Changes in PDB files used for clustering

Release 0.7 has 191 PDB files, release 0.8 has 191 PDB files, 191 of them are identical.

No equivalence class representatives have been replaced.

No new PDB files have been added.

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

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Changes in motif groups

Release 0.7 has 263 motif groups, release 0.8 has 263 motif groups, 263 of them are identical.

0 motif groups were updated, 0 groups are present only in release 0.7, 0 groups are only in release 0.8.

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_97217.2234
2IL_47174.220016S h34 ILa : Part of larger motif
3IL_39199.255Hoogsteen-edge Platform, Single bulged base
4IL_41766.249Tandem cWW pairs (Not AU or GC)
5IL_56465.245Single, unpaired intercalated base, consensus A
6IL_44540.243Sugar-edge, 1-base platform, consensus tHS
7IL_87904.231Triple sheared
8IL_06390.125cWH basepair with syn base
9IL_13959.224Double Sheared (tSH-tHS)
10IL_93424.222tSH-inserted-tHW
11IL_32390.22116S h19 IL and 23S H41 IL
12IL_65553.221Kink-turn
13IL_73276.120C-loop
14IL_55938.219LSU Helix 89 (H89) IL2. cSH Platform.
15IL_92027.21716S h21 S8 binding site
16IL_85647.216Sarcin-ricin parent motif with 15 Nts
17IL_06429.11616S h19 IL and 23S H41 IL | 1 or 2 bulged bases
18IL_31555.21516S decoding site
19IL_24982.315SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
20IL_49493.214Sarcin-ricin Parent Motif - bacterial LSU H95 IL
21IL_94430.21416S h32-h33-h34 3WJ
22IL_21304.111Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
23IL_46648.11123S H91 IL | Single-Base Intercalation Site
24IL_40090.21116S h34 ILa : Part of larger motif
25IL_27618.21123S H73 ILa : Part of larger Motif
26IL_24546.21023S H41 IL and 16S h18 IL : Has large bulge on one side
27IL_47444.29SRP Loop E-like motif
28IL_92114.29GAAA loop receptor "platform" motif
29IL_58291.29Recurrent Sub-motif found in junctions
30IL_92321.28Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
31IL_90459.28cWW AG or UU
32IL_02809.18REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
33IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
34IL_86357.27LSU Helix 61 IL2
35IL_73000.27cHS-cWS
36IL_24022.26
37IL_25230.26Bacterial 5S rRNA Loop E
38IL_89088.1616S h19 IL and 23S H41 IL
39IL_10007.16Single sheared with bulged bases
40IL_44067.26Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
41IL_08926.1623S H91 IL
42IL_97057.26
43IL_72158.26LSU Helix 62 (H62) IL
44IL_53635.26LSU Helix 32 (H32) IL
45IL_70237.36
46IL_13069.26LSU 3WJ H32-H33-H35A
47IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
48IL_79083.25
49IL_45262.25
50IL_07911.15
51IL_78732.35Double S-turn motif
52IL_02359.25
53IL_77263.15Kink-turn from U4
54IL_80179.25
55IL_01239.15
56IL_92484.15
57IL_82188.15LSU H68 IL from H.m.
58IL_40387.25
59IL_64184.24
60IL_22732.14tSH-inserted-tHS
61IL_98556.14
62IL_21333.14tSH-tHW-bulge
63IL_38807.24
64IL_62661.24Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
65IL_28572.1416S h18 kink-turn like motif
66IL_31066.24SSU Helix 44 (h44) extension
67IL_39526.24
68IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
69IL_98591.24
70IL_15840.13
71IL_80494.23LSU H58 IL2 H.m.
72IL_89028.13Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
73IL_09348.23
74IL_23262.33
75IL_79955.23SSU Helix (23) h23 IL1
76IL_95150.23
77IL_37053.13Kink-turn from 23S H58
78IL_34156.23cWW AG or UU
79IL_75447.13
80IL_16252.2323S H91 IL
81IL_62499.23
82IL_43946.13
83IL_82563.13Thi-box riboswitch T-loop
84IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
85IL_34363.13Kink-turn from 23S H42
86IL_30840.13
87IL_34628.23Kink-turn
88IL_52173.13
89IL_58586.23
