Motif Atlas Releases 0.6 and 0.7
Changes in PDB files used for clustering
Release 0.6 has 185 PDB files, release 0.7 has 191 PDB files, 180 of them are identical.
1 equivalence classes changed representatives: 3UXR → 3V2F.
10 new structures in release 0.7: 3SYW, 3SZX, 3TZR, 3U4M, 3V7E, 4AOB, 4E48, 4E5C, 4ERD, 4EYA.
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
Changes in motif groups
Release 0.6 has 260 motif groups, release 0.7 has 263 motif groups, 142 of them are identical.
59 motif groups were updated, 59 groups are present only in release 0.6, 62 groups are only in release 0.7.
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_92484.1 | 5 | |
2 | IL_01239.1 | 5 | |
3 | IL_82188.1 | 5 | LSU H68 IL from H.m. |
4 | IL_22732.1 | 4 | tSH-inserted-tHS |
5 | IL_31066.2 | 4 | SSU Helix 44 (h44) extension |
6 | IL_28572.1 | 4 | 16S h18 kink-turn like motif |
7 | IL_79955.2 | 3 | SSU Helix (23) h23 IL1 |
8 | IL_82563.1 | 3 | Thi-box riboswitch T-loop |
9 | IL_15840.1 | 3 | |
10 | IL_52173.1 | 3 | |
11 | IL_30840.1 | 3 | |
12 | IL_62499.2 | 3 | |
13 | IL_98421.1 | 3 | |
14 | IL_89028.1 | 3 | Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena |
15 | IL_95150.2 | 3 | |
16 | IL_95652.2 | 3 | SSU Helix 27 (h27) IL Sarcin-Ricin motif |
17 | IL_34363.1 | 3 | Kink-turn from 23S H42 |
18 | IL_37053.1 | 3 | Kink-turn from 23S H58 |
19 | IL_25271.1 | 2 | SSU Helix 8 (h8) IL E.c. and Yeast |
20 | IL_37197.1 | 2 | |
21 | IL_50521.1 | 2 | |
22 | IL_87173.1 | 2 | |
23 | IL_97833.1 | 2 | |
24 | IL_80093.1 | 2 | |
25 | IL_92459.1 | 2 | |
26 | IL_16166.1 | 2 | |
27 | IL_23414.1 | 2 | |
28 | IL_74876.1 | 2 | |
29 | IL_09882.1 | 2 | |
30 | IL_16330.1 | 2 | |
31 | IL_55287.1 | 2 | |
32 | IL_94744.1 | 2 | Sarcin-ricin motif with extra cWW GA pair |
33 | IL_98566.1 | 2 | |
34 | IL_45794.1 | 2 | |
35 | IL_52940.1 | 2 | |
36 | IL_90057.1 | 2 | |
37 | IL_12211.1 | 2 | |
38 | IL_81441.1 | 2 | |
39 | IL_25174.1 | 2 | |
40 | IL_46435.1 | 2 | |
41 | IL_78744.1 | 2 | Quadruple Sheared (tSH-tSH-tHS-tHS) |
42 | IL_28942.1 | 2 | |
43 | IL_40892.1 | 2 | |
44 | IL_70280.1 | 2 | Double sheared with wobble cWW. |
45 | IL_02835.1 | 1 | |
46 | IL_06808.1 | 1 | Double sheared (tSH-tSH) one bulged base. |
47 | IL_15205.1 | 1 | |
48 | IL_29949.1 | 1 | |
49 | IL_41009.1 | 1 | |
50 | IL_54450.1 | 1 | |
51 | IL_61730.1 | 1 | |
52 | IL_71685.1 | 1 | Sarcin-like with an intercalated basepair |
53 | IL_92280.1 | 1 | |
54 | IL_02957.1 | 1 | |
55 | IL_07375.1 | 1 | |
56 | IL_22858.1 | 1 | |
57 | IL_25307.1 | 1 | |
