	1
85	IL_89794.1	1
86	IL_80652.1	1
87	IL_54450.1	1
88	IL_77014.1	1
89	IL_91078.1	1
90	IL_37347.1	1
91	IL_46306.1	1
92	IL_21421.1	1
93	IL_40527.1	1	Kink-turn
94	IL_77296.1	1
95	IL_87394.1	1
96	IL_40845.1	1
97	IL_43316.1	1
98	IL_80505.1	1
99	IL_11302.1	1
100	IL_53988.1	1
101	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
102	IL_71942.1	1
103	IL_06306.1	1
104	IL_05221.1	1
105	IL_06471.1	1
106	IL_91904.1	1
107	IL_58454.1	1
108	IL_41139.1	1
109	IL_03282.1	1
110	IL_42891.1	1
111	IL_85805.1	1
112	IL_92280.1	1
113	IL_57977.1	1
114	IL_82650.1	1
115	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
116	IL_27243.1	1
117	IL_75328.1	1
118	IL_83856.1	1
119	IL_53323.1	1
120	IL_26971.1	1
121	IL_09491.1	1
122	IL_64589.1	1
123	IL_91089.1	1
124	IL_94973.1	1	Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
125	IL_47732.1	1
126	IL_83250.1	1	16S h40 3WJ T.th.
127	IL_41791.1	1
128	IL_25307.1	1
129	IL_59934.1	1	SSU Helix 23 (h23) Kink-turn E. coli
130	IL_52509.1	1
131	IL_61730.1	1
132	IL_81398.1	1
133	IL_98924.1	1
134	IL_59529.1	1
135	IL_02957.1	1
136	IL_82601.1	1	Tandem cWW water-inserted CU pairs
137	IL_23448.1	1
138	IL_57285.1	1
139	IL_30354.1	1
140	IL_63952.1	1
141	IL_03110.1	1
142	IL_76263.1	1
143	IL_91379.1	1
144	IL_52958.1	1
145	IL_78809.1	1
146	IL_13682.1	1
147	IL_25082.1	1
148	IL_71685.1	1	Sarcin-like with an intercalated basepair
149	IL_25181.1	1
150	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
151	IL_60643.1	1
152	IL_46721.1	1
153	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
154	IL_68827.1	1	Reverse Kink-Turn
155	IL_83920.1	1
156	IL_06468.1	1	16S h40 3WJ E.c.
157	IL_11778.1	1
158	IL_54576.1	1
159	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
160	IL_23639.1	1	tWH-tHS-L-cWW
161	IL_15205.1	1
162	IL_91044.1	1
163	IL_27668.1	1
164	IL_88865.1	1
165	IL_39324.1	1
166	IL_86059.1	1
167	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
168	IL_47687.1	1
169	IL_31006.1	1	tSH-tHW-L-bif-cWW
170	IL_55649.1	1
171	IL_20775.1	1	tSH-inserted
172	IL_75415.1	1	Pseudo-knot forming internal loop
173	IL_76486.1	1	Sarcin-ricin motif with syn G
174	IL_37990.1	1
175	IL_17603.1	1
176	IL_85510.1	1
177	IL_06847.1	1	Group II Intron IL
178	IL_30067.1	1
179	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
180	IL_02835.1	1
181	IL_28644.1	1
182	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
183	IL_03741.1	1
184	IL_97842.1	1
185	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
186	IL_56513.1	1
187	IL_88367.1	1
188	IL_60649.1	1	Kink-turn
189	IL_52610.1	1

Updated 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_44540.4	43	Sugar-edge, 1-base platform, consensus tHS
6	IL_87904.5	31	Triple sheared (tSH-tHS-tHS) no inserted bases
7	IL_13959.4	26	Double Sheared (tSH-tHS)
8	IL_65553.6	22	Kink-turn
9	IL_93424.4	21	tSH-inserted-tHW
10	IL_73276.4	21	C-loop
11	IL_55938.4	18	LSU Helix 89 (H89) IL2. cSH Platform.
12	IL_94430.5	16	16S h32-h33-h34 3WJ
13	IL_24982.5	16	SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
14	IL_92109.2	15	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
15	IL_49493.4	13	Sarcin-ricin Parent Motif - bacterial LSU H95 IL
16	IL_31555.4	13	Tandem sheared with inserted, unpaired purine.
17	IL_46648.3	10	23S H91 IL \| Single-Base Intercalation Site
18	IL_40090.5	10	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) \| 16S h34 ILa : Part of larger motif
19	IL_24546.4	10	23S H41 IL and 16S h18 IL : Has large bulge on one side
20	IL_58291.4	10	Recurrent Sub-motif found in junctions
21	IL_83451.3	7	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
22	IL_92321.4	7	Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
23	IL_90133.3	6
24	IL_77263.2	6	Kink-turn from U4
25	IL_08926.3	6	23S H91 IL
26	IL_44067.4	5	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
27	IL_95652.3	4	SSU Helix 27 (h27) IL Sarcin-Ricin motif
28	IL_71565.4	4
29	IL_47758.2	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
30	IL_31066.3	4	SSU Helix 44 (h44) extension
31	IL_45262.4	4
32	IL_28572.2	4	16S h18 kink-turn like motif
33	IL_82188.2	4	LSU H68 IL from H.m.
34	IL_94403.2	3	LSU H77
35	IL_25271.2	3	SSU Helix 8 (h8) IL E.c. and Yeast
36	IL_98421.4	3	SSU Helix 12 (h12) IL
37	IL_62499.7	3
38	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.
39	IL_16166.4	3	23S H91 IL
40	IL_30840.2	3
41	IL_07300.2	3
42	IL_95150.4	3
43	IL_16415.2	3	SSU Helix 23 (h23) Kink-turn T. thermophilus

