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0.1 | 0.9

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Changes in PDB files used for clustering

Release 0.1 has 142 PDB files, release 0.9 has 195 PDB files, 130 of them are identical.

10 equivalence classes changed representatives: 3F1H3V2F, 2GIS3GX5, 2IPY3SNP, 1L9A1MFQ, 3HHN3IVK, 3HL23RG5, 2O3Y3TD1, 1NUJ1NUV, 3MUR3UCZ, 2P7E2P7D.

55 new structures in release 0.9: 1J2B, 1KOG, 1NBS, 1T0K, 1U63, 1U6B, 1UN6, 1X8W, 1Y0Q, 2A64, 2AW7, 2IL9, 2QBG, 2XXA, 2XZM, 2Y9B, 387D, 3DHS, 3IWN, 3KTW, 3NPB, 3NVI, 3P49, 3Q1Q, 3Q3Z, 3R1D, 3R2D, 3R4F, 3RW6, 3SD3, 3SIU, 3SIV, 3SJ2, 3SN2, 3SUX, 3SYW, 3SZX, 3T4B, 3TD0, 3TZR, 3U4M, 3U5F, 3U5H, 3V7E, 4A1B, 4A1C, 4AOB, 4E48, 4E5C, 4ERD, 4EYA, 4FNJ, 4FRG, 4GMA, 4GXY.

Obsolete: 2IPY3SNP, 3F1H4V67.

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 0.1 has 172 motif groups, release 0.9 has 264 motif groups, 31 of them are identical.

7 motif groups were updated, 134 groups are present only in release 0.1, 226 groups are only in release 0.9.

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_54175.13
2IL_82563.13Thi-box riboswitch T-loop
3IL_09882.12
4IL_94744.12Sarcin-ricin motif with extra cWW GA pair
5IL_16360.12
6IL_74876.12
7IL_57785.12
8IL_41791.11
9IL_65493.11
10IL_12233.11
11IL_43316.11
12IL_67805.11
13IL_52375.11
14IL_20775.11tSH-inserted
15IL_53598.11
16IL_75582.11
17IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
18IL_76474.11
19IL_02835.11
20IL_26241.11
21IL_03110.11
22IL_39324.11
23IL_63952.11
24IL_83250.1116S h40 3WJ T.th.
25IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
26IL_41009.11
27IL_65332.11
28IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription
1IL_29070.1140
2IL_37431.1112
3IL_53935.129
4IL_85670.127
5IL_45564.126
6IL_69966.120
7IL_17030.117
8IL_30798.114
9IL_55389.112
10IL_17977.111
11IL_87158.111
12IL_29996.111
13IL_33742.110
14IL_33923.110
15IL_26410.19
16IL_36534.19
17IL_09381.18
18IL_63717.18
19IL_47950.18
20IL_65962.17
21IL_97204.16
22IL_20312.16
23IL_86322.16
24IL_36381.16
25IL_28652.16
26IL_92985.16
27IL_16628.16
28IL_51068.15
29IL_39216.15
30IL_39526.15
31IL_26097.15
32IL_06484.14
33IL_78938.14
34IL_22243.14
35IL_19813.14
36IL_49609.14
37IL_82768.14
38IL_16858.13
39IL_41412.13
40IL_10326.13
41IL_53203.13
42IL_78493.13
43IL_11419.13
44IL_18861.13
45IL_12437.13
46IL_19775.13
47IL_54308.13
48IL_85104.13
49IL_87744.13
50IL_08981.13
51IL_19801.13
52IL_55113.13
53IL_76095.13
54IL_40542.13
55IL_61616.13
56IL_20048.12
57IL_61636.12
58IL_82854.12
59IL_26781.12
60IL_78483.12
61IL_97453.12
62IL_10861.12
63IL_20796.12
64IL_57870.12
65IL_62527.12
66IL_83664.12
67IL_53918.12
68IL_62718.12
69IL_47648.12
70IL_64838.12
71IL_72026.12
72IL_82266.12
73IL_64979.12
74IL_03814.12
75IL_09020.12
76IL_04040.11
77IL_35361.11
78IL_50503.11
79IL_56170.11
80IL_77549.11
81IL_86213.11
82IL_88737.11
83IL_04151.11
84IL_31791.11
85IL_35496.11
86IL_44199.11
87IL_57863.11
88IL_61940.11
89IL_67328.11
90IL_83485.11
91IL_90018.11
92IL_05830.11
93IL_26786.11
94IL_32210.11
95IL_44893.11
96IL_69395.11
97IL_90243.11
98IL_98916.11
99IL_20940.11
100IL_28626.11
101IL_33041.11
102IL_58589.11
103IL_84308.11
104IL_87473.11
105IL_90454.11
106IL_06499.11
107IL_12278.11
108IL_19417.11
109IL_21031.11
110IL_33600.11
111IL_47295.11
112IL_60928.11
113IL_71076.11
114IL_81728.11
115IL_84453.11
116IL_87637.11
117IL_00209.11
118IL_08744.11
119IL_61032.11
120IL_95275.11
121IL_02449.11
122IL_14812.11
123IL_24704.11
124IL_29499.11
125IL_61226.11
126IL_82472.11
127IL_87816.11
128IL_95865.11
129IL_35355.11
130IL_65519.11
131IL_76973.11
132IL_85679.11
133IL_88360.11
134IL_96203.11

