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0.5 | 0.6

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Changes in PDB files used for clustering

Release 0.5 has 171 PDB files, release 0.6 has 185 PDB files, 158 of them are identical.

10 equivalence classes changed representatives: 1NUJ1NUV, 2P7E2P7D, 2GIS3GX5, 3A3A3RG5, 2IPY3SNP, 2O3Y3TD1, 3O303U5F, 3O583U5H, 3MUR3UCZ, 3PYO3UXR.

17 new structures in release 0.6: 2Y9B, 3NVI, 3Q3Z, 3R1C, 3R1D, 3R2D, 3RW6, 3SD3, 3SIU, 3SIV, 3SJ2, 3SN2, 3SUX, 3T4B, 3TD0, 4A1B, 4A1C.

Obsolete: 2IPY3SNP, 3O304V7R, 3O584V7R, 3PYO4V83.

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 0.5 has 357 motif groups, release 0.6 has 260 motif groups, 71 of them are identical.

12 motif groups were updated, 274 groups are present only in release 0.5, 177 groups are only in release 0.6.

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_82367.47
2IL_39526.15
3IL_01239.15
4IL_11167.34
5IL_82563.13Thi-box riboswitch T-loop
6IL_02691.12
7IL_50521.12
8IL_57870.12
9IL_62718.12
10IL_88684.12
11IL_16166.12
12IL_94744.12Sarcin-ricin motif with extra cWW GA pair
13IL_19202.12
14IL_97833.12
15IL_09882.12
16IL_74876.12
17IL_98566.12
18IL_11302.11
19IL_26241.11
20IL_39324.11
21IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
22IL_88403.11
23IL_02835.11
24IL_12233.11
25IL_26868.11
26IL_50767.11
27IL_80505.11
28IL_03110.11
29IL_12486.11
30IL_29949.11
31IL_40845.11
32IL_52509.11
33IL_63952.11
34IL_92280.11
35IL_05462.11
36IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
37IL_41009.11
38IL_52958.11
39IL_65788.11
40IL_06468.1116S h40 3WJ E.c.
41IL_31793.11Kink-turn from 16S H23
42IL_41791.11
43IL_53988.11
44IL_66744.11SSU Helix 21 (h21) IL2 E.coli
45IL_82650.11
46IL_97073.11
47IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
48IL_20775.11tSH-inserted
49IL_32080.11
50IL_43316.11
51IL_55167.11
52IL_71942.11
53IL_83250.1116S h40 3WJ T.th.
54IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
55IL_37715.11
56IL_47687.11
57IL_55649.11
58IL_85805.11
59IL_02690.11
60IL_22579.11
61IL_39230.11
62IL_48650.11
63IL_55934.11kink-turn-like
64IL_75415.11Pseudo-knot forming internal loop
65IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.

Updated motif groups

#Motif idInstancesDescription
1IL_24982.21616S h20 IL. Prokaryal Loop E Sub-motif
2IL_70237.26
3IL_78732.26Double S-turn motif
4IL_93335.25
5IL_31066.24SSU Helix 44 (h44) extension
6IL_95150.23
7IL_57785.43
8IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
9IL_62499.23
10IL_76095.23
11IL_23262.23
12IL_79955.23SSU Helix (23) h23 IL1