58 | IL_30390.1 | 1 | |
59 | IL_37347.1 | 1 | |
60 | IL_41139.1 | 1 | |
61 | IL_54576.1 | 1 | |
62 | IL_62352.1 | 1 | |
63 | IL_71942.1 | 1 | |
64 | IL_82650.1 | 1 | |
65 | IL_88367.1 | 1 | |
66 | IL_97842.1 | 1 | |
67 | IL_03110.1 | 1 | |
68 | IL_09333.1 | 1 | SSU Helix 8 (h8) IL T. thermophilus |
69 | IL_25739.1 | 1 | M-Box Riboswitch |
70 | IL_37715.1 | 1 | |
71 | IL_41791.1 | 1 | |
72 | IL_52509.1 | 1 | |
73 | IL_54954.1 | 1 | Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11. |
74 | IL_80505.1 | 1 | |
75 | IL_83250.1 | 1 | 16S h40 3WJ T.th. |
76 | IL_88403.1 | 1 | |
77 | IL_03741.1 | 1 | |
78 | IL_23639.1 | 1 | tWH-tHS-L-cWW |
79 | IL_26241.1 | 1 | |
80 | IL_37990.1 | 1 | |
81 | IL_43316.1 | 1 | |
82 | IL_52752.1 | 1 | |
83 | IL_63952.1 | 1 | |
84 | IL_75415.1 | 1 | Pseudo-knot forming internal loop |
85 | IL_80652.1 | 1 | |
86 | IL_83920.1 | 1 | |
87 | IL_05221.1 | 1 | |
88 | IL_11302.1 | 1 | |
89 | IL_17682.1 | 1 | Sarcin-ricin motif from Eukaryal LSU Helix 11 |
90 | IL_24143.1 | 1 | Yeast 18S |
91 | IL_26868.1 | 1 | |
92 | IL_31754.1 | 1 | Sarcin-ricin H95 23S rRNA E.c. |
93 | IL_39324.1 | 1 | |
94 | IL_55649.1 | 1 | |
95 | IL_65788.1 | 1 | |
96 | IL_75688.1 | 1 | Part of Helix 71 (H71) junction in 23S of D.r. |
97 | IL_81398.1 | 1 | |
98 | IL_85510.1 | 1 | |
99 | IL_98655.1 | 1 | Part of H71 Junction in 26S rRNA from Yeast |
100 | IL_05462.1 | 1 | |
101 | IL_20775.1 | 1 | tSH-inserted |
102 | IL_25082.1 | 1 | |
103 | IL_26971.1 | 1 | |
104 | IL_32080.1 | 1 | |
105 | IL_40527.1 | 1 | Kink-turn |
106 | IL_46306.1 | 1 | |
107 | IL_52958.1 | 1 | |
108 | IL_55934.1 | 1 | kink-turn-like |
109 | IL_66744.1 | 1 | SSU Helix 21 (h21) IL2 E.coli |
110 | IL_76486.1 | 1 | Sarcin-ricin motif with syn G |
111 | IL_85805.1 | 1 | |
112 | IL_91078.1 | 1 | |
113 | IL_98924.1 | 1 | |
114 | IL_06306.1 | 1 | |
115 | IL_12233.1 | 1 | |
116 | IL_21254.1 | 1 | SSU Helix 11 (h11) IL Kink-turn T. thermophilus |
117 | IL_40845.1 | 1 | |
118 | IL_53323.1 | 1 | |
119 | IL_59529.1 | 1 | |
120 | IL_67735.1 | 1 | |
121 | IL_82113.1 | 1 | |
122 | IL_86059.1 | 1 | |
123 | IL_91089.1 | 1 | |
124 | IL_96260.1 | 1 | |
125 | IL_02690.1 | 1 | |
126 | IL_06468.1 | 1 | 16S h40 3WJ E.c. |
127 | IL_12486.1 | 1 | |
128 | IL_22579.1 | 1 | |
129 | IL_25181.1 | 1 | |
130 | IL_47687.1 | 1 | |
131 | IL_53988.1 | 1 | |
132 | IL_61723.1 | 1 | |
133 | IL_78809.1 | 1 | |
134 | IL_86981.1 | 1 | Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18. |
135 | IL_91904.1 | 1 | |
136 | IL_97073.1 | 1 |
Updated motif groups
