1.0 | 1.10

Changes in PDB files used for clustering

Release 1.0 has 200 PDB files, release 1.10 has 214 PDB files, 196 of them are identical.

4 equivalence classes changed representatives: 3ZD3 → 3ZP8, 2XZM → 4BPP, 2ZJR → 4IOA, 3NPB → 4KQY.

14 new structures in release 1.10: 3WBM, 4BW0, 4C7O, 4JRC, 4K27, 4K31, 4KYY, 4L8H, 4LCK, 4LGT, 4M30, 4M4O, 4M6D, 4MGN.

Obsolete: 2XZM → 4V5O, 3NPB → 4KQY, 3ZD3 → 3ZP8.

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 1.0 has 267 motif groups, release 1.10 has 275 motif groups, 148 of them are identical.

56 motif groups were updated, 63 groups are present only in release 1.0, 71 groups are only in release 1.10.

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_47444.3	9	SRP Loop E-like motif
2	IL_92114.3	9	GAAA loop receptor "platform" motif
3	IL_73000.2	7	cHS-cWS
4	IL_70237.3	6
5	IL_22732.1	4	tSH-inserted-tHS
6	IL_39526.4	4
7	IL_58586.2	3
8	IL_43946.1	3
9	IL_89028.4	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.
10	IL_80494.2	3	LSU H58 IL2 H.m.
11	IL_62499.5	3
12	IL_37053.1	3	Kink-turn from 23S H58
13	IL_34628.2	3	Kink-turn
14	IL_74876.2	3	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
15	IL_79955.2	3	SSU Helix (23) h23 IL1
16	IL_05723.1	3
17	IL_16166.2	3
18	IL_82563.1	3	Thi-box riboswitch T-loop
19	IL_52173.1	3
20	IL_09882.1	2
21	IL_21495.1	2
22	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
23	IL_23414.1	2
24	IL_79870.1	2	tHS tHH bulge with S-turn
25	IL_97833.1	2
26	IL_80093.1	2
27	IL_37197.1	2
28	IL_50521.1	2
29	IL_52940.1	2
30	IL_76095.3	2	Motif from Hairpin Ribozyme
31	IL_64648.1	2	tHS tHH bulge with S-turn
32	IL_16377.1	2
33	IL_45794.1	2
34	IL_87548.1	2
35	IL_16330.1	2
36	IL_77076.1	2
37	IL_46435.1	2
38	IL_15840.2	2	Triple Sheared with unpaired, inserted A
39	IL_00998.1	2
40	IL_40892.1	2
41	IL_65137.1	2	Kink-turn like motif in Group I Intron
42	IL_90057.1	2
43	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
44	IL_87336.1	2	LSU Eukaryal Helix 96 (H96) IL1
45	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
46	IL_11751.1	2
47	IL_37406.1	2
48	IL_31707.1	2	Vitamin B12 aptamer
49	IL_98566.1	2
50	IL_12211.1	2
51	IL_96446.1	2
52	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
53	IL_85805.1	1
54	IL_02835.1	1
55	IL_25307.1	1
56	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
57	IL_25082.1	1
58	IL_98924.1	1
59	IL_25181.1	1
60	IL_15205.1	1
61	IL_91044.1	1
62	IL_27668.1	1
63	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
64	IL_83250.1	1	16S h40 3WJ T.th.
65	IL_57977.1	1
66	IL_76263.1	1
67	IL_91379.1	1
68	IL_59934.1	1	SSU Helix 23 (h23) Kink-turn E. coli
69	IL_31006.1	1	tSH-tHW-L-bif-cWW
70	IL_80652.1	1
71	IL_27243.1	1
72	IL_75415.1	1	Pseudo-knot forming internal loop
73	IL_77195.1	1
74	IL_71685.1	1	Sarcin-like with an intercalated basepair
75	IL_17603.1	1
76	IL_85510.1	1
77	IL_06847.1	1	Group II Intron IL
78	IL_03110.1	1
79	IL_68827.1	1	Reverse Kink-Turn
80	IL_06468.1	1	16S h40 3WJ E.c.
81	IL_89794.1	1
82	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
83	IL_61730.1	1
84	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
85	IL_23639.1	1	tWH-tHS-L-cWW
86	IL_56513.1	1
87	IL_88367.1	1
88	IL_60649.1	1	Kink-turn
89	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
90	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
91	IL_83920.1	1
92	IL_47687.1	1
93	IL_53988.1	1
94	IL_52509.1	1
95	IL_03741.1	1
96	IL_76486.1	1	Sarcin-ricin motif with syn G
97	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
98	IL_21421.1	1
99	IL_40527.1	1	Kink-turn
100	IL_77296.1	1
101	IL_63952.1	1
102	IL_39324.1	1
103	IL_82519.1	1	Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena
104	IL_11778.1	1
105	IL_91078.1	1
106	IL_97842.1	1
107	IL_46306.1	1
108	IL_58454.1	1
109	IL_41139.1	1
110	IL_03282.1	1
111	IL_86059.1	1
112	IL_12507.1	1
113	IL_61991.1	1
114	IL_52958.1	1
115	IL_20775.1	1	tSH-inserted
116	IL_77014.1	1
117	IL_06306.1	1
118	IL_37347.1	1
119	IL_06471.1	1
120	IL_18755.1	1
121	IL_63837.1	1	tHS tHH bulge with S-turn
122	IL_94973.1	1	Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
123	IL_41791.1	1
124	IL_43316.1	1
125	IL_80505.1	1
126	IL_26868.1	1
127	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
128	IL_71942.1	1
129	IL_83856.1	1
130	IL_05221.1	1
131	IL_26971.1	1
132	IL_91904.1	1
133	IL_82601.1	1	Tandem cWW water-inserted CU pairs
134	IL_91089.1	1
135	IL_57285.1	1
136	IL_40845.1	1
137	IL_88865.1	1
138	IL_82650.1	1
139	IL_11302.1	1
140	IL_55649.1	1
141	IL_54450.1	1
142	IL_75328.1	1
143	IL_81398.1	1
144	IL_53323.1	1
145	IL_59529.1	1
146	IL_02957.1	1
147	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
148	IL_23448.1	1

