1.4 | 1.5

Changes in PDB files used for clustering

Release 1.4 has 201 PDB files, release 1.5 has 203 PDB files, 200 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_92114.3	9	GAAA loop receptor "platform" motif
7	IL_47444.3	9	SRP Loop E-like motif
8	IL_02809.2	9	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
9	IL_90459.3	9	cWW AG or UU
10	IL_73000.2	7	cHS-cWS
11	IL_13069.3	6	LSU 3WJ H32-H33-H35A
12	IL_39585.1	6	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
13	IL_70237.3	6
14	IL_53635.3	6	LSU Helix 32 (H32) IL
15	IL_25230.3	6	Bacterial 5S rRNA Loop E
16	IL_97057.3	6
17	IL_72158.3	6	LSU Helix 62 (H62) IL
18	IL_02359.3	5
19	IL_79083.3	5
20	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
21	IL_86357.3	5	LSU Helix 61 IL2
22	IL_25300.1	5	16S h19 IL and 23S H41 IL
23	IL_01080.1	4
24	IL_38807.3	4
25	IL_34363.2	4	Kink-turn from 23S H42
26	IL_42251.1	4
27	IL_39526.4	4
28	IL_93568.2	4	Triple Sheared (tSH-tHS-tHS) with wobble cWW.
29	IL_98591.3	4
30	IL_21333.2	4	tSH-tHW-bulge
31	IL_22732.1	4	tSH-inserted-tHS
32	IL_58586.2	3
33	IL_05723.1	3
34	IL_74876.2	3	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
35	IL_09520.2	3	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
36	IL_34628.2	3	Kink-turn
37	IL_82563.1	3	Thi-box riboswitch T-loop
38	IL_37053.1	3	Kink-turn from 23S H58
39	IL_75447.1	3
40	IL_79955.2	3	SSU Helix (23) h23 IL1
41	IL_43946.1	3
42	IL_48918.2	3	Kink-turn variant
43	IL_80348.1	3	23S H91 IL
44	IL_52173.1	3
45	IL_80494.2	3	LSU H58 IL2 H.m.
46	IL_09348.5	2	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
47	IL_12211.1	2
48	IL_23262.4	2
49	IL_33964.1	2
50	IL_65137.1	2	Kink-turn like motif in Group I Intron
51	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
52	IL_19898.1	2
53	IL_23414.1	2
54	IL_52940.1	2
55	IL_55287.1	2
56	IL_90057.1	2
57	IL_98566.1	2
58	IL_69536.1	2	LSU Helix 96 (H96) IL2
59	IL_09587.1	2
60	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
61	IL_09882.1	2
62	IL_37197.1	2
63	IL_76095.3	2	Motif from Hairpin Ribozyme
64	IL_80093.1	2
65	IL_15840.2	2	Triple Sheared with unpaired, inserted A
66	IL_45794.1	2
67	IL_50521.1	2
68	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
69	IL_00998.1	2
70	IL_11751.1	2
71	IL_16330.1	2
72	IL_21495.1	2
73	IL_31707.1	2	Vitamin B12 aptamer
74	IL_37406.1	2
75	IL_40892.1	2
76	IL_77076.1	2
77	IL_87548.1	2
78	IL_01054.1	2
79	IL_46435.1	2
80	IL_97833.1	2
81	IL_05221.1	1
82	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
83	IL_26868.1	1
84	IL_41791.1	1
85	IL_46721.1	1
86	IL_52610.1	1
87	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
88	IL_80652.1	1
89	IL_85510.1	1
90	IL_89794.1	1
91	IL_97842.1	1
92	IL_09491.1	1
93	IL_12507.1	1
94	IL_26971.1	1
95	IL_39324.1	1
96	IL_59529.1	1
97	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
98	IL_78809.1	1
99	IL_81398.1	1
100	IL_92280.1	1
101	IL_06306.1	1
102	IL_20775.1	1	tSH-inserted
103	IL_23639.1	1	tWH-tHS-L-cWW
104	IL_28644.1	1
105	IL_47687.1	1
106	IL_52958.1	1