# | Motif id | Instances | Description |
---|---|---|---|
1 | IL_97217.2 | 234 | |
2 | IL_47174.2 | 200 | 16S h34 ILa : Part of larger motif |
3 | IL_39199.2 | 55 | Hoogsteen-edge Platform, Single bulged base |
4 | IL_41766.2 | 49 | Tandem cWW pairs (Not AU or GC) |
5 | IL_56465.2 | 45 | Single, unpaired intercalated base, consensus A |
6 | IL_44540.2 | 43 | Sugar-edge, 1-base platform, consensus tHS |
7 | IL_87904.2 | 31 | Triple sheared |
8 | IL_13959.2 | 24 | Double Sheared (tSH-tHS) |
9 | IL_93424.2 | 22 | tSH-inserted-tHW |
10 | IL_32390.2 | 21 | 16S h19 IL and 23S H41 IL |
11 | IL_65553.2 | 21 | Kink-turn |
12 | IL_55938.2 | 19 | LSU Helix 89 (H89) IL2. cSH Platform. |
13 | IL_92027.2 | 17 | 16S h21 S8 binding site |
14 | IL_85647.2 | 16 | Sarcin-ricin parent motif with 15 Nts |
15 | IL_31555.2 | 15 | 16S decoding site |
16 | IL_24982.3 | 15 | SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif |
17 | IL_49493.2 | 14 | Sarcin-ricin Parent Motif - bacterial LSU H95 IL |
18 | IL_94430.2 | 14 | 16S h32-h33-h34 3WJ |
19 | IL_27618.2 | 11 | 23S H73 ILa : Part of larger Motif |
20 | IL_40090.2 | 11 | 16S h34 ILa : Part of larger motif |
21 | IL_24546.2 | 10 | 23S H41 IL and 16S h18 IL : Has large bulge on one side |
22 | IL_47444.2 | 9 | SRP Loop E-like motif |
23 | IL_92114.2 | 9 | GAAA loop receptor "platform" motif |
24 | IL_58291.2 | 9 | Recurrent Sub-motif found in junctions |
25 | IL_90459.2 | 8 | cWW AG or UU |
26 | IL_92321.2 | 8 | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif |
27 | IL_83451.2 | 7 | cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1. |
28 | IL_73000.2 | 7 | cHS-cWS |
29 | IL_86357.2 | 7 | LSU Helix 61 IL2 |
30 | IL_13069.2 | 6 | LSU 3WJ H32-H33-H35A |
31 | IL_53635.2 | 6 | LSU Helix 32 (H32) IL |
32 | IL_70237.3 | 6 | |
33 | IL_24022.2 | 6 | |
34 | IL_44067.2 | 6 | Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2). |
35 | IL_72158.2 | 6 | LSU Helix 62 (H62) IL |
36 | IL_97057.2 | 6 | |
37 | IL_25230.2 | 6 | Bacterial 5S rRNA Loop E |
38 | IL_79083.2 | 5 | |
39 | IL_40387.2 | 5 | |
40 | IL_80179.2 | 5 | |
41 | IL_02359.2 | 5 | |
42 | IL_45262.2 | 5 | |
43 | IL_78732.3 | 5 | Double S-turn motif |
44 | IL_62661.2 | 4 | Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4. |
45 | IL_98591.2 | 4 | |
46 | IL_64184.2 | 4 | |
47 | IL_38807.2 | 4 | |
48 | IL_39526.2 | 4 | |
49 | IL_16252.2 | 3 | 23S H91 IL |
50 | IL_80494.2 | 3 | LSU H58 IL2 H.m. |
51 | IL_23262.3 | 3 | |
52 | IL_34156.2 | 3 | cWW AG or UU |
53 | IL_34628.2 | 3 | Kink-turn |
