Changes in PDB files used for clustering

Release 1.13 has 220 PDB files, release 1.14 has 223 PDB files, 219 of them are identical.

1 equivalence classes changed representatives: 3V2F4NVV.

3 new structures in release 1.14: 1VW3, 4KR6, 4KR7.

Obsolete: 3V2F4V8I.

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 1.13 has 278 motif groups, release 1.14 has 282 motif groups, 172 of them are identical.

53 motif groups were updated, 53 groups are present only in release 1.13, 57 groups are only in release 1.14.

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 idInstancesDescription
1IL_02809.39REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
2IL_47444.39SRP Loop E-like motif
3IL_92114.39GAAA loop receptor "platform" motif
4IL_92321.47Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
5IL_73000.27cHS-cWS
6IL_77263.26Kink-turn from U4
7IL_01080.14
8IL_39526.44
9IL_95652.34SSU Helix 27 (h27) IL Sarcin-Ricin motif
10IL_22732.14tSH-inserted-tHS
11IL_82188.24LSU H68 IL from H.m.
12IL_47758.24REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
13IL_31663.1423S H73 ILa : Part of larger Motif
14IL_48918.34Kink-turn variant
15IL_34363.24Kink-turn from 23S H42
16IL_28572.2416S h18 kink-turn like motif
17IL_42251.14
18IL_31066.34SSU Helix 44 (h44) extension
19IL_39980.14
20IL_37053.13Kink-turn from 23S H58
21IL_43946.13
22IL_80348.3323S H91 IL
23IL_34628.23Kink-turn
24IL_06180.13tHS tHH bulge with S-turn
25IL_52173.13
26IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
27IL_30840.23
28IL_25271.23SSU Helix 8 (h8) IL E.c. and Yeast
29IL_07300.23
30IL_06211.33
31IL_79955.23SSU Helix (23) h23 IL1
32IL_82563.13Thi-box riboswitch T-loop
33IL_11751.12
34IL_76095.32Motif from Hairpin Ribozyme
35IL_94744.12Sarcin-ricin motif with extra cWW GA pair
36IL_90735.12
37IL_21495.12
38IL_96446.12
39IL_70401.12
40IL_65137.12Kink-turn like motif in Group I Intron
41IL_77076.12
42IL_33842.12
43IL_50521.12
44IL_90057.12
45IL_30381.12tHS tHH bulge with S-turn
46IL_37197.12
47IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
48IL_87548.12
49IL_09587.12
50IL_21639.12
51IL_45794.12
52IL_52940.12
53IL_09882.12
54IL_98566.12
55IL_46435.12
56IL_31707.12Vitamin B12 aptamer
57IL_12147.12Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
58IL_16330.12
59IL_40892.12
60IL_97833.12
61IL_80093.12
62IL_12211.12
63IL_23414.12
64IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
65IL_03110.11
66IL_06177.11cWW AG or UU
67IL_82650.11
68IL_26868.11
69IL_06421.11Single sheared with bulged bases
70IL_75415.11Pseudo-knot forming internal loop
71IL_37347.11
72IL_06471.11
73IL_91904.11
74IL_85510.11
75IL_49527.11
76IL_57285.11
77IL_27640.11
78IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
79IL_80714.11
80IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
81IL_25307.11
82IL_11302.11
83IL_80652.11
84IL_27243.11
85IL_91078.11
86IL_31224.1123S H91 IL
87IL_05221.11
88IL_26971.11
89IL_09491.11
90IL_88367.11
91IL_23448.11
92IL_40845.11
93IL_39324.11
94IL_02897.11Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th.
95IL_76263.11
96IL_91379.11
97IL_66744.11SSU Helix 21 (h21) IL2 E.coli
98IL_31006.11tSH-tHW-L-bif-cWW
99IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
100IL_61730.11
101IL_86336.11
102IL_25082.11
103IL_53323.11
104IL_59529.11
105IL_02957.11
106IL_40527.11Kink-turn
107IL_91044.11
108IL_27668.11
109IL_85805.11
110IL_41791.11
111IL_68827.11Reverse Kink-Turn
112IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
113IL_89794.11
114IL_52509.11
115IL_88119.11
116IL_98924.11
117IL_41139.11
118IL_06847.11Group II Intron IL
119IL_30067.11
120IL_05513.11
121IL_83250.1116S h40 3WJ T.th.
122IL_88865.11
123IL_86059.11
124IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
125IL_83920.11
126IL_53988.11
127IL_11778.11
128IL_71685.11Sarcin-like with an intercalated basepair
129IL_64589.11
130IL_54470.11tHS tHH bulge with S-turn
131IL_60649.11Kink-turn
132IL_52610.11
133IL_78513.11
134IL_63952.11
135IL_57977.11
136IL_63253.11LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
137IL_06468.1116S h40 3WJ E.c.
138IL_52958.11
139IL_20775.11tSH-inserted
140IL_77014.11
141IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
142IL_23639.11tWH-tHS-L-cWW
143IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
144IL_82601.11Tandem cWW water-inserted CU pairs
145IL_91089.11
146IL_77296.11
147IL_87394.11
148IL_02835.11
149IL_43316.11
150IL_12507.11
151IL_47687.11
152IL_55649.11
153IL_06808.11Double sheared (tSH-tSH) one bulged base.
154IL_75328.11
155IL_06306.11
156IL_76486.11Sarcin-ricin motif with syn G
157IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
158IL_87523.11
159IL_03282.11
160IL_42891.11
161IL_80505.11
162IL_22909.11
163IL_28644.11
164IL_54450.11
165IL_81398.11
166IL_97842.11
167IL_46306.11
168IL_68767.11
169IL_15205.11
170IL_21077.11
171IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
172IL_63133.11Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)

