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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_01239.15
3IL_39526.15
4IL_11167.34
5IL_82563.13Thi-box riboswitch T-loop
6IL_16166.12
7IL_94744.12Sarcin-ricin motif with extra cWW GA pair
8IL_19202.12
9IL_97833.12
10IL_09882.12
11IL_74876.12
12IL_98566.12
13IL_02691.12
14IL_50521.12
15IL_57870.12
16IL_62718.12
17IL_88684.12
18IL_03110.11
19IL_12486.11
20IL_29949.11
21IL_40845.11
22IL_52509.11
23IL_63952.11
24IL_92280.11
25IL_05462.11
26IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
27IL_41009.11
28IL_52958.11
29IL_65788.11
30IL_06468.1116S h40 3WJ E.c.
31IL_31793.11Kink-turn from 16S H23
32IL_41791.11
33IL_53988.11
34IL_66744.11SSU Helix 21 (h21) IL2 E.coli
35IL_82650.11
36IL_97073.11
37IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
38IL_20775.11tSH-inserted
39IL_32080.11
40IL_43316.11
41IL_55167.11
42IL_71942.11
43IL_83250.1116S h40 3WJ T.th.
44IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
45IL_37715.11
46IL_47687.11
47IL_55649.11
48IL_85805.11
49IL_02690.11
50IL_22579.11
51IL_39230.11
52IL_48650.11
53IL_55934.11kink-turn-like
54IL_75415.11Pseudo-knot forming internal loop
55IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
56IL_11302.11
57IL_26241.11
58IL_39324.11
59IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
60IL_88403.11
61IL_02835.11
62IL_12233.11
63IL_26868.11
64IL_50767.11
65IL_80505.11

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_62499.23
7IL_76095.23
8IL_23262.23
9IL_79955.23SSU Helix (23) h23 IL1
10IL_95150.23
11IL_57785.43
12IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif

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_78374.112
13IL_93479.112
14IL_33235.112
15IL_97493.111
16IL_34442.19
17IL_06751.19
18IL_33032.19
19IL_87738.19
20IL_95015.19
21IL_70242.19
22IL_79143.19
23IL_47067.19
24IL_16498.18
25IL_95965.18
26IL_60288.18
27IL_62873.18
28IL_38336.18
29IL_68211.18
30IL_28693.17
31IL_80407.17
32IL_37996.17
33IL_98047.17
34IL_87608.16
35IL_94031.16
36IL_07547.16
37IL_29784.16
38IL_33144.16
39IL_82768.26
40IL_55276.16
41IL_61831.15
42IL_97736.15
43IL_76133.15
44IL_58440.15
45IL_96804.15
46IL_14611.15
47IL_66688.15
48IL_52210.14
49IL_89295.14
50IL_23428.14
51IL_20328.14
52IL_81468.14
53IL_38028.14
54IL_76795.14
55IL_94438.14
56IL_86121.14
57IL_99388.14
58IL_19771.14
59IL_30092.14
60IL_86221.14
61IL_09233.23
62IL_13468.13
63IL_28399.13
64IL_34435.13
65IL_68345.13
66IL_01628.13
67IL_47671.13
68IL_62437.13
69IL_89586.13
70IL_10326.23
71IL_16722.13
72IL_44213.13
73IL_58388.13
74IL_78493.33
75IL_89613.13
76IL_29583.13
77IL_60708.13
78IL_74605.13
79IL_81608.13
80IL_67582.13
81IL_97554.13
82IL_21341.13
83IL_55113.23
84IL_13224.13
85IL_61616.13
86IL_36852.12
87IL_43333.12
88IL_56029.12
89IL_66718.12
90IL_80202.12
91IL_99637.12
92IL_16614.12
93IL_19935.12
94IL_44024.12
95IL_52634.12
96IL_68486.12
97IL_73213.12
98IL_01955.12
99IL_52844.12
100IL_76618.12
101IL_14562.12
102IL_20679.12
103IL_25228.12
104IL_69110.12
105IL_76760.12
106IL_50828.12
107IL_18488.12
108IL_39081.12
109IL_42644.12
110IL_45797.12
111IL_54567.12
112IL_67609.12
113IL_75000.12
114IL_77104.12
115IL_03978.12
116IL_46873.12
117IL_51412.12
