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_06429.11616S h19 IL and 23S H41 IL | 1 or 2 bulged bases
17IL_85647.216Sarcin-ricin parent motif with 15 Nts
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_73000.27cHS-cWS
34IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
35IL_86357.27LSU Helix 61 IL2
36IL_25230.26Bacterial 5S rRNA Loop E
37IL_89088.1616S h19 IL and 23S H41 IL
38IL_10007.16Single sheared with bulged bases
39IL_44067.26Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
40IL_08926.1623S H91 IL
41IL_97057.26
42IL_72158.26LSU Helix 62 (H62) IL
43IL_53635.26LSU Helix 32 (H32) IL
44IL_70237.36
45IL_13069.26LSU 3WJ H32-H33-H35A
46IL_24022.26
47IL_40387.25
48IL_45262.25
49IL_79083.25
50IL_77263.15Kink-turn from U4
51IL_80179.25
52IL_01239.15
53IL_92484.15
54IL_07911.15
55IL_78732.35Double S-turn motif
56IL_02359.25
57IL_82188.15LSU H68 IL from H.m.
58IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
59IL_98556.14
60IL_21333.14tSH-tHW-bulge
61IL_38807.24
62IL_28572.1416S h18 kink-turn like motif
63IL_31066.24SSU Helix 44 (h44) extension
64IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
65IL_98591.24
66IL_62661.24Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
67IL_39526.24
68IL_64184.24
69IL_22732.14tSH-inserted-tHS
70IL_79955.23SSU Helix (23) h23 IL1
71IL_95150.23
72IL_37053.13Kink-turn from 23S H58
73IL_53774.13Single sheared with bulged bases
74IL_34156.23cWW AG or UU
75IL_09348.23
76IL_23262.33
77IL_62499.23
78IL_43946.13
79IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
80IL_34363.13Kink-turn from 23S H42
81IL_75447.13
82IL_16252.2323S H91 IL
83IL_82563.13Thi-box riboswitch T-loop
84IL_52173.13
85IL_58586.23
86IL_30840.13
87IL_34628.23Kink-turn
88IL_98421.13
89IL_71565.13
90IL_15840.13
91IL_80494.23LSU H58 IL2 H.m.
92IL_89028.13Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
93IL_45808.13
94IL_50521.12
95IL_09882.12
96IL_12269.12
97IL_12211.12
98IL_37406.12
99IL_12068.12
100IL_55287.12
101IL_37197.12
102IL_87548.12
103IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
104IL_52940.12
105IL_90057.12
106IL_01054.12
107IL_70280.12Double sheared with wobble cWW.
108IL_45794.12
109IL_65137.12Kink-turn like motif in Group I Intron
110IL_74291.12
111IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
112IL_25174.12
113IL_23414.12
114IL_43933.12
115IL_91026.12
116IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
117IL_97833.12
118IL_16166.12
119IL_81441.12
120IL_92459.12
121IL_94744.12Sarcin-ricin motif with extra cWW GA pair
122IL_16330.12
123IL_40892.12
124IL_76095.32Motif from Hairpin Ribozyme
125IL_98566.12
126IL_87173.12
127IL_00998.12
128IL_14023.12
129IL_31707.12Vitamin B12 aptamer
130IL_82831.22Kink-turn from 16S H23
131IL_48285.12Leadzyme Motif
132IL_80093.12
133IL_28942.12
134IL_74876.12
135IL_99575.12
136IL_46435.12
137IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
138IL_21495.12
139IL_78674.12tHS tHH bulge with S-turn
140IL_41397.22LSU Helix 96 (H96) IL2
141IL_83250.1116S h40 3WJ T.th.
142IL_57977.11
143IL_39324.11
144IL_41791.11
145IL_86059.11
146IL_12507.11
147IL_47687.11
148IL_52509.11
149IL_12486.11
150IL_26241.11
151IL_53423.11
152IL_24143.11Yeast 18S
153IL_71685.11Sarcin-like with an intercalated basepair
154IL_90880.11
155IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
156IL_96260.11
157IL_13942.11
158IL_80505.11
159IL_55649.11
160IL_54450.11
161IL_31241.11
162IL_41849.11
163IL_13682.11
164IL_67735.11
165IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
166IL_23639.11tWH-tHS-L-cWW
167IL_17603.11
168IL_15205.11
169IL_91089.11
170IL_63952.11
171IL_52752.11
172IL_82650.11
173IL_26868.11
174IL_89794.11
175IL_07675.11tHS tHH bulge with S-turn
176IL_25739.11M-Box Riboswitch
177IL_37715.11
178IL_22579.11
179IL_61730.11
180IL_76486.11Sarcin-ricin motif with syn G
181IL_37990.11
182IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
183IL_47457.11
184IL_60643.11
185IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
186IL_76263.11
187IL_25307.11
188IL_11302.11
189IL_53988.11
190IL_20775.11tSH-inserted
191IL_78809.11
192IL_75415.11Pseudo-knot forming internal loop
193IL_06306.11
194IL_97842.11
195IL_56513.11
196IL_30390.11
197IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
198IL_40845.11
199IL_22858.11
200IL_66744.11SSU Helix 21 (h21) IL2 E.coli
201IL_05462.11
202IL_06808.11Double sheared (tSH-tSH) one bulged base.
203IL_65788.11
204IL_55934.11kink-turn-like
205IL_61723.11
206IL_54576.11
207IL_81398.11
208IL_37347.11
209IL_46306.11
210IL_91904.11
211IL_21421.11
212IL_85510.11
213IL_92280.11
214IL_02835.11
215IL_68827.11Reverse Kink-Turn
216IL_80652.11
217IL_32080.11
218IL_29949.11
219IL_03741.11
220IL_82113.11
221IL_05221.11
222IL_26971.11
223IL_07375.11
224IL_58454.11
225IL_88367.11
226IL_03110.11
227IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
228IL_83920.11
229IL_88403.11
230IL_52958.11
231IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
232IL_97073.11
233IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
234IL_41009.11
235IL_91078.11
236IL_56779.11
237IL_53323.11
238IL_59529.11
239IL_02957.11
240IL_18755.11
241IL_40527.11Kink-turn
242IL_85805.11
243IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
244IL_43316.11
245IL_06468.1116S h40 3WJ E.c.
246IL_62352.11
247IL_02690.11
248IL_11869.11
249IL_12233.11
250IL_71942.11
251IL_95939.11
252IL_25082.11
253IL_98924.11
254IL_25181.11
255IL_82601.11Tandem cWW water-inserted CU pairs
256IL_41139.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription