Changes in PDB files used for clustering

Release 1.17 has 243 PDB files, release 1.18 has 246 PDB files, 240 of them are identical.

1 equivalence classes changed representatives: 4LCK4TZZ.

5 new structures in release 1.18: 4PDB, 4QJH, 4R0D, 4W21, 4W23.

Obsolete: 1VWW4W1Z, 1VX24W28.

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 1.17 has 364 motif groups, release 1.18 has 372 motif groups, 193 of them are identical.

75 motif groups were updated, 96 groups are present only in release 1.17, 104 groups are only in release 1.18.

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_67038.11523S H91 IL | Single-Base Intercalation Site
2IL_18271.112Single, unpaired intercalated base, consensus A | 23S H91 IL
3IL_53635.69LSU Helix 32 (H32) IL
4IL_64847.27Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
5IL_02359.66
6IL_51439.16
7IL_15123.36Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th.
8IL_25230.56Bacterial 5S rRNA Loop E
9IL_55114.35Double S-turn motif | tHS tHH bulge with S-turn | Double S-turn motif
10IL_39980.25
11IL_98421.75SSU Helix 12 (h12) IL | SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
12IL_04397.25
13IL_71229.25
14IL_39526.44
15IL_48918.34Kink-turn variant
16IL_94519.24
17IL_32508.1423S H91 IL
18IL_77076.34
19IL_43727.14tSH-inserted-tHS | tHS tHH bulge with S-turn | tSH-inserted-tHS
20IL_16166.5423S H91 IL
21IL_83339.14
22IL_62499.10323S H91 IL
23IL_19268.13
24IL_45592.2323S H91 IL
25IL_82563.13Thi-box riboswitch T-loop
26IL_43946.13
27IL_21639.23
28IL_34628.23Kink-turn
29IL_40892.23
30IL_22025.13
31IL_98073.23Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
32IL_03362.12
33IL_06692.12
34IL_68034.12
35IL_74462.12
36IL_91942.12
37IL_98172.12
38IL_31707.12Vitamin B12 aptamer
39IL_35558.12
40IL_50521.12
41IL_21062.12Sarcin-ricin motif with cWW UU instead of tSH basepair.
42IL_23414.12
43IL_40041.12
44IL_76095.32Motif from Hairpin Ribozyme
45IL_94744.12Sarcin-ricin motif with extra cWW GA pair
46IL_28003.22
47IL_43363.12
48IL_46435.12
49IL_70401.12
50IL_28028.12
51IL_65137.12Kink-turn like motif in Group I Intron
52IL_21495.12
53IL_28058.12
54IL_33842.12
55IL_39175.12
56IL_52940.12
57IL_09882.12
58IL_44092.12
59IL_67024.12
60IL_06675.12Triple Sheared with unpaired, inserted A
61IL_16330.12
62IL_39439.12
63IL_44977.12LSU H58 IL2 H.m. | SSU Helix (23) h23 IL1
64IL_01562.11
65IL_11302.11
66IL_22909.11
67IL_26868.11
68IL_31160.11
69IL_35267.11
70IL_41215.11
71IL_45432.11
72IL_80652.11
73IL_84276.11
74IL_88367.11
75IL_02257.11
76IL_03808.11
77IL_06808.11Double sheared (tSH-tSH) one bulged base.
78IL_11778.11
79IL_22953.11Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
80IL_26971.11
81IL_41371.11
82IL_55649.11
83IL_62617.11
84IL_69482.11
85IL_75415.11Pseudo-knot forming internal loop
86IL_80714.11
87IL_84995.11
88IL_89463.11
89IL_06847.11Group II Intron IL
90IL_12507.11
91IL_27640.11
92IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
93IL_36006.11
94IL_41516.11
95IL_45617.11
96IL_57334.11
97IL_63952.11
98IL_70069.11tHS tHH bulge with S-turn
99IL_81280.11
100IL_85510.11
101IL_89794.11
102IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
103IL_02835.11
104IL_05221.11
105IL_07252.11
106IL_21077.11
107IL_23639.11tWH-tHS-L-cWW
108IL_37347.11
109IL_40364.11
110IL_51572.11
111IL_57977.11
112IL_81587.11
113IL_86059.11
114IL_90633.11
115IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
116IL_98924.11
117IL_02897.11Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th.
118IL_05513.11
119IL_08588.11
120IL_15205.11
121IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
122IL_33217.11
123IL_37970.11tHS tHH bulge with S-turn | tSH-inserted-tHS
124IL_40527.11Kink-turn
125IL_47687.11
126IL_52610.11
127IL_58270.11
128IL_70529.11
129IL_77296.11
130IL_86060.11
131IL_91044.11
132IL_96591.11
133IL_99784.11
134IL_02957.11
135IL_06306.11
136IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
137IL_15884.11
138IL_25420.11
139IL_40845.11
140IL_47702.11
141IL_59907.11
142IL_66744.11SSU Helix 21 (h21) IL2 E.coli
143IL_77862.11
144IL_82601.11Tandem cWW water-inserted CU pairs
145IL_86336.11
146IL_91061.11
147IL_97803.11
148IL_99937.11
149IL_03110.11
150IL_06468.1116S h40 3WJ E.c.
151IL_25808.11
152IL_28644.11
153IL_39324.11
154IL_48036.11
155IL_52958.11
156IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
157IL_73656.11
158IL_79910.11
159IL_82650.11
160IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
161IL_91078.11
162IL_97842.11
163IL_00346.11
164IL_03282.11
165IL_11268.11
166IL_25926.11
167IL_29058.11
168IL_34816.11
169IL_41139.11
170IL_48268.11
171IL_62296.11
172IL_74400.11
173IL_80505.11
174IL_87523.11
175IL_91089.11