Updated motif groups

#Motif idInstancesDescription
1IL_97217.122621-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_41766.757Tandem cWW pairs (Not AU or GC)
3IL_39199.556Hoogsteen-edge Platform, Single bulged base
4IL_56465.551Single, unpaired intercalated base, consensus A
5IL_44540.545Sugar-edge, 1-base platform, consensus tHS
6IL_87904.632Triple sheared (tSH-tHS-tHS) no inserted bases
7IL_82444.228cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base | 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
8IL_13959.527Double Sheared (tSH-tHS)
9IL_73276.624C-loop
10IL_28947.32423S 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
11IL_65553.923Kink-turn
12IL_93424.522tSH-inserted-tHW
13IL_92027.41916S h21 S8 binding site
14IL_85647.418Sarcin-ricin parent motif with 15 Nts
15IL_55938.517LSU Helix 89 (H89) IL2. cSH Platform.
16IL_24982.616SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
17IL_49493.515Sarcin-ricin Parent Motif - bacterial LSU H95 IL
18IL_94430.61416S h32-h33-h34 3WJ
19IL_46648.71423S H91 IL | Single-Base Intercalation Site
20IL_43124.31323S H73 ILa : Part of larger Motif | Single sheared with bulged bases
21IL_31555.613Tandem sheared with inserted, unpaired purine. | 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.
22IL_37104.413Single sheared with bulged bases | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 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)
23IL_24546.51023S H41 IL and 16S h18 IL : Has large bulge on one side
24IL_58291.510Recurrent Sub-motif found in junctions
25IL_97057.47
26IL_08926.4723S H91 IL
27IL_53635.47LSU Helix 32 (H32) IL
28IL_86357.46LSU Helix 61 IL2
29IL_70237.46
30IL_72158.46LSU Helix 62 (H62) IL
31IL_25230.46Bacterial 5S rRNA Loop E
32IL_13069.46LSU 3WJ H32-H33-H35A
33IL_93568.36Triple Sheared (tSH-tHS-tHS) with wobble cWW.
34IL_02359.45
35IL_44067.55Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
36IL_90133.45
37IL_09530.25Double S-turn motif
38IL_79083.45
39IL_87065.2423S H91 IL | Single-Base Intercalation Site
40IL_16166.5423S H91 IL
41IL_69536.23LSU Helix 96 (H96) IL2
42IL_05723.23
43IL_58586.33
44IL_62499.83
45IL_97509.23Double sheared with wobble cWW.
46IL_98421.53SSU Helix 12 (h12) IL | SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
47IL_67887.23
48IL_69106.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
49IL_94403.63LSU H77
50IL_16415.32SSU Helix 23 (h23) Kink-turn T. thermophilus
51IL_95150.72
52IL_28003.22
53IL_80494.32LSU H58 IL2 H.m.

