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_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.
7IL_51439.16
8IL_25230.56Bacterial 5S rRNA Loop E
9IL_71229.25
10IL_39980.25
11IL_55114.35Double S-turn motif | tHS tHH bulge with S-turn | Double S-turn motif
12IL_04397.25
13IL_98421.75SSU Helix 12 (h12) IL | SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
14IL_16166.5423S H91 IL
15IL_77076.34
16IL_39526.44
17IL_48918.34Kink-turn variant
18IL_83339.14
19IL_32508.1423S H91 IL
20IL_43727.14tSH-inserted-tHS | tHS tHH bulge with S-turn | tSH-inserted-tHS
21IL_94519.24
22IL_21639.23
23IL_34628.23Kink-turn
24IL_40892.23
25IL_43946.13
26IL_22025.13
27IL_82563.13Thi-box riboswitch T-loop
28IL_19268.13
29IL_62499.10323S H91 IL
30IL_45592.2323S H91 IL
31IL_98073.23Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
32IL_09882.12
33IL_52940.12
34IL_94744.12Sarcin-ricin motif with extra cWW GA pair
35IL_06675.12Triple Sheared with unpaired, inserted A
36IL_16330.12
37IL_39439.12
38IL_44092.12
39IL_67024.12
40IL_03362.12
41IL_06692.12
42IL_44977.12LSU H58 IL2 H.m. | SSU Helix (23) h23 IL1
43IL_31707.12Vitamin B12 aptamer
44IL_35558.12
45IL_68034.12
46IL_21062.12Sarcin-ricin motif with cWW UU instead of tSH basepair.
47IL_23414.12
48IL_40041.12
49IL_50521.12
50IL_74462.12
51IL_28003.22
52IL_28028.12
53IL_43363.12
54IL_46435.12
55IL_76095.32Motif from Hairpin Ribozyme
56IL_91942.12
57IL_98172.12
58IL_21495.12
59IL_28058.12
60IL_33842.12
61IL_39175.12
62IL_65137.12Kink-turn like motif in Group I Intron
63IL_70401.12
64IL_00346.11
65IL_03110.11
66IL_06468.1116S h40 3WJ E.c.
67IL_25808.11
68IL_28644.11
69IL_39324.11
70IL_47702.11
71IL_59907.11
72IL_66744.11SSU Helix 21 (h21) IL2 E.coli
73IL_70529.11
74IL_81587.11
75IL_86059.11
76IL_89794.11
77IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
78IL_01562.11
79IL_03282.11
80IL_11268.11
81IL_25926.11
82IL_29058.11
83IL_34816.11
84IL_41139.11
85IL_48036.11
86IL_52958.11
87IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
88IL_77296.11
89IL_86060.11
90IL_90633.11
91IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
92IL_98924.11
93IL_02257.11
94IL_11302.11
95IL_22909.11
96IL_26868.11
97IL_31160.11
98IL_35267.11
99IL_41215.11
100IL_48268.11
101IL_62296.11
102IL_73656.11
103IL_77862.11
104IL_82601.11Tandem cWW water-inserted CU pairs
105IL_86336.11
106IL_91044.11
107IL_96591.11
108IL_99784.11
109IL_03808.11
110IL_06808.11Double sheared (tSH-tSH) one bulged base.
111IL_11778.11
112IL_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)
113IL_26971.11
114IL_41371.11
115IL_45432.11
116IL_74400.11
117IL_79910.11
118IL_82650.11
119IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
120IL_91061.11
121IL_97803.11
122IL_99937.11
123IL_02835.11
124IL_06847.11Group II Intron IL
125IL_12507.11
126IL_27640.11
127IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
128IL_36006.11
129IL_41516.11
130IL_55649.11
131IL_62617.11
132IL_68827.11Reverse Kink-Turn
133IL_80505.11
134IL_87394.11
135IL_91078.11
136IL_97842.11
137IL_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.
