Changes in PDB files used for clustering

Release 0.6 has 185 PDB files, release 0.7 has 192 PDB files, 181 of them are identical.

1 equivalence classes changed representatives: 3UXR3V2F.

10 new structures in release 0.7: 3SYW, 3SZX, 3TZR, 3U4M, 3V7E, 4AOB, 4E48, 4E5C, 4ERD, 4EYA.

Obsolete: 3UXR4V8A.

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 0.6 has 260 motif groups, release 0.7 has 263 motif groups, 142 of them are identical.

59 motif groups were updated, 59 groups are present only in release 0.6, 62 groups are only in release 0.7.

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_92484.15
2IL_82188.15LSU H68 IL from H.m.
3IL_01239.15
4IL_22732.14tSH-inserted-tHS
5IL_31066.24SSU Helix 44 (h44) extension
6IL_28572.1416S h18 kink-turn like motif
7IL_34363.13Kink-turn from 23S H42
8IL_37053.13Kink-turn from 23S H58
9IL_98421.13
10IL_15840.13
11IL_89028.13Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
12IL_30840.13
13IL_52173.13
14IL_95150.23
15IL_62499.23
16IL_95652.23SSU Helix 27 (h27) IL Sarcin-Ricin motif
17IL_79955.23SSU Helix (23) h23 IL1
18IL_82563.13Thi-box riboswitch T-loop
19IL_28942.12
20IL_46435.12
21IL_92459.12
22IL_25271.12SSU Helix 8 (h8) IL E.c. and Yeast
23IL_40892.12
24IL_37197.12
25IL_50521.12
26IL_70280.12Double sheared with wobble cWW.
27IL_94744.12Sarcin-ricin motif with extra cWW GA pair
28IL_98566.12
29IL_16166.12
30IL_23414.12
31IL_81441.12
32IL_90057.12
33IL_09882.12
34IL_16330.12
35IL_78744.12Quadruple Sheared (tSH-tSH-tHS-tHS)
36IL_55287.12
37IL_74876.12
38IL_12211.12
39IL_45794.12
40IL_52940.12
41IL_87173.12
42IL_25174.12
43IL_80093.12
44IL_97833.12
45IL_02690.11
46IL_06468.1116S h40 3WJ E.c.
47IL_12486.11
48IL_22579.11
49IL_25181.11
50IL_40845.11
51IL_53323.11
52IL_59529.11
53IL_67735.11
54IL_75688.11Part of Helix 71 (H71) junction in 23S of D.r.
55IL_80505.11
56IL_83250.1116S h40 3WJ T.th.
57IL_88403.11
58IL_97842.11
59IL_02835.11
60IL_06808.11Double sheared (tSH-tSH) one bulged base.
61IL_15205.11
62IL_29949.11
63IL_47687.11
64IL_53988.11
65IL_61723.11
66IL_68827.11Reverse Kink-Turn
67IL_76263.11
68IL_80652.11
69IL_83920.11
70IL_88865.11
71IL_02957.11
72IL_07375.11
73IL_22858.11
74IL_25307.11
75IL_30390.11
76IL_41009.11
77IL_54450.11
78IL_61730.11
79IL_76486.11Sarcin-ricin motif with syn G
80IL_81398.11
81IL_85510.11
82IL_03110.11
83IL_09333.11SSU Helix 8 (h8) IL T. thermophilus
84IL_25739.11M-Box Riboswitch
85IL_37347.11
86IL_41139.11
87IL_54576.11
88IL_62352.11
89IL_71685.11Sarcin-like with an intercalated basepair
90IL_77014.11
91IL_85805.11
92IL_98655.11Part of H71 Junction in 26S rRNA from Yeast
93IL_03741.11
94IL_23639.11tWH-tHS-L-cWW
95IL_26241.11
96IL_31006.11tSH-tHW-L-bif-cWW
97IL_37715.11
98IL_41791.11
99IL_52509.11
100IL_54954.11Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
101IL_71942.11
102IL_82113.11
103IL_86059.11
104IL_91078.11
105IL_98924.11
106IL_05221.11
107IL_11302.11
108IL_17682.11Sarcin-ricin motif from Eukaryal LSU Helix 11
109IL_24143.11Yeast 18S
110IL_26868.11
111IL_37990.11
112IL_43316.11
113IL_52752.11
114IL_63952.11
115IL_78809.11
116IL_86981.11Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
117IL_91089.11
118IL_96260.11
119IL_05462.11
120IL_20775.11tSH-inserted
121IL_25082.11
122IL_26971.11
123IL_31754.11Sarcin-ricin H95 23S rRNA E.c.
124IL_39324.11
125IL_55649.11
126IL_65788.11
127IL_75328.11
128IL_91904.11
129IL_97073.11
130IL_06306.11
131IL_12233.11
132IL_21254.11SSU Helix 11 (h11) IL Kink-turn T. thermophilus
133IL_32080.11
134IL_40527.11Kink-turn
135IL_46306.11
136IL_52958.11
137IL_55934.11kink-turn-like
138IL_66744.11SSU Helix 21 (h21) IL2 E.coli
139IL_75415.11Pseudo-knot forming internal loop
140IL_82650.11
141IL_88367.11
142IL_92280.11