90IL_45808.13
91IL_98421.13
92IL_71565.13
93IL_53774.13Single sheared with bulged bases
94IL_99575.12
95IL_01054.12
96IL_70280.12Double sheared with wobble cWW.
97IL_45794.12
98IL_50521.12
99IL_09882.12
100IL_12269.12
101IL_12211.12
102IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
103IL_25174.12
104IL_23414.12
105IL_43933.12
106IL_91026.12
107IL_87548.12
108IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
109IL_52940.12
110IL_90057.12
111IL_81441.12
112IL_92459.12
113IL_94744.12Sarcin-ricin motif with extra cWW GA pair
114IL_16330.12
115IL_40892.12
116IL_65137.12Kink-turn like motif in Group I Intron
117IL_74291.12
118IL_00998.12
119IL_14023.12
120IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
121IL_97833.12
122IL_16166.12
123IL_87173.12
124IL_82831.22Kink-turn from 16S H23
125IL_76095.32Motif from Hairpin Ribozyme
126IL_98566.12
127IL_28942.12
128IL_74876.12
129IL_31707.12Vitamin B12 aptamer
130IL_46435.12
131IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
132IL_21495.12
133IL_78674.12tHS tHH bulge with S-turn
134IL_41397.22LSU Helix 96 (H96) IL2
135IL_48285.12Leadzyme Motif
136IL_80093.12
137IL_37406.12
138IL_12068.12
139IL_55287.12
140IL_37197.12
141IL_85805.11
142IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
143IL_43316.11
144IL_80505.11
145IL_55649.11
146IL_54450.11
147IL_31241.11
148IL_41849.11
149IL_13682.11
150IL_67735.11
151IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
152IL_23639.11tWH-tHS-L-cWW
153IL_17603.11
154IL_15205.11
155IL_91089.11
156IL_83250.1116S h40 3WJ T.th.
157IL_57977.11
158IL_39324.11
159IL_41791.11
160IL_86059.11
161IL_82650.11
162IL_26868.11
163IL_89794.11
164IL_07675.11tHS tHH bulge with S-turn
165IL_25739.11M-Box Riboswitch
166IL_37715.11
167IL_22579.11
168IL_61730.11
169IL_76486.11Sarcin-ricin motif with syn G
170IL_37990.11
171IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
172IL_47457.11
173IL_60643.11
174IL_13942.11
175IL_25307.11
176IL_11302.11
177IL_53988.11
178IL_20775.11tSH-inserted
179IL_78809.11
180IL_75415.11Pseudo-knot forming internal loop
181IL_06306.11
182IL_97842.11
183IL_56513.11
184IL_30390.11
185IL_63952.11
186IL_52752.11
187IL_22858.11
188IL_66744.11SSU Helix 21 (h21) IL2 E.coli
189IL_05462.11
190IL_06808.11Double sheared (tSH-tSH) one bulged base.
191IL_65788.11
192IL_55934.11kink-turn-like
193IL_61723.11
194IL_54576.11
195IL_81398.11
196IL_37347.11
197IL_46306.11
198IL_91904.11
199IL_21421.11
200IL_85510.11
201IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
202IL_80652.11
203IL_32080.11
204IL_29949.11
205IL_03741.11
206IL_82113.11
207IL_05221.11
208IL_26971.11
209IL_07375.11
210IL_58454.11
211IL_88367.11
212IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
213IL_40845.11
214IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
215IL_83920.11
216IL_88403.11
217IL_52958.11
218IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
219IL_97073.11
220IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
221IL_41009.11
222IL_91078.11
223IL_56779.11
224IL_53323.11
225IL_59529.11
226IL_02957.11
227IL_18755.11
228IL_40527.11Kink-turn
229IL_92280.11
230IL_02835.11
231IL_06468.1116S h40 3WJ E.c.
232IL_62352.11
233IL_02690.11
234IL_11869.11
235IL_12233.11
236IL_71942.11
237IL_95939.11
238IL_25082.11
239IL_98924.11
240IL_25181.11
241IL_82601.11Tandem cWW water-inserted CU pairs
242IL_41139.11
243IL_03110.11
244IL_12507.11
245IL_47687.11
246IL_52509.11
247IL_12486.11
248IL_26241.11
249IL_53423.11
250IL_24143.11Yeast 18S
251IL_71685.11Sarcin-like with an intercalated basepair
252IL_90880.11
253IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
254IL_96260.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription