Changes in PDB files used for clustering

Release 1.0 has 200 PDB files, release 1.1 has 200 PDB files, 198 of them are identical.

1 equivalence classes changed representatives: 2ZJR4IOA.

1 new structures in release 1.1: 3ZP8.

Obsolete: 3ZD33ZP8.

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 1.0 has 267 motif groups, release 1.1 has 271 motif groups, 179 of them are identical.

51 motif groups were updated, 37 groups are present only in release 1.0, 41 groups are only in release 1.1.

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_31555.315Tandem sheared with inserted, unpaired purine.
2IL_02809.29REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
3IL_47444.39SRP Loop E-like motif
4IL_92114.39GAAA loop receptor "platform" motif
5IL_73000.27cHS-cWS
6IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
7IL_54420.16
8IL_70237.36
9IL_77263.15Kink-turn from U4
10IL_25300.1516S h19 IL and 23S H41 IL
11IL_82188.15LSU H68 IL from H.m.
12IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
13IL_78732.35Double S-turn motif
14IL_92484.15
15IL_28572.1416S h18 kink-turn like motif
16IL_31066.24SSU Helix 44 (h44) extension
17IL_22732.14tSH-inserted-tHS
18IL_71565.24
19IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
20IL_39526.44
21IL_52173.13
22IL_80494.23LSU H58 IL2 H.m.
23IL_34628.23Kink-turn
24IL_37053.13Kink-turn from 23S H58
25IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
26IL_95150.33
27IL_79955.23SSU Helix (23) h23 IL1
28IL_05723.13
29IL_58586.23
30IL_75447.13
31IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
32IL_82563.13Thi-box riboswitch T-loop
33IL_43946.13
34IL_30840.13
35IL_89231.12LSU H77
36IL_21495.12
37IL_31707.12Vitamin B12 aptamer
38IL_52940.12
39IL_09882.12
40IL_77076.12
41IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
42IL_70280.12Double sheared with wobble cWW.
43IL_90057.12
44IL_46435.12
45IL_15840.22Triple Sheared with unpaired, inserted A
46IL_37197.12
47IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
48IL_01054.12
49IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
50IL_16252.3223S H91 IL
51IL_94744.12Sarcin-ricin motif with extra cWW GA pair
52IL_45794.12
53IL_11751.12
54IL_97833.12
55IL_00998.12
56IL_27892.12
57IL_07300.12
58IL_16330.12
59IL_76095.32Motif from Hairpin Ribozyme
60IL_98566.12
61IL_12211.12
62IL_55287.12
63IL_40892.12
64IL_96446.12
65IL_50521.12
66IL_65137.12Kink-turn like motif in Group I Intron
67IL_37406.12
68IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
69IL_87548.12
70IL_80093.12
71IL_28942.12
72IL_23414.12
73IL_63952.11
74IL_83250.1116S h40 3WJ T.th.
75IL_03110.11
76IL_68827.11Reverse Kink-Turn
77IL_83920.11
78IL_06468.1116S h40 3WJ E.c.
79IL_05462.11
80IL_97073.11
81IL_02690.11
82IL_75415.11Pseudo-knot forming internal loop
83IL_82113.11
84IL_98924.11
85IL_59529.11
86IL_17603.11
87IL_88367.11
88IL_60649.11Kink-turn
89IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
90IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
91IL_47687.11
92IL_31006.11tSH-tHW-L-bif-cWW
93IL_80652.11
94IL_12486.11
95IL_03741.11
96IL_25082.11
97IL_71685.11Sarcin-like with an intercalated basepair
98IL_25181.11
99IL_56513.11
100IL_40527.11Kink-turn
101IL_77296.11
102IL_39324.11
103IL_89794.11
104IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
105IL_37715.11
106IL_54450.11
107IL_77014.11
108IL_91078.11
109IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
110IL_23639.11tWH-tHS-L-cWW
111IL_21421.11
112IL_41139.11
113IL_03282.11
114IL_88865.11
115IL_86059.11
116IL_12507.11
117IL_53988.11
118IL_52509.11
119IL_71942.11
120IL_67735.11
121IL_76486.11Sarcin-ricin motif with syn G
122IL_37990.11
123IL_58454.11
124IL_91089.11
125IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
126IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
127IL_41791.11
128IL_43316.11
129IL_80505.11
130IL_26868.11
131IL_11778.11
132IL_27243.11
133IL_75328.11
134IL_97842.11
135IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
136IL_82601.11Tandem cWW water-inserted CU pairs
137IL_23448.11
138IL_57285.11
139IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
140IL_82650.11
141IL_11302.11
142IL_52958.11
143IL_20775.11tSH-inserted
144IL_65788.11
145IL_61730.11
146IL_06306.11
147IL_37347.11
148IL_46306.11
149IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
150IL_60643.11
151IL_40845.11
152IL_92280.11
153IL_57977.11
154IL_02835.11
155IL_25307.11
156IL_66744.11SSU Helix 21 (h21) IL2 E.coli
157IL_06808.11Double sheared (tSH-tSH) one bulged base.
158IL_03931.1116S h19 IL and 23S H41 IL
159IL_78809.11
160IL_13682.11
161IL_83856.11
162IL_05221.11
163IL_06471.11
164IL_91904.11
165IL_15205.11
166IL_91044.11
167IL_27668.11
168IL_85805.11
169IL_76263.11
170IL_91379.11
171IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
172IL_55649.11
173IL_54576.11
174IL_81398.11
175IL_53323.11
176IL_26971.11
177IL_02957.11
178IL_85510.11
179IL_06847.11Group II Intron IL