Added motif groups

#Motif idInstancesDescription
1IL_97217.3235
2IL_47174.320216S 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_65553.323Kink-turn
11IL_93424.222tSH-inserted-tHW
12IL_32390.22116S h19 IL and 23S H41 IL
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_94430.31516S h32-h33-h34 3WJ
19IL_31555.21516S decoding site
20IL_24982.315SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
21IL_49493.214Sarcin-ricin Parent Motif - bacterial LSU H95 IL
22IL_21304.111Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
23IL_46648.11123S H91 IL | Single-Base Intercalation Site
24IL_27618.21123S H73 ILa : Part of larger Motif
25IL_40090.21116S h34 ILa : Part of larger motif
26IL_24546.21023S H41 IL and 16S h18 IL : Has large bulge on one side
27IL_92114.29GAAA loop receptor "platform" motif
28IL_58291.29Recurrent Sub-motif found in junctions
29IL_90459.28cWW AG or UU
30IL_92321.28Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
31IL_02809.18REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
32IL_73000.27cHS-cWS
33IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
34IL_86357.27LSU Helix 61 IL2
35IL_08926.1623S H91 IL
36IL_54420.16
37IL_72158.26LSU Helix 62 (H62) IL
38IL_24022.26
39IL_70237.36
40IL_10007.16Single sheared with bulged bases
41IL_97057.26
42IL_13069.26LSU 3WJ H32-H33-H35A
43IL_44067.26Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
44IL_53635.26LSU Helix 32 (H32) IL
45IL_89088.1616S h19 IL and 23S H41 IL
46IL_01239.15
47IL_77263.15Kink-turn from U4
48IL_90133.15
49IL_02359.25
50IL_79083.25
51IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
52IL_92484.15
53IL_45262.25
54IL_82188.15LSU H68 IL from H.m.
55IL_80179.25
56IL_38807.24
57IL_21333.14tSH-tHW-bulge
58IL_98556.24
59IL_39526.34
60IL_98591.24
61IL_28572.1416S h18 kink-turn like motif
62IL_40387.34
63IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
64IL_62661.24Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
65IL_22732.14tSH-inserted-tHS
66IL_93568.14Triple Sheared (tSH-tHS-tHS) with wobble cWW.
67IL_31066.24SSU Helix 44 (h44) extension
68IL_36254.13
69IL_98421.23SSU Helix 12 (h12) IL
70IL_09348.33cWW-L-cWW-cWW
71IL_16166.23
72IL_37053.13Kink-turn from 23S H58
73IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
74IL_16252.2323S H91 IL
75IL_62499.33
76IL_79955.23SSU Helix (23) h23 IL1
77IL_71565.13
78IL_89028.23Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
79IL_23262.33
80IL_30840.13
81IL_34363.13Kink-turn from 23S H42
82IL_53774.13Single sheared with bulged bases
83IL_58586.23
84IL_34628.23Kink-turn
85IL_52173.13
86IL_86826.13tHS tHH bulge with S-turn
87IL_01054.12
88IL_12269.12
89IL_15840.22Triple Sheared with unpaired, inserted A
90IL_41397.22LSU Helix 96 (H96) IL2