Updated motif groups

#Motif idInstancesDescription
1IL_48256.23711-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | 23S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 1-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 1-3 bulged nucleotides
2IL_92602.2321Non-canonical cWW basepair
3IL_41766.1088Stacked cWW-cWH pairs | Tandem cWW pairs (Not AU or GC)
4IL_39199.874Hoogsteen-edge Platform, Single bulged base
5IL_67828.26523S H91 IL | Single-Base Intercalation Site | Single, unpaired intercalated base, consensus A | 16S h32-h33-h34 3WJ
6IL_44540.862One or more bulged nucleotides | Sugar-edge, 1-base platform, consensus tHS
7IL_13959.839Double Sheared (tSH-tHS)
8IL_82822.235One or more bulged bases
9IL_73276.931C-loop
10IL_93424.831tSH-inserted-tHW
11IL_65553.1229Kink-turn
12IL_55938.827LSU Helix 89 (H89) IL2. cSH Platform.
13IL_85647.725Sarcin-ricin parent motif with 15 Nts
14IL_92027.72516S h21 S8 binding site
15IL_34098.221cWW with bulged base | tHS and base triple with flanking pair
16IL_37104.719Single sheared with bulged bases
17IL_49493.818Sarcin-ricin Parent Motif - bacterial LSU H95 IL
18IL_53587.218Base triple, intercalated pair, and bulged bases making long-range interactions. | IL_53587.1 is a mixed group with either one cSW pair or an intercalated base
19IL_37964.216Recurrent Sub-motif found in junctions
20IL_19986.215Pair and triple
21IL_31555.815Tandem sheared with inserted, unpaired purine
22IL_58261.213SRP Loop E-like motif | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
23IL_92114.511GAAA loop receptor "platform" motif
24IL_92122.210
25IL_11015.310tHS and base triple with flanking pair
26IL_02809.510REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
27IL_70237.79
28IL_86933.29Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
29IL_72158.79LSU Helix 62 (H62) IL
30IL_13069.79LSU 3WJ H32-H33-H35A
31IL_32902.29Stacked cWW-cWH pairs
32IL_39212.28
33IL_12849.28
34IL_89033.2823S H41 IL and 16S h18 IL : Has large bulge on one side
35IL_74856.48LSU Helix 89 (H89) IL2
36IL_08926.6723S H91 IL
37IL_77263.37Kink-turn from U4
38IL_73000.47cHS-cWS
39IL_31066.67SSU Helix 44 (h44) extension
40IL_82188.57LSU H68 IL from H.m.
41IL_93568.67Triple Sheared (tSH-tHS-tHS) with wobble cWW.
42IL_95652.67SSU Helix 27 (h27) IL Sarcin-Ricin motif
43IL_98016.26One or more bulged nucleotides
44IL_34363.46Kink-turn from 23S H42
45IL_26321.26LSU H58 IL2 H.m. | SRP Loop E-like motif | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
46IL_28572.5616S h18 kink-turn like motif
47IL_32261.46LSU Helix 89 (H89) IL2
48IL_85010.2623S H91 IL | Single-Base Intercalation Site
49IL_86694.25SSU Helix 8 (h8) IL E.c. and Yeast | LSU H68 IL from H.m.
50IL_99363.25
51IL_37053.45Kink-turn from 23S H58
52IL_60760.25
53IL_12211.45
54IL_73281.25Sarcin-like with an intercalated basepair
55IL_15702.25
56IL_70089.24
57IL_40053.24
58IL_37197.44
59IL_94403.74LSU H77
60IL_69536.54LSU Helix 96 (H96) IL2
61IL_09530.43Double S-turn motif
62IL_78744.23Quadruple Sheared (tSH-tSH-tHS-tHS)
63IL_87548.23
64IL_92205.23cWW AG or water inserted cWW Y-Y. | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | cWW AG or UU | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
65IL_87899.23SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
66IL_90735.33
67IL_91102.23
68IL_74876.43Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
69IL_24955.22
70IL_59563.32Sarcin-ricin motif with syn G
71IL_79398.22cWW AG or UU | cWH basepair with syn base | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif
72IL_62504.22Triple Sheared with unpaired, inserted A
73IL_80494.52LSU H58 IL2 H.m.
74IL_63917.22
75IL_37914.32