118IL_56765.12
119IL_63749.12
120IL_67617.12
121IL_16360.12
122IL_34305.12
123IL_43113.12
124IL_49468.12
125IL_71985.12
126IL_75870.12
127IL_82794.12
128IL_97713.12
129IL_99404.12
130IL_01618.11
131IL_05754.11
132IL_19830.11
133IL_23044.11
134IL_30763.11
135IL_40287.11
136IL_47493.11
137IL_49866.11
138IL_57517.11
139IL_59424.11
140IL_63867.11
141IL_72595.11
142IL_76093.11
143IL_78215.11
144IL_82910.11
145IL_86397.11
146IL_92311.11
147IL_05865.11
148IL_10310.11
149IL_13608.11
150IL_37987.11
151IL_40303.11
152IL_49911.11
153IL_56093.11
154IL_58040.11
155IL_59905.11
156IL_64796.11
157IL_66760.11
158IL_83485.11
159IL_87056.11
160IL_92348.11
161IL_96468.11
162IL_97912.11
163IL_99663.11
164IL_00209.11
165IL_13649.11
166IL_28819.11
167IL_31920.11
168IL_34469.11
169IL_40672.11
170IL_47741.11
171IL_56096.11
172IL_64973.11
173IL_67277.11
174IL_74594.11
175IL_84234.11
176IL_96697.11
177IL_98023.11
178IL_99755.11
179IL_00439.11
180IL_02478.11
181IL_07220.11
182IL_10746.11
183IL_17247.11
184IL_34589.11
185IL_40914.11
186IL_44362.11
187IL_48662.11
188IL_50779.11
189IL_53202.11
190IL_56170.11
191IL_63594.11
192IL_65001.11
193IL_67286.11
194IL_78858.11
195IL_84341.11
196IL_87637.11
197IL_89769.11
198IL_99757.11
199IL_00739.11
200IL_02980.11
201IL_17323.11
202IL_20815.11
203IL_25897.11
204IL_35012.11
205IL_42300.11
206IL_45155.11
207IL_48709.11
208IL_54320.11
209IL_56237.11
210IL_58545.11
211IL_60867.11
212IL_63624.11
213IL_65375.11
214IL_69599.11
215IL_74622.11
216IL_81728.11
217IL_84840.11
218IL_90734.11
219IL_98249.11
220IL_01251.11
221IL_08624.11
222IL_12536.11
223IL_14812.11
224IL_21025.11
225IL_26134.11
226IL_29920.11
227IL_35361.11
228IL_48723.11
229IL_50881.11
230IL_56427.11
231IL_58626.11
232IL_63662.11
233IL_65519.11
234IL_69835.11
235IL_79119.11
236IL_82472.11
237IL_85789.11
238IL_87841.11
239IL_98615.11
240IL_01299.11
241IL_08947.11
242IL_12912.11
243IL_15075.11
244IL_18581.11
245IL_26929.11
246IL_30028.11
247IL_33509.11
248IL_36240.11
249IL_39643.11
250IL_49431.11
251IL_58873.11
252IL_61401.11
253IL_65931.11
254IL_75765.11
255IL_77549.11
256IL_89238.11
257IL_95735.11
258IL_97624.11
259IL_01594.11
260IL_04040.11
261IL_09107.11
262IL_22907.11
263IL_27364.11
264IL_36331.11
265IL_40073.11
266IL_51922.11
267IL_57195.11
268IL_59183.11
269IL_63760.11
270IL_77562.11
271IL_79913.11
272IL_89283.11
273IL_91604.11
274IL_95813.11

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_99515.11123S H91 IL
23IL_27618.11123S H73 ILa : Part of larger Motif
24IL_48187.111Single sheared with bulged bases
25IL_92114.110GAAA loop receptor "platform" motif
26IL_24546.11023S H41 IL and 16S h18 IL : Has large bulge on one side
27IL_47444.110SRP Loop E-like motif
28IL_58291.110Recurrent Sub-motif found in junctions
29IL_68939.19Kink-turn from U4
30IL_76831.18REV element IL with syn G
31IL_90459.18cWW AG or UU
32IL_86357.18
33IL_92321.18Triple sheared with wobble
34IL_73000.18
35IL_40239.18Leadzyme Motif
36IL_25230.17
37IL_80179.17
38IL_13069.16
39IL_24022.16
40IL_29610.16
41IL_97057.16
42IL_44067.16
43IL_53635.16
44IL_40387.16
45IL_45262.15
46IL_59016.15
47IL_78157.15
48IL_72158.15
49IL_02359.15
50IL_79083.15
51IL_82188.15LSU H68 IL from H.m.
