Changes in PDB files used for clustering

Release 1.1 has 199 PDB files, release 1.2 has 200 PDB files, 199 of them are identical.

No equivalence class representatives have been replaced.

1 new structures in release 1.2: 4JRC.

No equivalence class representatives have been obsoleted.

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 1.1 has 271 motif groups, release 1.2 has 271 motif groups, 268 of them are identical.

2 motif groups were updated, 1 groups are present only in release 1.1, 1 groups are only in release 1.2.

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_97217.62391-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_47174.6201cWW AG or water inserted cWW Y-Y.
3IL_39199.354Hoogsteen-edge Platform, Single bulged base
4IL_41766.349Tandem cWW pairs (Not AU or GC)
5IL_56465.346Single, unpaired intercalated base, consensus A
6IL_44540.343Sugar-edge, 1-base platform, consensus tHS
7IL_87904.431Triple sheared (tSH-tHS-tHS) no inserted bases
8IL_06390.326cWH basepair with syn base
9IL_13959.324Double Sheared (tSH-tHS)
10IL_65553.522Kink-turn
11IL_93424.322tSH-inserted-tHW
12IL_28947.12123S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
13IL_55938.318LSU Helix 89 (H89) IL2. cSH Platform.
14IL_92027.31716S h21 S8 binding site
15IL_24982.416SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
16IL_85647.316Sarcin-ricin parent motif with 15 Nts
17IL_92109.115cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
18IL_94430.41516S h32-h33-h34 3WJ
19IL_31555.315Tandem sheared with inserted, unpaired purine.
20IL_49493.314Sarcin-ricin Parent Motif - bacterial LSU H95 IL
21IL_21304.211Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
22IL_46648.21123S H91 IL | Single-Base Intercalation Site
23IL_40090.31116S h34 ILa : Part of larger motif
24IL_43124.11123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
25IL_24546.31023S H41 IL and 16S h18 IL : Has large bulge on one side
26IL_02809.29REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
27IL_92114.39GAAA loop receptor "platform" motif
28IL_58291.39Recurrent Sub-motif found in junctions
29IL_90459.39cWW AG or UU
30IL_47444.39SRP Loop E-like motif
31IL_92321.37Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
32IL_73000.27cHS-cWS
33IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
34IL_53635.36LSU Helix 32 (H32) IL
35IL_90133.26
36IL_72158.36LSU Helix 62 (H62) IL
37IL_13069.36LSU 3WJ H32-H33-H35A
38IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
39IL_70237.36
40IL_54420.16
41IL_25230.36Bacterial 5S rRNA Loop E
42IL_44067.36Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
43IL_97057.36
44IL_08926.2523S H91 IL
45IL_77263.15Kink-turn from U4
46IL_02359.35
47IL_92484.15
48IL_78732.35Double S-turn motif
49IL_82188.15LSU H68 IL from H.m.
50IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
51IL_25300.1516S h19 IL and 23S H41 IL
52IL_45262.35
53IL_79083.35
54IL_86357.35LSU Helix 61 IL2
55IL_16207.15Single sheared with bulged bases
56IL_28572.1416S h18 kink-turn like motif
57IL_21333.24tSH-tHW-bulge
58IL_16166.3423S H91 IL
59IL_31066.24SSU Helix 44 (h44) extension
60IL_08559.14LSU Helix 89 (H89) IL2
61IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
62IL_01080.14
63IL_98591.34
64IL_39526.44
65IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
66IL_22732.14tSH-inserted-tHS
67IL_42251.14
68IL_38807.34
69IL_34363.24Kink-turn from 23S H42
70IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
71IL_75447.13
72IL_48918.23Kink-turn variant
73IL_82563.13Thi-box riboswitch T-loop
74IL_10647.13tHS tHH bulge with S-turn
75IL_80348.1323S H91 IL
76IL_52173.13
77IL_58586.23
78IL_30840.13
79IL_98421.33SSU Helix 12 (h12) IL
80IL_05723.13
81IL_95150.33
82IL_80494.23LSU H58 IL2 H.m.
83IL_89028.53Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th.
84IL_34628.23Kink-turn
85IL_79955.23SSU Helix (23) h23 IL1
86IL_37053.13Kink-turn from 23S H58
87IL_92267.1323S H73 ILa : Part of larger Motif
88IL_56077.13
89IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
90IL_34156.63cWW AG or UU
91IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
92IL_62499.63
93IL_43946.13
94IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