Removed motif groups

#Motif idInstancesDescription
1IL_47174.11219cWW AG or water inserted cWW Y-Y.
2IL_92109.315cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
3IL_17212.211cWW 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
4IL_90459.39cWW AG or UU
5IL_46301.17Leadzyme 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.
6IL_25300.3716S h19 IL and 23S H41 IL
7IL_70173.16Single 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)
8IL_25380.16LSU Helix 89 (H89) IL2
9IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
10IL_05684.15tHS tHH bulge with S-turn | Double S-turn motif
11IL_21333.24tSH-tHW-bulge
12IL_45262.44
13IL_97296.14Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
14IL_54966.14cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
15IL_98591.34
16IL_38807.34
17IL_47875.13LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
18IL_35043.13cWW AG or UU | cWH basepair with syn base | cWH basepair with syn base
19IL_89028.63Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th.
20IL_31039.12
21IL_00998.12
22IL_33964.12
23IL_43877.12Single 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)
24IL_96206.32
25IL_23262.42
26IL_46034.32
27IL_15840.22Triple Sheared with unpaired, inserted A
28IL_24293.1223S H73 ILa : Part of larger Motif | Single sheared with bulged bases | 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)
29IL_37406.12
30IL_39355.12SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
31IL_46990.12
32IL_87507.12tHS tHH bulge with S-turn
33IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
34IL_18675.11cWW-bulge-cWW
35IL_41153.11
36IL_47732.11
37IL_58454.11
38IL_69799.11
39IL_21421.11
40IL_49976.11
41IL_13777.11cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
42IL_37325.11
43IL_50911.1116S h34 ILa : Part of larger motif
44IL_70299.11
45IL_71942.11
46IL_17066.11
47IL_25181.11
48IL_46721.11
49IL_56513.11
50IL_83856.11
51IL_99397.11cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
52IL_57364.11LSU Helix 89 (H89) IL2
53IL_17603.11

Added motif groups

#Motif idInstancesDescription
1IL_78141.1228cWW AG or UU | cWW AG or water inserted cWW Y-Y. | 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
2IL_37056.1161-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
3IL_67813.115cWW AG or water inserted cWW Y-Y. | 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 | cWH basepair with syn base | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | 16S h34 ILa : Part of larger motif
4IL_71837.18cWW AG or UU | 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) | 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 | 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) | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
5IL_65554.18cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1. | Tandem sheared with inserted, unpaired purine. | 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.
6IL_55214.18Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
7IL_74856.18LSU Helix 89 (H89) IL2
8IL_64847.17Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
9IL_16029.15cWW AG or water inserted cWW Y-Y. | 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)
10IL_59864.15
11IL_82133.15SSU Decoding Site -- Human. Bulge-cSW-tHS | 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.
12IL_71229.15
13IL_04397.15
14IL_46960.1516S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
15IL_48183.15tSH-tHW-bulge
16IL_32261.14LSU Helix 89 (H89) IL2
17IL_08763.14LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL
18IL_55114.14tHS tHH bulge with S-turn | Double S-turn motif
19IL_66654.14Single 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) | 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)
20IL_15123.14Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th.
21IL_56594.14cWW AG or UU
22IL_89252.13
23IL_37171.13LSU H58 IL2 H.m.
24IL_72641.13cWW 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
25IL_95908.13LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
26IL_30534.12
27IL_43545.12Leadzyme 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.
28IL_60613.12
29IL_16977.12
30IL_87064.12tHS tHH bulge with S-turn
31IL_05641.12
32IL_90877.12
33IL_25541.12Triple Sheared with unpaired, inserted A
34IL_39175.12
35IL_92422.12
36IL_12204.12
37IL_92576.12
38IL_67024.12
39IL_96920.11SSU Helix 12 (h12) IL
40IL_03625.11
41IL_16921.11
42IL_45432.11
43IL_86453.1123S H73 ILa : Part of larger Motif | Single sheared with bulged bases | 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)
44IL_99937.11
45IL_03808.11
46IL_36006.11
47IL_46151.11Triple Sheared with unpaired, inserted A
48IL_62296.11
49IL_23302.11
50IL_64213.11SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
51IL_72293.11
52IL_25420.11
53IL_73656.11
54IL_25771.11
55IL_41027.11
56IL_26448.11
57IL_41516.11