107	IL_55649.1	1
108	IL_59934.1	1	SSU Helix 23 (h23) Kink-turn E. coli
109	IL_75415.1	1	Pseudo-knot forming internal loop
110	IL_85805.1	1
111	IL_02835.1	1
112	IL_06468.1	1	16S h40 3WJ E.c.
113	IL_13682.1	1
114	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
115	IL_25082.1	1
116	IL_43316.1	1
117	IL_47732.1	1
118	IL_53323.1	1
119	IL_60643.1	1
120	IL_82601.1	1	Tandem cWW water-inserted CU pairs
121	IL_86059.1	1
122	IL_91044.1	1
123	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
124	IL_02957.1	1
125	IL_06471.1	1
126	IL_15205.1	1
127	IL_25181.1	1
128	IL_30067.1	1
129	IL_40527.1	1	Kink-turn
130	IL_56513.1	1
131	IL_60649.1	1	Kink-turn
132	IL_82650.1	1
133	IL_91078.1	1
134	IL_94973.1	1	Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
135	IL_98924.1	1
136	IL_03110.1	1
137	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
138	IL_11302.1	1
139	IL_21421.1	1
140	IL_30354.1	1
141	IL_37347.1	1
142	IL_40845.1	1
143	IL_53988.1	1
144	IL_61730.1	1
145	IL_71685.1	1	Sarcin-like with an intercalated basepair
146	IL_76486.1	1	Sarcin-ricin motif with syn G
147	IL_83250.1	1	16S h40 3WJ T.th.
148	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
149	IL_91089.1	1
150	IL_03282.1	1
151	IL_06847.1	1	Group II Intron IL
152	IL_46306.1	1
153	IL_54450.1	1
154	IL_57977.1	1
155	IL_63952.1	1
156	IL_71942.1	1
157	IL_83856.1	1
158	IL_91904.1	1
159	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
160	IL_03741.1	1
161	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
162	IL_11778.1	1
163	IL_17603.1	1
164	IL_25307.1	1
165	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
166	IL_37990.1	1
167	IL_41139.1	1
168	IL_52509.1	1
169	IL_54576.1	1
170	IL_58454.1	1
171	IL_64589.1	1
172	IL_77296.1	1
173	IL_80505.1	1
174	IL_83920.1	1
175	IL_88367.1	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_73276.4	21	C-loop
10	IL_93424.4	21	tSH-inserted-tHW
11	IL_55938.4	18	LSU Helix 89 (H89) IL2. cSH Platform.
12	IL_24982.5	16	SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
13	IL_94430.5	16	16S h32-h33-h34 3WJ
14	IL_92109.2	15	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
15	IL_31555.4	13	Tandem sheared with inserted, unpaired purine.
16	IL_49493.4	13	Sarcin-ricin Parent Motif - bacterial LSU H95 IL
17	IL_46648.3	10	23S H91 IL \| Single-Base Intercalation Site
18	IL_24546.4	10	23S H41 IL and 16S h18 IL : Has large bulge on one side
19	IL_40090.5	10	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) \| 16S h34 ILa : Part of larger motif
20	IL_58291.4	10	Recurrent Sub-motif found in junctions
21	IL_92321.4	7	Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
22	IL_83451.3	7	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
23	IL_77263.2	6	Kink-turn from U4
24	IL_08926.3	6	23S H91 IL
25	IL_90133.3	6
26	IL_44067.4	5	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
27	IL_31066.3	4	SSU Helix 44 (h44) extension
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_82188.2	4	LSU H68 IL from H.m.