52IL_24476.15
53IL_83451.15
54IL_92484.15
55IL_92936.15
56IL_28572.1416S h18 kink-turn like motif
57IL_49111.14tHS tHH bulge with S-turn
58IL_69124.14
59IL_38807.14
60IL_18947.14
61IL_34628.14Kink-turn
62IL_92333.14
63IL_62661.14Double-sheared with stacked As
64IL_22732.14tSH-inserted-tHS
65IL_11594.14
66IL_80494.14
67IL_98591.14
68IL_34156.13
69IL_52173.13
70IL_13740.13
71IL_34363.13Kink-turn from 23S H42
72IL_41397.13
73IL_99434.13Single-Base Intercalation Site
74IL_37053.13Kink-turn from 23S H58
75IL_82831.13Kink-turn from 16S H23
76IL_10804.13
77IL_30840.13
78IL_98421.13
79IL_15840.13
80IL_30979.13
81IL_58586.13
82IL_64184.13
83IL_89028.13Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
84IL_16252.12
85IL_23414.12
86IL_25174.12
87IL_89461.12
88IL_12211.12
89IL_16330.12
90IL_28942.12
91IL_40892.12
92IL_45794.12
93IL_70280.12Double sheared with wobble cWW.
94IL_90057.12
95IL_67117.12
96IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
97IL_81441.12
98IL_92123.12
99IL_09348.12
100IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
101IL_46435.12
102IL_55287.12
103IL_09390.12
104IL_52940.12
105IL_87173.12
106IL_19889.12
107IL_47247.12
108IL_68736.12
109IL_80093.12
110IL_92459.12
111IL_37197.12
112IL_63741.12
113IL_75449.12
114IL_91543.12
115IL_44742.12
116IL_69009.12
117IL_06306.11
118IL_37990.11
119IL_40527.11Kink-turn
120IL_54450.11
121IL_80652.11
122IL_85510.11
123IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
124IL_06808.11Double sheared (tSH-tSH) one bulged base.
125IL_23639.11tWH-tHS-L-cWW
126IL_25181.11
127IL_38333.11
128IL_54576.11
129IL_59529.11
130IL_65978.11
131IL_81398.11
132IL_98924.11
133IL_07375.11
134IL_17109.11
135IL_41139.11
136IL_46306.11
137IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
138IL_61723.11
139IL_71685.11Sarcin-like with an intercalated basepair
140IL_86059.11
141IL_96260.11
142IL_99165.11
143IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
144IL_24143.11Yeast 18S
145IL_29877.11
146IL_39165.11
147IL_52752.11
148IL_61730.11
149IL_67697.11
150IL_78809.11
151IL_82113.11
152IL_91078.11
153IL_24335.11
154IL_25307.11
155IL_30390.11
156IL_62352.11
157IL_67735.11
158IL_91089.11
159IL_02957.11
160IL_10109.11H71 junction in 23S rRNA of T.th.
161IL_14225.11
162IL_25739.11M-Box Riboswitch
163IL_30650.11
164IL_53323.11
165IL_91513.11
166IL_97842.11
167IL_03741.11
168IL_15205.11
169IL_26971.11
170IL_88367.11
171IL_05221.11
172IL_22858.11
173IL_25082.11
174IL_37347.11
175IL_76486.11Sarcin-ricin motif with syn G
176IL_83920.11
177IL_91904.11