Changes in PDB files used for clustering

Release 1.0 has 199 PDB files, release 1.1 has 199 PDB files, 197 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

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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_47444.39SRP Loop E-like motif
3IL_92114.39GAAA loop receptor "platform" motif
4IL_02809.29REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
5IL_73000.27cHS-cWS
6IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
7IL_70237.36
8IL_54420.16
9IL_92484.15
10IL_77263.15Kink-turn from U4
11IL_82188.15LSU H68 IL from H.m.
12IL_25300.1516S h19 IL and 23S H41 IL
13IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
14IL_78732.35Double S-turn motif
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_80494.23LSU H58 IL2 H.m.
22IL_52173.13
23IL_37053.13Kink-turn from 23S H58
24IL_95150.33
25IL_79955.23SSU Helix (23) h23 IL1
26IL_05723.13
27IL_75447.13
28IL_58586.23
29IL_82563.13Thi-box riboswitch T-loop
30IL_30840.13
31IL_34628.23Kink-turn
32IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
33IL_43946.13
34IL_74876.23Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
35IL_50521.12
36IL_65137.12Kink-turn like motif in Group I Intron
37IL_80093.12
38IL_21495.12
39IL_70280.12Double sheared with wobble cWW.
40IL_07300.12
41IL_16330.12
42IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
43IL_87548.12
44IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
45IL_55287.12
46IL_40892.12
47IL_89231.12LSU H77
48IL_15840.22Triple Sheared with unpaired, inserted A
49IL_16252.3223S H91 IL
50IL_94744.12Sarcin-ricin motif with extra cWW GA pair
51IL_31707.12Vitamin B12 aptamer
52IL_52940.12
53IL_09882.12
54IL_77076.12
55IL_46435.12
56IL_01054.12
57IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS
58IL_00998.12
59IL_27892.12
60IL_23414.12
61IL_90057.12
62IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
63IL_37406.12
64IL_11751.12
65IL_97833.12
66IL_98566.12
67IL_12211.12
68IL_28942.12
69IL_37197.12
70IL_76095.32Motif from Hairpin Ribozyme
71IL_45794.12
72IL_40845.11
73IL_92280.11
74IL_76263.11
75IL_83920.11
76IL_06468.1116S h40 3WJ E.c.
77IL_80652.11
78IL_12486.11
79IL_71942.11
80IL_97842.11
81IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
82IL_82601.11Tandem cWW water-inserted CU pairs
83IL_60643.11
84IL_85805.11
85IL_03110.11
86IL_68827.11Reverse Kink-Turn
87IL_47687.11
88IL_89794.11
89IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
90IL_37715.11
91IL_54450.11
92IL_06306.11
93IL_37347.11
94IL_46306.11
95IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
96IL_91044.11
97IL_63952.11
98IL_83250.1116S h40 3WJ T.th.
99IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
100IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
101IL_53988.11
102IL_52509.11
103IL_13682.11
104IL_83856.11
105IL_05221.11
106IL_06471.11
107IL_91904.11
108IL_15205.11
109IL_06847.11Group II Intron IL
110IL_39324.11
111IL_11778.11
112IL_61730.11
113IL_81398.11
114IL_53323.11
115IL_26971.11
116IL_02957.11
117IL_85510.11
118IL_60649.11Kink-turn
119IL_86059.11
120IL_12507.11
121IL_26868.11
122IL_52958.11
123IL_20775.11tSH-inserted
124IL_65788.11
125IL_78809.11
126IL_75415.11Pseudo-knot forming internal loop
127IL_82113.11
128IL_98924.11
129IL_59529.11
130IL_17603.11
131IL_88367.11
132IL_77296.11
133IL_41791.11
134IL_43316.11
135IL_80505.11
136IL_11302.11
137IL_06808.11Double sheared (tSH-tSH) one bulged base.
138IL_03931.1116S h19 IL and 23S H41 IL
139IL_54576.11
140IL_03741.11
141IL_25082.11
142IL_71685.11Sarcin-like with an intercalated basepair
143IL_25181.11
144IL_56513.11
145IL_40527.11Kink-turn
146IL_03282.11
147IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
148IL_82650.11
149IL_66744.11SSU Helix 21 (h21) IL2 E.coli
150IL_55649.11
151IL_91078.11
152IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
153IL_23639.11tWH-tHS-L-cWW
154IL_21421.11
155IL_41139.11
156IL_94973.11Sarcin-Ricin from Group II Intron with inserted base and poor modeling:
157IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
158IL_57977.11
159IL_02835.11
160IL_25307.11
161IL_59934.11SSU Helix 23 (h23) Kink-turn E. coli
162IL_05462.11
163IL_97073.11
164IL_02690.11
165IL_67735.11
166IL_76486.11Sarcin-ricin motif with syn G
167IL_37990.11
168IL_58454.11
169IL_91089.11