31	IL_28572.2	4	16S h18 kink-turn like motif
32	IL_95652.3	4	SSU Helix 27 (h27) IL Sarcin-Ricin motif
33	IL_45262.4	4
34	IL_98421.4	3	SSU Helix 12 (h12) IL
35	IL_16166.4	3	23S H91 IL
36	IL_16415.2	3	SSU Helix 23 (h23) Kink-turn T. thermophilus
37	IL_94403.2	3	LSU H77
38	IL_25271.2	3	SSU Helix 8 (h8) IL E.c. and Yeast
39	IL_95150.4	3
40	IL_07300.2	3
41	IL_62499.7	3
42	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.
43	IL_30840.2	3

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_16207.1	5	Single sheared with bulged bases
5	IL_92484.1	5
6	IL_78732.3	5	Double S-turn motif
7	IL_08559.1	4	LSU Helix 89 (H89) IL2
8	IL_56077.1	3
9	IL_92267.1	3	23S H73 ILa : Part of larger Motif
10	IL_34156.6	3	cWW AG or UU
11	IL_10647.1	3	tHS tHH bulge with S-turn
12	IL_28942.1	2
13	IL_91273.1	2
14	IL_16252.3	2	23S H91 IL
15	IL_33925.1	2
16	IL_09901.1	2	tHS tHH bulge with S-turn
17	IL_70280.1	2	Double sheared with wobble cWW.
18	IL_24358.1	2
19	IL_27892.1	2
20	IL_49550.1	2	tHS tHH bulge with S-turn
21	IL_88180.1	2	cWW-bulge-cWW
22	IL_04550.1	1	tHS tHH bulge with S-turn
23	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.
24	IL_05462.1	1
25	IL_31290.1	1
26	IL_65788.1	1
27	IL_21221.1	1	SSU Helix 12 (h12) IL
28	IL_67735.1	1
29	IL_95774.1	1	tHS tHH bulge with S-turn
30	IL_34868.1	1	LSU Eukaryal Helix 96 (H96) IL1
31	IL_97073.1	1
32	IL_37715.1	1
33	IL_02690.1	1
34	IL_12486.1	1
35	IL_41341.1	1	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
36	IL_82113.1	1
37	IL_03931.1	1	16S h19 IL and 23S H41 IL
38	IL_13434.1	1
39	IL_28468.1	1	Single sheared with bulged bases

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_39980.1	4
6	IL_09530.1	4	Double S-turn motif
7	IL_15768.1	4	cWW AG or UU \| cWH basepair with syn base
8	IL_31663.1	4	23S H73 ILa : Part of larger Motif
9	IL_06180.1	3	tHS tHH bulge with S-turn
10	IL_06211.1	3
11	IL_87065.1	3	23S H91 IL \| Single-Base Intercalation Site
12	IL_35994.1	2	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
13	IL_87507.1	2	tHS tHH bulge with S-turn
14	IL_21639.1	2
15	IL_39355.1	2	SSU Helix 12 (h12) IL \| LSU Eukaryal Helix 96 (H96) IL1
16	IL_67887.1	2
17	IL_90735.1	2
18	IL_30381.1	2	tHS tHH bulge with S-turn
19	IL_46034.1	2
20	IL_12685.1	2	cWW AG or UU \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
21	IL_96206.1	2
22	IL_97509.1	2	Double sheared with wobble cWW.
23	IL_35595.1	2	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
24	IL_06177.1	1	cWW AG or UU
25	IL_20530.1	1
26	IL_54470.1	1	tHS tHH bulge with S-turn
27	IL_21077.1	1
28	IL_57364.1	1	LSU Helix 89 (H89) IL2
29	IL_87523.1	1
30	IL_59018.1	1
31	IL_88119.1	1
32	IL_06421.1	1	Single sheared with bulged bases
33	IL_68767.1	1
34	IL_96182.1	1	cWH basepair with syn base
35	IL_31224.1	1	23S H91 IL
36	IL_49527.1	1
37	IL_69799.1	1
38	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.
39	IL_49976.1	1
40	IL_18675.1	1	cWW-bulge-cWW
41	IL_50911.1	1	16S h34 ILa : Part of larger motif
42	IL_99438.1	1