Updated motif groups

#	Motif id	Instances	Description
1	IL_92027.3	17	16S h21 S8 binding site
2	IL_85647.3	16	Sarcin-ricin parent motif with 15 Nts
3	IL_90459.3	9	cWW AG or UU
4	IL_02809.3	9	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
5	IL_77263.2	6	Kink-turn from U4
6	IL_25300.2	6	16S h19 IL and 23S H41 IL
7	IL_72158.3	6	LSU Helix 62 (H62) IL
8	IL_97057.3	6
9	IL_53635.3	6	LSU Helix 32 (H32) IL
10	IL_13069.3	6	LSU 3WJ H32-H33-H35A
11	IL_25230.3	6	Bacterial 5S rRNA Loop E
12	IL_02359.3	5
13	IL_86357.3	5	LSU Helix 61 IL2
14	IL_79083.3	5
15	IL_28572.2	4	16S h18 kink-turn like motif
16	IL_21333.2	4	tSH-tHW-bulge
17	IL_98591.3	4
18	IL_82188.2	4	LSU H68 IL from H.m.
19	IL_93568.2	4	Triple Sheared (tSH-tHS-tHS) with wobble cWW.
20	IL_95652.3	4	SSU Helix 27 (h27) IL Sarcin-Ricin motif
21	IL_38807.3	4
22	IL_47758.2	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
23	IL_31066.3	4	SSU Helix 44 (h44) extension
24	IL_34363.2	4	Kink-turn from 23S H42
25	IL_30840.2	3
26	IL_07300.2	3
27	IL_16415.2	3	SSU Helix 23 (h23) Kink-turn T. thermophilus
28	IL_25271.2	3	SSU Helix 8 (h8) IL E.c. and Yeast
29	IL_23262.4	2