Removed motif groups

#Motif idInstancesDescription
1IL_61133.1221
2IL_24421.1160
3IL_78918.151
4IL_42829.140
5IL_91286.139
6IL_91075.127
7IL_11266.125
8IL_68930.120
9IL_03728.117
10IL_49994.115
11IL_31491.113
12IL_33235.112
13IL_78374.112
14IL_93479.112
15IL_97493.111
16IL_87738.19
17IL_95015.19
18IL_70242.19
19IL_79143.19
20IL_47067.19
21IL_34442.19
22IL_06751.19
23IL_33032.19
24IL_38336.18
25IL_68211.18
26IL_16498.18
27IL_95965.18
28IL_60288.18
29IL_62873.18
30IL_28693.17
31IL_80407.17
32IL_37996.17
33IL_98047.17
34IL_07547.16
35IL_29784.16
36IL_33144.16
37IL_82768.26
38IL_55276.16
39IL_87608.16
40IL_94031.16
41IL_14611.15
42IL_66688.15
43IL_61831.15
44IL_97736.15
45IL_76133.15
46IL_58440.15
47IL_96804.15
48IL_76795.14
49IL_94438.14
50IL_86121.14
51IL_99388.14
52IL_19771.14
53IL_30092.14
54IL_86221.14
55IL_52210.14
56IL_89295.14
57IL_23428.14
58IL_20328.14
59IL_81468.14
60IL_38028.14
61IL_67582.13
62IL_97554.13
63IL_21341.13
64IL_55113.23
65IL_13224.13
66IL_61616.13
67IL_09233.23
68IL_13468.13
69IL_28399.13
70IL_34435.13
71IL_68345.13
72IL_01628.13
73IL_47671.13
74IL_62437.13
75IL_89586.13
76IL_10326.23
77IL_16722.13
78IL_44213.13
79IL_58388.13
80IL_78493.33
81IL_89613.13
82IL_29583.13
83IL_60708.13
84IL_74605.13
85IL_81608.13
86IL_50828.12
87IL_18488.12
88IL_39081.12
89IL_42644.12
90IL_45797.12
91IL_54567.12
92IL_67609.12
93IL_75000.12
94IL_77104.12
95IL_03978.12
96IL_46873.12
97IL_51412.12
98IL_56765.12
99IL_63749.12
100IL_67617.12
101IL_16360.12
102IL_34305.12
103IL_43113.12
104IL_49468.12
105IL_71985.12
106IL_75870.12
107IL_82794.12
108IL_97713.12
109IL_99404.12
110IL_36852.12
111IL_43333.12
112IL_56029.12
113IL_66718.12
114IL_80202.12
115IL_99637.12
116IL_16614.12
117IL_19935.12
118IL_44024.12
119IL_52634.12
120IL_68486.12
121IL_73213.12
122IL_01955.12
123IL_52844.12
124IL_76618.12
125IL_14562.12
126IL_20679.12
127IL_25228.12
128IL_69110.12
129IL_76760.12
130IL_00739.11
131IL_02980.11
132IL_17323.11
133IL_20815.11
134IL_25897.11
135IL_35012.11
136IL_42300.11
137IL_45155.11
138IL_48709.11
139IL_54320.11
140IL_56237.11
141IL_58545.11
142IL_60867.11
143IL_63624.11
144IL_65375.11
145IL_69599.11
146IL_74622.11
147IL_81728.11
148IL_84840.11
149IL_90734.11
150IL_98249.11
151IL_01251.11
152IL_08624.11
153IL_12536.11
154IL_14812.11
155IL_21025.11
156IL_26134.11
157IL_29920.11
158IL_35361.11
159IL_48723.11
160IL_50881.11
161IL_56427.11
162IL_58626.11
163IL_63662.11
164IL_65519.11
165IL_69835.11
166IL_79119.11
167IL_82472.11
168IL_85789.11
169IL_87841.11
170IL_98615.11
171IL_01299.11
172IL_08947.11
173IL_12912.11
174IL_15075.11
175IL_18581.11
176IL_26929.11
177IL_30028.11
178IL_33509.11
179IL_36240.11
180IL_39643.11
181IL_49431.11
182IL_58873.11
183IL_61401.11
184IL_65931.11
185IL_75765.11
186IL_77549.11
187IL_89238.11
188IL_95735.11
189IL_97624.11
190IL_01594.11
191IL_04040.11
192IL_09107.11
193IL_22907.11
194IL_27364.11
195IL_36331.11
196IL_40073.11
197IL_51922.11
198IL_57195.11
199IL_59183.11
200IL_63760.11
201IL_77562.11
202IL_79913.11
203IL_89283.11
204IL_91604.11
205IL_95813.11
206IL_01618.11
207IL_05754.11
208IL_19830.11
209IL_23044.11
210IL_30763.11
211IL_40287.11
212IL_47493.11
213IL_49866.11
214IL_57517.11
215IL_59424.11
216IL_63867.11
217IL_72595.11
218IL_76093.11
219IL_78215.11
220IL_82910.11
221IL_86397.11
222IL_92311.11
223IL_05865.11
224IL_10310.11
225IL_13608.11
226IL_37987.11
227IL_40303.11
228IL_49911.11
229IL_56093.11
230IL_58040.11
231IL_59905.11
232IL_64796.11
233IL_66760.11
234IL_83485.11
235IL_87056.11
236IL_92348.11
237IL_96468.11
238IL_97912.11
239IL_99663.11
240IL_00209.11
241IL_13649.11
242IL_28819.11
243IL_31920.11
244IL_34469.11
245IL_40672.11
246IL_47741.11
247IL_56096.11
248IL_64973.11
249IL_67277.11
250IL_74594.11
251IL_84234.11
252IL_96697.11
253IL_98023.11
254IL_99755.11
255IL_00439.11
256IL_02478.11
257IL_07220.11
258IL_10746.11
259IL_17247.11
260IL_34589.11
261IL_40914.11
262IL_44362.11
263IL_48662.11
264IL_50779.11
265IL_53202.11
266IL_56170.11
267IL_63594.11
268IL_65001.11
269IL_67286.11
270IL_78858.11
271IL_84341.11
272IL_87637.11
273IL_89769.11
274IL_99757.11