54 | IL_09348.2 | 3 | |
55 | IL_58586.2 | 3 | |
56 | IL_41397.2 | 2 | LSU Helix 96 (H96) IL2 |
57 | IL_82831.2 | 2 | Kink-turn from 16S H23 |
58 | IL_57785.5 | 2 | SSU Decoding Site -- Human. Bulge-cSW-tHS |
59 | IL_76095.3 | 2 | Motif from Hairpin Ribozyme |
Removed motif groups
Added motif groups
# | Motif id | Instances | Description |
---|---|---|---|
1 | IL_06390.1 | 25 | cWH basepair with syn base |
2 | IL_73276.1 | 20 | C-loop |
3 | IL_06429.1 | 16 | 16S h19 IL and 23S H41 IL | 1 or 2 bulged bases |
4 | IL_21304.1 | 11 | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) |
5 | IL_46648.1 | 11 | 23S H91 IL | Single-Base Intercalation Site |
6 | IL_02809.1 | 8 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
7 | IL_89088.1 | 6 | 16S h19 IL and 23S H41 IL |
8 | IL_08926.1 | 6 | 23S H91 IL |
9 | IL_10007.1 | 6 | Single sheared with bulged bases |
10 | IL_71288.1 | 5 | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. |
11 | IL_07911.1 | 5 | |
12 | IL_77263.1 | 5 | Kink-turn from U4 |
13 | IL_21333.1 | 4 | tSH-tHW-bulge |
14 | IL_47758.1 | 4 | REV element IL with syn G | Tandem cWW pairs (Not AU or GC) |
15 | IL_98556.1 | 4 | |
16 | IL_53774.1 | 3 | Single sheared with bulged bases |
17 | IL_71565.1 | 3 | |
18 | IL_43946.1 | 3 | |
19 | IL_45808.1 | 3 | |
20 | IL_75447.1 | 3 | |
21 | IL_12068.1 | 2 | |
22 | IL_87548.1 | 2 | |
23 | IL_99575.1 | 2 | |
24 | IL_12269.1 | 2 | |
25 | IL_43933.1 | 2 | |
26 | IL_74291.1 | 2 | |
27 | IL_21495.1 | 2 | |
28 | IL_91026.1 | 2 | |
29 | IL_14023.1 | 2 | |
30 | IL_00998.1 | 2 | |
31 | IL_16415.1 | 2 | SSU Helix 23 (h23) Kink-turn T. thermophilus |
32 | IL_31707.1 | 2 | Vitamin B12 aptamer |
33 | IL_78674.1 | 2 | tHS tHH bulge with S-turn |
34 | IL_01054.1 | 2 | |
35 | IL_37406.1 | 2 | |
36 | IL_48285.1 | 2 | Leadzyme Motif |
37 | IL_65137.1 | 2 | Kink-turn like motif in Group I Intron |
38 | IL_18755.1 | 1 | |
39 | IL_41849.1 | 1 | |
40 | IL_53423.1 | 1 | |
41 | IL_12507.1 | 1 | |
42 | IL_56513.1 | 1 | |
43 | IL_89794.1 | 1 | |
44 | IL_07675.1 | 1 | tHS tHH bulge with S-turn |
45 | IL_13682.1 | 1 | |
46 | IL_21421.1 | 1 | |
47 | IL_56779.1 | 1 | |
48 | IL_90880.1 | 1 | |
49 | IL_13942.1 | 1 | |
50 | IL_57977.1 | 1 | |
51 | IL_31241.1 | 1 | |
52 | IL_47457.1 | 1 | |
53 | IL_58454.1 | 1 | |
54 | IL_95939.1 | 1 | |
55 | IL_60643.1 | 1 | |
56 | IL_97191.1 | 1 | Sarcin-ricin motif with cWW UU instead of tSH basepair. |
57 | IL_11869.1 | 1 | |
58 | IL_17603.1 | 1 | |
59 | IL_82601.1 | 1 | Tandem cWW water-inserted CU pairs |