Removed motif groups

#	Motif id	Instances	Description
1	IL_06390.2	26	cWH basepair with syn base
2	IL_91487.1	21	16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
3	IL_21304.1	11	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
4	IL_46648.1	11	23S H91 IL \| Single-Base Intercalation Site
5	IL_27618.2	11	23S H73 ILa : Part of larger Motif
6	IL_40090.2	11	16S h34 ILa : Part of larger motif
7	IL_10007.2	7	Single sheared with bulged bases
8	IL_83451.2	7	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
9	IL_38960.1	6	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
10	IL_54420.1	6
11	IL_45262.2	5
12	IL_78732.3	5	Double S-turn motif
13	IL_01239.1	5
14	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
15	IL_92484.1	5
16	IL_98556.4	4
17	IL_40387.4	4	LSU Helix 89 (H89) IL2
18	IL_71565.2	4
19	IL_87218.1	4	23S H91 IL
20	IL_75447.1	3
21	IL_36254.1	3
22	IL_57216.1	3	tHS tHH bulge with S-turn
23	IL_09348.4	3	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
24	IL_48918.1	3	Kink-turn variant
25	IL_53774.1	3	Single sheared with bulged bases
26	IL_16252.3	2	23S H91 IL
27	IL_34156.5	2	cWW AG or UU
28	IL_89231.1	2	LSU H77
29	IL_01054.1	2
30	IL_09520.1	2	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
31	IL_25174.1	2
32	IL_91132.1	2
33	IL_81441.1	2
34	IL_27892.1	2
35	IL_70280.1	2	Double sheared with wobble cWW.
36	IL_28942.1	2
37	IL_41397.2	2	LSU Helix 96 (H96) IL2
38	IL_55287.1	2
39	IL_05462.1	1
40	IL_44803.1	1
41	IL_55934.1	1	kink-turn-like
42	IL_88403.1	1
43	IL_75688.1	1	Part of Helix 71 (H71) junction in 23S of D.r.
44	IL_98688.1	1
45	IL_22579.1	1
46	IL_37715.1	1
47	IL_60643.1	1
48	IL_90880.1	1
49	IL_37990.1	1
50	IL_65788.1	1
51	IL_78809.1	1
52	IL_67735.1	1
53	IL_02690.1	1
54	IL_11869.1	1
55	IL_82113.1	1
56	IL_92280.1	1
57	IL_03914.1	1
58	IL_12486.1	1
59	IL_54576.1	1
60	IL_03931.1	1	16S h19 IL and 23S H41 IL
61	IL_13682.1	1
62	IL_31241.1	1
63	IL_97073.1	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_28947.2	22	23S H91 IL \| cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW \| LSU H77 \| cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
3	IL_46648.6	13	23S H91 IL \| Single-Base Intercalation Site
4	IL_43124.2	11	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
5	IL_37104.2	11	Single sheared with bulged bases \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
6	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
7	IL_46301.1	7	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW \| Leadzyme Motif. LSU H101 IL2. SSU Decoding site. \| Tandem sheared with inserted, unpaired purine. \| cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
8	IL_39585.1	6	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
9	IL_25380.1	6	LSU Helix 89 (H89) IL2
10	IL_70173.1	6	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)
11	IL_05684.1	5	tHS tHH bulge with S-turn \| Double S-turn motif
12	IL_01080.1	4
13	IL_42251.1	4
14	IL_54966.1	4	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
15	IL_94403.5	4	LSU H77
16	IL_48918.3	4	Kink-turn variant
17	IL_45262.4	4
18	IL_97296.1	4	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW \| Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
19	IL_39980.1	4
20	IL_09530.1	4	Double S-turn motif
21	IL_31663.1	4	23S H73 ILa : Part of larger Motif
22	IL_28003.1	3
23	IL_35043.1	3	cWW AG or UU \| cWH basepair with syn base \| cWH basepair with syn base
24	IL_06211.2	3
25	IL_87065.1	3	23S H91 IL \| Single-Base Intercalation Site
26	IL_46034.2	3
27	IL_09587.1	2
28	IL_33842.1	2
29	IL_74214.1	2	cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
30	IL_33964.1	2
31	IL_47475.1	2	LSU H77 \| cWW-bulge-cWW \| 16S h19 IL and 23S H41 IL \| cWW-bulge-cWW
32	IL_80348.2	2	23S H91 IL
33	IL_95884.1	2
34	IL_21639.1	2
35	IL_43877.1	2	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) \| cWW AG or UU \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
36	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)
37	IL_22358.1	2
38	IL_69106.1	2	Leadzyme Motif. SSU Decoding site motif, extended. \| cWW-L-cWW-cWW
39	IL_69536.1	2	LSU Helix 96 (H96) IL2
40	IL_97509.1	2	Double sheared with wobble cWW.
41	IL_31473.1	2
42	IL_70401.1	2
43	IL_90735.1	2
44	IL_46721.1	1
45	IL_91956.1	1
46	IL_05513.1	1
47	IL_28644.1	1
48	IL_42891.1	1
49	IL_57364.1	1	LSU Helix 89 (H89) IL2
50	IL_21077.1	1
51	IL_34076.1	1
52	IL_47732.1	1
53	IL_64589.1	1
54	IL_06177.1	1	cWW AG or UU
55	IL_30067.1	1
56	IL_68767.1	1
57	IL_95980.1	1	23S H73 ILa : Part of larger Motif \| Single sheared with bulged bases
58	IL_30354.1	1
59	IL_49527.1	1
60	IL_06421.1	1	Single sheared with bulged bases
61	IL_22909.1	1
62	IL_31224.1	1	23S H91 IL
63	IL_49976.1	1
64	IL_87394.1	1
65	IL_09491.1	1
66	IL_50911.1	1	16S h34 ILa : Part of larger motif
67	IL_87523.1	1
68	IL_99397.1	1	cWW AG or UU \| Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
69	IL_27503.1	1
70	IL_41153.1	1
71	IL_52610.1	1