Added motif groups

#Motif idInstancesDescription
1IL_97217.1260
2IL_47174.1198
3IL_39199.159Hoogsteen-edge Platform, Single-base
4IL_11616.155cWH basepair with syn base
5IL_41766.149Tandem cWW pairs (Not AU or GC)
6IL_56465.148Single, unpaired intercalated base, consensus A
7IL_44540.146Sugar-edge, 1-base platform, consensus tHS
8IL_87904.131Triple sheared
9IL_54307.127C-loop
10IL_13959.126Double sheared
11IL_93424.123tWH-inserted-tHS
12IL_32390.12216S h19 IL and 23S H41 IL
13IL_55938.12023S H89 IL1 and others
14IL_65553.119Kink-turn
15IL_92027.11816S h21 S8 binding site
16IL_85647.118Sarcin-ricin
17IL_31555.11716S decoding site
18IL_73663.1151 or 2 bulged bases
19IL_49493.114Sarcin-ricin H95 23S rRNA H.m.
20IL_94430.11416S h32-h33-h34 3WJ
21IL_40090.11216S h34 ILa : Part of larger motif
22IL_27618.11123S H73 ILa : Part of larger Motif
23IL_48187.111Single sheared with bulged bases
24IL_99515.11123S H91 IL
25IL_24546.11023S H41 IL and 16S h18 IL : Has large bulge on one side
26IL_47444.110SRP Loop E-like motif
27IL_58291.110Recurrent Sub-motif found in junctions
28IL_92114.110GAAA loop receptor "platform" motif
29IL_68939.19Kink-turn from U4
30IL_40239.18Leadzyme Motif
31IL_76831.18REV element IL with syn G
32IL_90459.18cWW AG or UU
33IL_86357.18
34IL_92321.18Triple sheared with wobble
35IL_73000.18
36IL_80179.17
37IL_25230.17
38IL_53635.16
39IL_40387.16
40IL_13069.16
41IL_24022.16
42IL_29610.16
43IL_97057.16
44IL_44067.16
45IL_83451.15
46IL_92484.15
47IL_92936.15
48IL_45262.15
49IL_59016.15
50IL_78157.15
51IL_72158.15
52IL_02359.15
53IL_79083.15
54IL_82188.15LSU H68 IL from H.m.
55IL_24476.15
56IL_22732.14tSH-inserted-tHS
57IL_11594.14
58IL_80494.14
59IL_98591.14
60IL_28572.1416S h18 kink-turn like motif
61IL_49111.14tHS tHH bulge with S-turn
62IL_69124.14
63IL_38807.14
64IL_18947.14
65IL_34628.14Kink-turn
66IL_92333.14
67IL_62661.14Double-sheared with stacked As
68IL_10804.13
69IL_30840.13
70IL_98421.13
71IL_15840.13
72IL_30979.13
73IL_58586.13
74IL_64184.13
75IL_89028.13Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
76IL_34156.13
77IL_52173.13
78IL_13740.13
79IL_34363.13Kink-turn from 23S H42
80IL_41397.13
81IL_99434.13Single-Base Intercalation Site
82IL_37053.13Kink-turn from 23S H58
83IL_82831.13Kink-turn from 16S H23
84IL_37197.12
85IL_63741.12
86IL_75449.12
87IL_91543.12
88IL_44742.12
89IL_69009.12
90IL_16252.12
91IL_23414.12
92IL_25174.12
93IL_89461.12
94IL_12211.12
95IL_16330.12
96IL_28942.12
97IL_40892.12
98IL_45794.12
99IL_70280.12Double sheared with wobble cWW.
100IL_90057.12
101IL_67117.12
102IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
103IL_81441.12
104IL_92123.12
105IL_09348.12
106IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
107IL_46435.12
108IL_55287.12
109IL_09390.12
110IL_52940.12
111IL_87173.12
112IL_19889.12
113IL_47247.12
114IL_68736.12
115IL_80093.12
116IL_92459.12
117IL_03741.11
118IL_15205.11
119IL_26971.11
120IL_88367.11
121IL_05221.11
122IL_22858.11
123IL_25082.11
124IL_37347.11
125IL_76486.11Sarcin-ricin motif with syn G
126IL_83920.11
127IL_91904.11
128IL_06306.11
129IL_37990.11
130IL_40527.11Kink-turn
131IL_54450.11
132IL_80652.11
133IL_85510.11
134IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
135IL_06808.11Double sheared (tSH-tSH) one bulged base.
136IL_23639.11tWH-tHS-L-cWW
137IL_25181.11
138IL_38333.11
139IL_54576.11
140IL_59529.11
141IL_65978.11
142IL_81398.11
143IL_98924.11
144IL_07375.11
145IL_17109.11
146IL_41139.11
147IL_46306.11
148IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
149IL_61723.11
150IL_71685.11Sarcin-like with an intercalated basepair
151IL_86059.11
152IL_96260.11
153IL_99165.11
154IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
155IL_24143.11Yeast 18S
156IL_29877.11
157IL_39165.11
158IL_52752.11
159IL_61730.11
160IL_67697.11
161IL_78809.11
162IL_82113.11
163IL_91078.11
164IL_24335.11
165IL_25307.11
166IL_30390.11
167IL_62352.11
168IL_67735.11
169IL_91089.11
170IL_02957.11
171IL_10109.11H71 junction in 23S rRNA of T.th.
172IL_14225.11
173IL_25739.11M-Box Riboswitch
174IL_30650.11
175IL_53323.11
176IL_91513.11
177IL_97842.11