138IL_05221.11
139IL_07252.11
140IL_21077.11
141IL_23639.11tWH-tHS-L-cWW
142IL_37347.11
143IL_40364.11
144IL_42891.11
145IL_45617.11
146IL_57334.11
147IL_63952.11
148IL_69482.11
149IL_75415.11Pseudo-knot forming internal loop
150IL_80652.11
151IL_84276.11
152IL_87523.11
153IL_91089.11
154IL_02957.11
155IL_05513.11
156IL_08588.11
157IL_15205.11
158IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
159IL_33217.11
160IL_37970.11tHS tHH bulge with S-turn | tSH-inserted-tHS
161IL_40527.11Kink-turn
162IL_51572.11
163IL_57977.11
164IL_70069.11tHS tHH bulge with S-turn
165IL_80714.11
166IL_84995.11
167IL_88367.11
168IL_03030.11tSH-inserted-tHS
169IL_06306.11
170IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
171IL_15884.11
172IL_25420.11
173IL_40845.11
174IL_47687.11
175IL_52610.11
176IL_58270.11
177IL_76263.11
178IL_81280.11
179IL_85510.11
180IL_89463.11

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_02809.510REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
25IL_92122.210
26IL_11015.310tHS and base triple with flanking pair
27IL_32902.29Stacked cWW-cWH pairs
28IL_70237.79
29IL_86933.29Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
30IL_72158.79LSU Helix 62 (H62) IL
31IL_13069.79LSU 3WJ H32-H33-H35A
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_95652.67SSU Helix 27 (h27) IL Sarcin-Ricin motif
37IL_08926.6723S H91 IL
38IL_77263.37Kink-turn from U4
39IL_73000.47cHS-cWS
40IL_31066.67SSU Helix 44 (h44) extension
41IL_82188.57LSU H68 IL from H.m.
42IL_93568.67Triple Sheared (tSH-tHS-tHS) with wobble cWW.
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_15702.25
50IL_86694.25SSU Helix 8 (h8) IL E.c. and Yeast | LSU H68 IL from H.m.
51IL_99363.25
52IL_37053.45Kink-turn from 23S H58
53IL_60760.25
54IL_12211.45
55IL_73281.25Sarcin-like with an intercalated basepair
56IL_69536.54LSU Helix 96 (H96) IL2
57IL_70089.24
58IL_40053.24
59IL_37197.44
60IL_94403.74LSU H77
61IL_74876.43Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
62IL_09530.43Double S-turn motif
63IL_78744.23Quadruple Sheared (tSH-tSH-tHS-tHS)
64IL_87548.23
65IL_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)
66IL_87899.23SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
67IL_90735.33
68IL_91102.23
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_31772.16SRP Loop E-like motif | SSU Helix (23) h23 IL1
14IL_77920.16
15IL_01551.16
16IL_10743.16
17IL_67399.16REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
18IL_52024.15
19IL_37688.15Stacked bases not quite making a basepair.
20IL_10554.15SSU Helix 23 (h23) Kink-turn T. thermophilus
21IL_59276.15
22IL_72062.15
23IL_13023.14
24IL_00520.14
25IL_45593.14
26IL_61513.14One or more bulged nucleotides
27IL_50787.14tSH-tHW-bulge
28IL_62615.14cWS plus stacked base
29IL_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
30IL_14081.13Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. | tSH-inserted
31IL_48070.13C-loop
32IL_01827.13Base triple, intercalated pair, and bulged bases making long-range interactions.
33IL_17204.23
34IL_74163.13cWS making long-range triple
35IL_07300.32
36IL_44847.12
37IL_64894.1223S H91 IL | Single-Base Intercalation Site
38IL_68945.12
39IL_88416.12
40IL_00697.12
41IL_10119.12
42IL_69668.12
43IL_92422.12
44IL_79636.12Kink-turn
45IL_24583.12
46IL_38488.12
47IL_86033.12
48IL_06413.12LSU Helix 89 (H89) IL2 | SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
49IL_67005.12
50IL_73348.12Triple sheared (tSH-tHS-tHS) no inserted bases
51IL_94799.12tHS tHH bulge with S-turn
52IL_06527.12
53IL_51576.12
54IL_00519.11Triple sheared (tSH-tHS-tHS) no inserted bases
55IL_41920.11
56IL_63723.11
57IL_76024.11
58IL_88263.11
59IL_09430.11
60IL_20608.11
61IL_34548.11
62IL_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
63IL_83250.1116S h40 3WJ T.th.