Removed motif groups

#Motif idInstancesDescription
1IL_81965.144Triple sheared (tSH-tHS-tHS) no inserted bases | Double sheared with wobble cWW.
2IL_82444.442cWH basepair
3IL_24982.821SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
4IL_68200.118One or more bulged nucleotides
5IL_94430.81516S h32-h33-h34 3WJ
6IL_49203.114Double sheared with wobble cWW.
7IL_27005.112Non-canonical cWW
8IL_65542.110SRP Loop E-like motif | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
9IL_38078.19
10IL_86357.69LSU Helix 61 IL2
11IL_51342.18Non-canonical cWW with inserted stacked base.
12IL_18916.17One or more bulged nucleotides
13IL_77920.16
14IL_01551.16
15IL_10743.16
16IL_67399.16REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
17IL_31772.16SRP Loop E-like motif | SSU Helix (23) h23 IL1
18IL_37688.15Stacked bases not quite making a basepair.
19IL_10554.15SSU Helix 23 (h23) Kink-turn T. thermophilus
20IL_59276.15
21IL_72062.15
22IL_52024.15
23IL_00520.14
24IL_45593.14
25IL_61513.14One or more bulged nucleotides
26IL_50787.14tSH-tHW-bulge
27IL_62615.14cWS plus stacked base
28IL_13023.14
29IL_14081.13Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. | tSH-inserted
30IL_48070.13C-loop
31IL_01827.13Base triple, intercalated pair, and bulged bases making long-range interactions.
32IL_17204.23
33IL_74163.13cWS making long-range triple
34IL_82600.13cWW AG or UU | cWH basepair with syn base | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif
35IL_44847.12
36IL_64894.1223S H91 IL | Single-Base Intercalation Site
37IL_68945.12
38IL_88416.12
39IL_00697.12
40IL_10119.12
41IL_69668.12
42IL_92422.12
43IL_79636.12Kink-turn
44IL_24583.12
45IL_38488.12
46IL_86033.12
47IL_06413.12LSU Helix 89 (H89) IL2 | SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
48IL_67005.12
49IL_73348.12Triple sheared (tSH-tHS-tHS) no inserted bases
50IL_94799.12tHS tHH bulge with S-turn
51IL_06527.12
52IL_51576.12
53IL_07300.32
54IL_09430.11
55IL_20608.11
56IL_34548.11
57IL_55210.111-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | 23S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | LSU H77 | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 1-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
58IL_83250.1116S h40 3WJ T.th.
59IL_14240.11
60IL_22601.11
61IL_57625.11
62IL_78984.11
63IL_85707.11
64IL_15219.11
65IL_22731.11
66IL_65681.11
67IL_70102.11
68IL_85805.11
69IL_92957.11
70IL_10628.11
71IL_15813.11
72IL_66407.11
73IL_72055.11
74IL_81512.11
75IL_85975.11
76IL_92986.11
77IL_06177.11cWW AG or UU
78IL_39296.11
79IL_62008.11
80IL_66775.11
81IL_81956.11
82IL_11529.11
83IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
84IL_40987.1123S H91 IL | Single-Base Intercalation Site
85IL_11989.11
86IL_18506.11
87IL_27713.11
88IL_41027.11
89IL_63366.11
90IL_87168.11
91IL_94958.11
92IL_00519.11Triple sheared (tSH-tHS-tHS) no inserted bases
93IL_41920.11
94IL_63723.11
95IL_76024.11
96IL_88263.11