91IL_46435.12
92IL_82831.22Kink-turn from 16S H23
93IL_87336.12LSU Eukaryal Helix 96 (H96) IL1
94IL_90057.12
95IL_52940.12
96IL_80755.12
97IL_87548.12
98IL_31707.12Vitamin B12 aptamer
99IL_37197.12
100IL_70280.12Double sheared with wobble cWW.
101IL_98566.12
102IL_16330.12
103IL_21495.12
104IL_73816.12tHS tHH bulge with S-turn
105IL_81441.12
106IL_11751.12
107IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
108IL_37406.12
109IL_54965.12Leadzyme Motif. SSU Decoding site motif, extended.
110IL_25174.12
111IL_28942.12
112IL_34156.32cWW AG or UU
113IL_55287.12
114IL_80093.12
115IL_12068.12
116IL_14023.12
117IL_37737.12
118IL_40892.12
119IL_45794.12
120IL_50521.12
121IL_76095.32Motif from Hairpin Ribozyme
122IL_91132.12
123IL_97833.12
124IL_00998.12
125IL_07300.12
126IL_12211.12
127IL_23414.12
128IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
129IL_93782.12
130IL_99575.12
131IL_05462.11
132IL_23639.11tWH-tHS-L-cWW
133IL_25307.11
134IL_31241.11
135IL_52509.11
136IL_60643.11
137IL_67735.11
138IL_76486.11Sarcin-ricin motif with syn G
139IL_80652.11
140IL_06306.11
141IL_12486.11
142IL_26868.11
143IL_54450.11
144IL_61730.11
145IL_12507.11
146IL_21421.11
147IL_26971.11
148IL_41849.11
149IL_52958.11
150IL_54576.11
151IL_56513.11
152IL_61991.11
153IL_78809.11
154IL_81398.11
155IL_83856.11
156IL_92280.11
157IL_02690.11
158IL_11302.11
159IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
160IL_37347.11
161IL_47687.11
162IL_53323.11
163IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
164IL_57977.11
165IL_70550.11
166IL_83920.11
167IL_88367.11
168IL_90880.11
169IL_97073.11
170IL_06468.1116S h40 3WJ E.c.
171IL_13682.11
172IL_22579.11
173IL_25082.11
174IL_53423.11
175IL_75415.11Pseudo-knot forming internal loop
176IL_82113.11
177IL_85510.11
178IL_88403.11
179IL_91078.11
180IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
181IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
182IL_02957.11
183IL_06471.11
184IL_11869.11
185IL_17603.11
186IL_37715.11
187IL_40527.11Kink-turn
188IL_58454.11
189IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
190IL_91089.11
191IL_98688.11
192IL_03741.11
193IL_06780.11
194IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
195IL_25181.11
196IL_55649.11
197IL_65788.11
198IL_71685.11Sarcin-like with an intercalated basepair
199IL_82601.11Tandem cWW water-inserted CU pairs
200IL_98924.11
201IL_05221.11
202IL_15205.11
203IL_18755.11
204IL_37990.11
205IL_41139.11
206IL_46306.11
207IL_53988.11
208IL_55934.11kink-turn-like
209IL_59529.11
210IL_66744.11SSU Helix 21 (h21) IL2 E.coli
211IL_71942.11
212IL_76256.11
213IL_80505.11
214IL_82650.11
215IL_89794.11
216IL_91904.11
217IL_97842.11
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