95IL_98566.12
96IL_00998.12
97IL_16252.3223S H91 IL
98IL_94744.12Sarcin-ricin motif with extra cWW GA pair
99IL_97833.12
100IL_91273.12
101IL_27892.12
102IL_23414.12
103IL_37197.12
104IL_31707.12Vitamin B12 aptamer
105IL_76095.32Motif from Hairpin Ribozyme
106IL_09587.12
107IL_07300.12
108IL_45794.12
109IL_33964.12
110IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
111IL_80093.12
112IL_46435.12
113IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
114IL_09901.12tHS tHH bulge with S-turn
115IL_24358.12
116IL_16330.12
117IL_50521.12
118IL_21495.12
119IL_37406.12
120IL_69536.12LSU Helix 96 (H96) IL2
121IL_28942.12
122IL_40892.12
123IL_87548.12
124IL_09882.12
125IL_77076.12
126IL_12211.12
127IL_01054.12
128IL_15840.22Triple Sheared with unpaired, inserted A
129IL_23262.42
130IL_49550.12tHS tHH bulge with S-turn
131IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
132IL_52940.12
133IL_90057.12
134IL_33925.12
135IL_70280.12Double sheared with wobble cWW.
136IL_88180.12cWW-bulge-cWW
137IL_11751.12
138IL_65137.12Kink-turn like motif in Group I Intron
139IL_19898.12
140IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
141IL_55287.12
142IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
143IL_76263.11
144IL_04550.11tHS tHH bulge with S-turn
145IL_66744.11SSU Helix 21 (h21) IL2 E.coli
146IL_05462.11
147IL_20775.11tSH-inserted
148IL_13682.11
149IL_31290.11
150IL_13434.11
151IL_71685.11Sarcin-like with an intercalated basepair
152IL_25181.11
153IL_58454.11
154IL_40527.11Kink-turn
155IL_77296.11
156IL_30354.11
157IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
158IL_40845.11
159IL_68827.11Reverse Kink-Turn
160IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
161IL_06808.11Double sheared (tSH-tSH) one bulged base.
162IL_61730.11
163IL_67735.11
164IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
165IL_23639.11tWH-tHS-L-cWW
166IL_64589.11
167IL_41139.11
168IL_03282.11
169IL_46721.11
170IL_02835.11
171IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
172IL_83920.11
173IL_52958.11
174IL_80652.11
175IL_65788.11
176IL_78809.11
177IL_75415.11Pseudo-knot forming internal loop
178IL_76486.11Sarcin-ricin motif with syn G
179IL_37990.11
180IL_82601.11Tandem cWW water-inserted CU pairs
181IL_34868.11LSU Eukaryal Helix 96 (H96) IL1
182IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
183IL_92280.11
184IL_03110.11
185IL_06468.1116S h40 3WJ E.c.
186IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
187IL_97073.11
188IL_03931.1116S h19 IL and 23S H41 IL
189IL_54576.11
190IL_06306.11
191IL_97842.11
192IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
193IL_17603.11
194IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
195IL_91089.11
196IL_30067.11
197IL_85805.11
198IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
199IL_41791.11
200IL_43316.11
201IL_12507.11
202IL_47687.11
203IL_21221.11SSU Helix 12 (h12) IL
204IL_03741.11
205IL_83856.11
206IL_37347.11
207IL_46306.11
208IL_15674.11Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th.
209IL_15205.11
210IL_60643.11
211IL_52610.11
212IL_83250.1116S h40 3WJ T.th.
213IL_57977.11
214IL_39324.11
215IL_80505.11
216IL_55649.11
217IL_52509.11
218IL_02690.11
219IL_91078.11
220IL_81398.11
221IL_05221.11
222IL_06471.11
223IL_91904.11
224IL_56513.11
225IL_91044.11
226IL_87394.11
227IL_63952.11
228IL_86059.11
229IL_82650.11
230IL_26868.11
231IL_89794.11
232IL_95774.11tHS tHH bulge with S-turn
233IL_12486.11
234IL_71942.11
235IL_82113.11
236IL_53323.11
237IL_26971.11
238IL_09491.11
239IL_21421.11
240IL_85510.11
241IL_06847.11Group II Intron IL
242IL_42891.11
243IL_25307.11
244IL_11302.11
245IL_53988.11
246IL_28644.11
247IL_11778.11
248IL_37715.11
249IL_54450.11
250IL_41341.11Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
251IL_25082.11
252IL_98924.11
253IL_59529.11
254IL_02957.11
255IL_28468.11Single sheared with bulged bases
256IL_88367.11
257IL_60649.11Kink-turn
258IL_47732.11

Updated motif groups

#Motif idInstancesDescription
1IL_73276.321C-loop
2IL_71565.33

Removed motif groups

#Motif idInstancesDescription
1IL_89231.12LSU H77

Added motif groups

#Motif idInstancesDescription
1IL_94403.14LSU H77