Updated motif groups

#Motif idInstancesDescription
1IL_97217.62391-3 bulged nucleotides, same chain | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_47174.6201cWW AG or water inserted cWW Y-Y.
3IL_39199.354Hoogsteen-edge Platform, Single bulged base
4IL_41766.349Tandem cWW pairs (Not AU or GC)
5IL_56465.346Single, unpaired intercalated base, consensus A
6IL_44540.343Sugar-edge, 1-base platform, consensus tHS
7IL_87904.431Triple sheared (tSH-tHS-tHS) no inserted bases
8IL_06390.326cWH basepair with syn base
9IL_13959.324Double Sheared (tSH-tHS)
10IL_93424.322tSH-inserted-tHW
11IL_65553.522Kink-turn
12IL_73276.220C-loop
13IL_55938.318LSU Helix 89 (H89) IL2. cSH Platform.
14IL_92027.31716S h21 S8 binding site
15IL_24982.416SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
16IL_85647.316Sarcin-ricin parent motif with 15 Nts
17IL_94430.41516S h32-h33-h34 3WJ
18IL_49493.314Sarcin-ricin Parent Motif - bacterial LSU H95 IL
19IL_46648.21123S H91 IL | Single-Base Intercalation Site
20IL_40090.31116S h34 ILa : Part of larger motif
21IL_21304.211Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
22IL_24546.31023S H41 IL and 16S h18 IL : Has large bulge on one side
23IL_58291.39Recurrent Sub-motif found in junctions
24IL_90459.39cWW AG or UU
25IL_92321.37Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
26IL_97057.36
27IL_53635.36LSU Helix 32 (H32) IL
28IL_13069.36LSU 3WJ H32-H33-H35A
29IL_72158.36LSU Helix 62 (H62) IL
30IL_44067.36Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
31IL_25230.36Bacterial 5S rRNA Loop E
32IL_90133.26
33IL_45262.35
34IL_86357.35LSU Helix 61 IL2
35IL_02359.35
36IL_79083.35
37IL_08926.2523S H91 IL
38IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
39IL_21333.24tSH-tHW-bulge
40IL_16166.3423S H91 IL
41IL_98591.34
42IL_38807.34
43IL_34363.24Kink-turn from 23S H42
44IL_34156.63cWW AG or UU
45IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
46IL_98421.33SSU Helix 12 (h12) IL
47IL_62499.63
48IL_89028.53Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th.
49IL_48918.23Kink-turn variant
50IL_23262.42
51IL_09348.52Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW

Removed motif groups

#Motif idInstancesDescription
1IL_91487.12116S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_06429.315cWW-bulge-cWW
3IL_27618.21123S H73 ILa : Part of larger Motif
4IL_10007.27Single sheared with bulged bases
5IL_38960.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
6IL_01239.15
7IL_87218.1423S H91 IL
8IL_40387.44LSU Helix 89 (H89) IL2
9IL_98556.44
10IL_36254.13
11IL_57216.13tHS tHH bulge with S-turn
12IL_53774.13Single sheared with bulged bases
13IL_16377.12
14IL_87336.12LSU Eukaryal Helix 96 (H96) IL1
15IL_41397.22LSU Helix 96 (H96) IL2
16IL_64648.12tHS tHH bulge with S-turn
17IL_42397.12
18IL_25174.12
19IL_91132.12
20IL_79870.12tHS tHH bulge with S-turn
21IL_06635.12
22IL_81441.12
23IL_82519.11Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena
24IL_98688.11
25IL_11869.11
26IL_61991.11
27IL_63837.11tHS tHH bulge with S-turn
28IL_18755.11
29IL_88403.11
30IL_22579.11
31IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
32IL_90880.11
33IL_03914.11
34IL_44803.11
35IL_77195.11
36IL_31241.11
37IL_55934.11kink-turn-like

Added motif groups

#Motif idInstancesDescription
1IL_28947.12123S H91 IL | cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
2IL_92109.115cWW-bulge-cWW | 16S h19 IL and 23S H41 IL | cWW-bulge-cWW
3IL_43124.11123S H73 ILa : Part of larger Motif | Single sheared with bulged bases
4IL_39585.16Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
5IL_16207.15Single sheared with bulged bases
6IL_01080.14
7IL_42251.14
8IL_08559.14LSU Helix 89 (H89) IL2
9IL_10647.13tHS tHH bulge with S-turn
10IL_56077.13
11IL_92267.1323S H73 ILa : Part of larger Motif
12IL_80348.1323S H91 IL
13IL_09587.12
14IL_24358.12
15IL_33964.12
16IL_88180.12cWW-bulge-cWW
17IL_09901.12tHS tHH bulge with S-turn
18IL_49550.12tHS tHH bulge with S-turn
19IL_91273.12
20IL_69536.12LSU Helix 96 (H96) IL2
21IL_19898.12
22IL_33925.12
23IL_47732.11
24IL_28468.11Single sheared with bulged bases
25IL_34868.11LSU Eukaryal Helix 96 (H96) IL1
26IL_28644.11
27IL_52610.11
28IL_13434.11
29IL_41341.11Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
30IL_15674.11Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena | Part of H71 junction in 23S rRNA from T.th.
31IL_30067.11
32IL_64589.11
33IL_95774.11tHS tHH bulge with S-turn
34IL_04550.11tHS tHH bulge with S-turn
35IL_30354.11
36IL_42891.11
37IL_31290.11
38IL_09491.11
39IL_21221.11SSU Helix 12 (h12) IL
40IL_46721.11
41IL_87394.11