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_65553.522Kink-turn
11IL_93424.322tSH-inserted-tHW
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_90459.39cWW AG or UU
24IL_58291.39Recurrent Sub-motif found in junctions
25IL_92321.37Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
26IL_25230.36Bacterial 5S rRNA Loop E
27IL_90133.26
28IL_97057.36
29IL_53635.36LSU Helix 32 (H32) IL
30IL_13069.36LSU 3WJ H32-H33-H35A
31IL_72158.36LSU Helix 62 (H62) IL
32IL_44067.36Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
33IL_08926.2523S H91 IL
34IL_45262.35
35IL_86357.35LSU Helix 61 IL2
36IL_02359.35
37IL_79083.35
38IL_34363.24Kink-turn from 23S H42
39IL_93568.24Triple Sheared (tSH-tHS-tHS) with wobble cWW.
40IL_21333.24tSH-tHW-bulge
41IL_16166.3423S H91 IL
42IL_98591.34
43IL_38807.34
44IL_48918.23Kink-turn variant
45IL_34156.63cWW AG or UU
46IL_09520.23Leadzyme Motif. SSU Decoding site motif, extended. | cWW-L-cWW-cWW
47IL_98421.33SSU Helix 12 (h12) IL
48IL_62499.63
49IL_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.
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_98556.44
8IL_87218.1423S H91 IL
9IL_40387.44LSU Helix 89 (H89) IL2
10IL_53774.13Single sheared with bulged bases
11IL_36254.13
12IL_57216.13tHS tHH bulge with S-turn
13IL_79870.12tHS tHH bulge with S-turn
14IL_06635.12
15IL_81441.12
16IL_16377.12
17IL_87336.12LSU Eukaryal Helix 96 (H96) IL1
18IL_41397.22LSU Helix 96 (H96) IL2
19IL_64648.12tHS tHH bulge with S-turn
20IL_42397.12
21IL_25174.12
22IL_91132.12
23IL_31241.11
24IL_55934.11kink-turn-like
25IL_82519.11Part of Helix 71 (H71) junction in 23S rRNA E.c. H.m. and Tetrahymena
26IL_98688.11
27IL_11869.11
28IL_61991.11
29IL_63837.11tHS tHH bulge with S-turn
30IL_18755.11
31IL_88403.11
32IL_22579.11
33IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
34IL_90880.11
35IL_03914.11
36IL_44803.11
37IL_77195.11

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_08559.14LSU Helix 89 (H89) IL2
7IL_01080.14
8IL_42251.14
9IL_80348.1323S H91 IL
10IL_10647.13tHS tHH bulge with S-turn
11IL_56077.13
12IL_92267.1323S H73 ILa : Part of larger Motif
13IL_19898.12
14IL_33925.12
15IL_09587.12
16IL_24358.12
17IL_33964.12
18IL_88180.12cWW-bulge-cWW
19IL_09901.12tHS tHH bulge with S-turn
20IL_49550.12tHS tHH bulge with S-turn
21IL_91273.12
22IL_69536.12LSU Helix 96 (H96) IL2
23IL_31290.11
24IL_09491.11
25IL_21221.11SSU Helix 12 (h12) IL
26IL_46721.11
27IL_87394.11
28IL_47732.11
29IL_28468.11Single sheared with bulged bases
30IL_34868.11LSU Eukaryal Helix 96 (H96) IL1
31IL_28644.11
32IL_52610.11
33IL_13434.11
34IL_41341.11Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
35IL_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.
36IL_30067.11
37IL_64589.11
38IL_95774.11tHS tHH bulge with S-turn
39IL_04550.11tHS tHH bulge with S-turn
40IL_30354.11
41IL_42891.11