Added motif groups

#Motif idInstancesDescription
1IL_37976.144Triple sheared (tSH-tHS-tHS) no inserted bases | Double sheared with wobble cWW. | Triple sheared (tSH-tHS-tHS) no inserted bases | SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
2IL_85638.143cWH basepair | Non-canonical cWW basepair | IL_53587.1 is a mixed group with either one cSW pair or an intercalated base
3IL_77895.120Triple sheared (tSH-tHS-tHS) no inserted bases | Double sheared with wobble cWW. | SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
4IL_21137.118Sugar-edge, 1-base platform, consensus tHS | cHS-cWS | 16S h32-h33-h34 3WJ
5IL_66381.117One or more bulged nucleotides | 1-3 bulged nucleotides | 23S H41 IL and 16S h18 IL : Has large bulge on one side
6IL_68859.116Triple sheared (tSH-tHS-tHS) no inserted bases | Double sheared with wobble cWW. | Double sheared with wobble cWW.
7IL_93635.113Non-canonical cWW
8IL_68638.112One or more bulged nucleotides
9IL_75508.112LSU Helix 61 IL2 | IL_53587.1 is a mixed group with either one cSW pair or an intercalated base
10IL_98284.19SRP Loop E-like motif | SSU Helix (23) h23 IL1 | SRP Loop E-like motif | Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
11IL_72032.18LSU Helix 96 (H96) IL2
12IL_96532.17cWS plus stacked base
13IL_22529.16cWW AG or UU | cWW AG or UU | cWH basepair with syn base | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif | Stacked bases not quite making a basepair. | IL_53587.1 is a mixed group with either one cSW pair or an intercalated base
14IL_41366.16
15IL_99561.16Double Sheared (tSH-tHS) | Stacked cWW-cWH pairs | tSH-tHW-bulge
16IL_74753.16Non-canonical cWW with inserted stacked base.
17IL_04238.15cWH basepair | Stacked bases not quite making a basepair.
18IL_70108.15REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
19IL_84284.15
20IL_99840.15Triple sheared (tSH-tHS-tHS) no inserted bases | Double sheared with wobble cWW. | Triple sheared (tSH-tHS-tHS) no inserted bases
21IL_07837.15Non-canonical cWW with inserted stacked base. | cWS plus stacked base | Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. | tSH-inserted
22IL_04466.14
23IL_77152.14
24IL_77382.14SRP Loop E-like motif | SSU Helix (23) h23 IL1
25IL_06584.14
26IL_52184.14Base triple, intercalated pair, and bulged bases making long-range interactions.
27IL_10822.14cWS making long-range triple
28IL_92942.14cWW AG or UU | cWH basepair with syn base | Single sheared (tHS) with bulged bases. LSU Helix 75 (H75) | 16S h34 ILa : Part of larger motif
29IL_75951.13Non-canonical cWW with inserted stacked base. | cWS plus stacked base
30IL_84401.13cWW with bulged base
31IL_96898.13
32IL_53504.13
33IL_68139.13One or more bulged nucleotides
34IL_35279.12
35IL_58695.12
36IL_87433.12
37IL_19589.12
38IL_22611.12LSU Helix 89 (H89) IL2 | SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
39IL_41740.12
40IL_93090.12
41IL_20094.12
42IL_37400.12SSU Helix 23 (h23) Kink-turn T. thermophilus
43IL_55583.1223S H91 IL | Single-Base Intercalation Site | 16S h32-h33-h34 3WJ
44IL_27536.12Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. | tSH-inserted
45IL_70320.1216S h40 3WJ T.th.
46IL_28666.12
47IL_37481.12
48IL_51413.12Sarcin-ricin motif from Eukaryal LSU Helix 11
49IL_77809.12C-loop
50IL_22165.12
51IL_32815.12REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
52IL_57674.12
53IL_92630.12tHS tHH bulge with S-turn
54IL_79341.12Non-canonical cWW basepair
55IL_86090.12
56IL_03783.12
57IL_34637.12
58IL_81791.12
59IL_04023.11
60IL_14652.11
61IL_54405.11
62IL_83427.11
63IL_93035.11
64IL_36321.11
65IL_54542.11
66IL_58965.11
67IL_83917.11
68IL_87776.11
69IL_99739.11
70IL_24658.11
71IL_45126.11
72IL_60334.11
73IL_90660.11
74IL_05920.11One or more bulged nucleotides
75IL_37408.11Kink-turn from 23S H58
76IL_48045.11
77IL_56083.11
78IL_64749.11
79IL_91857.11Kink-turn
80IL_94312.11
81IL_21577.11LSU Helix 89 (H89) IL2 | SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
82IL_56616.11
83IL_84773.11
84IL_92115.11
85IL_66408.11
86IL_96604.11
87IL_22247.11
88IL_33156.11
89IL_39044.11
90IL_53415.1123S H91 IL
91IL_57780.11
92IL_67360.11
93IL_75176.11
94IL_92733.11
95IL_12192.11
96IL_22368.11
97IL_40852.11
98IL_58203.11cWH basepair
99IL_75231.1116S h32-h33-h34 3WJ
100IL_86167.11