64IL_14240.11
65IL_22601.11
66IL_57625.11
67IL_78984.11
68IL_85707.11
69IL_15219.11
70IL_22731.11
71IL_65681.11
72IL_70102.11
73IL_85805.11
74IL_92957.11
75IL_10628.11
76IL_15813.11
77IL_66407.11
78IL_72055.11
79IL_81512.11
80IL_85975.11
81IL_92986.11
82IL_06177.11cWW AG or UU
83IL_39296.11
84IL_62008.11
85IL_66775.11
86IL_81956.11
87IL_11529.11
88IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
89IL_40987.1123S H91 IL | Single-Base Intercalation Site
90IL_11989.11
91IL_18506.11
92IL_27713.11
93IL_41027.11
94IL_63366.11
95IL_87168.11
96IL_94958.11

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_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
23IL_04466.14
24IL_77152.14
25IL_77382.14SRP Loop E-like motif | SSU Helix (23) h23 IL1
26IL_06584.14
27IL_52184.14Base triple, intercalated pair, and bulged bases making long-range interactions.
28IL_10822.14cWS making long-range triple
29IL_53504.13
30IL_68139.13One or more bulged nucleotides
31IL_75951.13Non-canonical cWW with inserted stacked base. | cWS plus stacked base
32IL_84401.13cWW with bulged base
33IL_96898.13
34IL_03783.12
35IL_34637.12
36IL_81791.12
37IL_35279.12
38IL_58695.12
39IL_87433.12
40IL_19589.12
41IL_22611.12LSU Helix 89 (H89) IL2 | SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
42IL_41740.12
43IL_93090.12
44IL_20094.12
45IL_37400.12SSU Helix 23 (h23) Kink-turn T. thermophilus
46IL_55583.1223S H91 IL | Single-Base Intercalation Site | 16S h32-h33-h34 3WJ
47IL_27536.12Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW | Leadzyme Motif. LSU H101 IL2. SSU Decoding site. | tSH-inserted
48IL_70320.1216S h40 3WJ T.th.
49IL_28666.12
50IL_37481.12
51IL_51413.12Sarcin-ricin motif from Eukaryal LSU Helix 11
52IL_77809.12C-loop
53IL_22165.12
54IL_32815.12REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
55IL_57674.12
56IL_92630.12tHS tHH bulge with S-turn
57IL_79341.12Non-canonical cWW basepair
58IL_86090.12
59IL_12192.11
60IL_22368.11
61IL_40852.11
62IL_58203.11cWH basepair
63IL_75231.1116S h32-h33-h34 3WJ
64IL_86167.11
65IL_04023.11
66IL_14652.11
67IL_54405.11
68IL_83427.11
69IL_93035.11
70IL_36321.11
71IL_54542.11
72IL_58965.11
73IL_83917.11
74IL_87776.11
75IL_99739.11
76IL_24658.11
77IL_45126.11
78IL_60334.11
79IL_90660.11
80IL_05920.11One or more bulged nucleotides
81IL_37408.11Kink-turn from 23S H58
82IL_48045.11
83IL_56083.11
84IL_64749.11
85IL_91857.11Kink-turn
86IL_94312.11
87IL_21577.11LSU Helix 89 (H89) IL2 | SSU Helix 12 (h12) IL | LSU Eukaryal Helix 96 (H96) IL1
88IL_56616.11
89IL_84773.11
90IL_92115.11
91IL_66408.11
92IL_96604.11
93IL_22247.11
94IL_33156.11
95IL_39044.11
96IL_53415.1123S H91 IL
97IL_57780.11
98IL_67360.11
99IL_75176.11
100IL_92733.11