Removed motif groups

#	Motif id	Instances	Description
1	IL_06390.3	26	cWH basepair with syn base
2	IL_21304.2	11	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
3	IL_54420.1	6
4	IL_78732.3	5	Double S-turn motif
5	IL_16207.1	5	Single sheared with bulged bases
6	IL_92484.1	5
7	IL_08559.1	4	LSU Helix 89 (H89) IL2
8	IL_34156.6	3	cWW AG or UU
9	IL_10647.1	3	tHS tHH bulge with S-turn
10	IL_56077.1	3
11	IL_92267.1	3	23S H73 ILa : Part of larger Motif
12	IL_09901.1	2	tHS tHH bulge with S-turn
13	IL_70280.1	2	Double sheared with wobble cWW.
14	IL_24358.1	2
15	IL_27892.1	2
16	IL_49550.1	2	tHS tHH bulge with S-turn
17	IL_88180.1	2	cWW-bulge-cWW
18	IL_28942.1	2
19	IL_91273.1	2
20	IL_16252.3	2	23S H91 IL
21	IL_33925.1	2
22	IL_21221.1	1	SSU Helix 12 (h12) IL
23	IL_67735.1	1
24	IL_95774.1	1	tHS tHH bulge with S-turn
25	IL_34868.1	1	LSU Eukaryal Helix 96 (H96) IL1
26	IL_97073.1	1
27	IL_37715.1	1
28	IL_02690.1	1
29	IL_12486.1	1
30	IL_41341.1	1	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
31	IL_82113.1	1
32	IL_03931.1	1	16S h19 IL and 23S H41 IL
33	IL_13434.1	1
34	IL_28468.1	1	Single sheared with bulged bases
35	IL_04550.1	1	tHS tHH bulge with S-turn
36	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.
37	IL_05462.1	1
38	IL_31290.1	1
39	IL_65788.1	1

Added motif groups

#	Motif id	Instances	Description
1	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
2	IL_37104.1	11	Single sheared with bulged bases \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
3	IL_25380.1	6	LSU Helix 89 (H89) IL2
4	IL_05684.1	5	tHS tHH bulge with S-turn \| Double S-turn motif
5	IL_09530.1	4	Double S-turn motif
6	IL_15768.1	4	cWW AG or UU \| cWH basepair with syn base
7	IL_31663.1	4	23S H73 ILa : Part of larger Motif
8	IL_39980.1	4
9	IL_87065.1	3	23S H91 IL \| Single-Base Intercalation Site
10	IL_06180.1	3	tHS tHH bulge with S-turn
11	IL_06211.1	3
12	IL_30381.1	2	tHS tHH bulge with S-turn
13	IL_46034.1	2
14	IL_12685.1	2	cWW AG or UU \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
15	IL_96206.1	2
16	IL_97509.1	2	Double sheared with wobble cWW.
17	IL_35595.1	2	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
18	IL_35994.1	2	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
19	IL_87507.1	2	tHS tHH bulge with S-turn
20	IL_21639.1	2
21	IL_39355.1	2	SSU Helix 12 (h12) IL \| LSU Eukaryal Helix 96 (H96) IL1
22	IL_67887.1	2
23	IL_90735.1	2
24	IL_68767.1	1
25	IL_96182.1	1	cWH basepair with syn base
26	IL_31224.1	1	23S H91 IL
27	IL_49527.1	1
28	IL_69799.1	1
29	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.
30	IL_49976.1	1
31	IL_18675.1	1	cWW-bulge-cWW
32	IL_50911.1	1	16S h34 ILa : Part of larger motif
33	IL_99438.1	1
34	IL_06177.1	1	cWW AG or UU
35	IL_20530.1	1
36	IL_54470.1	1	tHS tHH bulge with S-turn
37	IL_21077.1	1
38	IL_57364.1	1	LSU Helix 89 (H89) IL2
39	IL_87523.1	1
40	IL_59018.1	1
41	IL_88119.1	1
42	IL_06421.1	1	Single sheared with bulged bases