Updated motif groups

#Motif idInstancesDescription
1IL_97217.2234
2IL_47174.220016S 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_13959.224Double Sheared (tSH-tHS)
9IL_93424.222tSH-inserted-tHW
10IL_32390.22116S h19 IL and 23S H41 IL
11IL_65553.221Kink-turn
12IL_55938.219LSU Helix 89 (H89) IL2. cSH Platform.
13IL_92027.21716S h21 S8 binding site
14IL_85647.216Sarcin-ricin parent motif with 15 Nts
15IL_31555.21516S decoding site
16IL_24982.315SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
17IL_49493.214Sarcin-ricin Parent Motif - bacterial LSU H95 IL
18IL_94430.21416S h32-h33-h34 3WJ
19IL_27618.21123S H73 ILa : Part of larger Motif
20IL_40090.21116S h34 ILa : Part of larger motif
21IL_24546.21023S H41 IL and 16S h18 IL : Has large bulge on one side
22IL_58291.29Recurrent Sub-motif found in junctions
23IL_47444.29SRP Loop E-like motif
24IL_92114.29GAAA loop receptor "platform" motif
25IL_92321.28Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
26IL_90459.28cWW AG or UU
27IL_83451.27cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
28IL_73000.27cHS-cWS
29IL_86357.27LSU Helix 61 IL2
30IL_53635.26LSU Helix 32 (H32) IL
31IL_72158.26LSU Helix 62 (H62) IL
32IL_13069.26LSU 3WJ H32-H33-H35A
33IL_24022.26
34IL_25230.26Bacterial 5S rRNA Loop E
35IL_44067.26Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
36IL_97057.26
37IL_70237.36
38IL_78732.35Double S-turn motif
39IL_80179.25
40IL_40387.25
41IL_02359.25
42IL_45262.25
43IL_79083.25
44IL_62661.24Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
45IL_98591.24
46IL_39526.24
47IL_38807.24
48IL_64184.24
49IL_34628.23Kink-turn
50IL_58586.23
51IL_34156.23cWW AG or UU
52IL_23262.33
53IL_80494.23LSU H58 IL2 H.m.
54IL_09348.23
55IL_16252.2323S H91 IL
56IL_82831.22Kink-turn from 16S H23
57IL_41397.22LSU Helix 96 (H96) IL2
58IL_76095.32Motif from Hairpin Ribozyme
59IL_57785.52SSU Decoding Site -- Human. Bulge-cSW-tHS

Removed motif groups

#Motif idInstancesDescription
1IL_11616.155cWH basepair with syn base
2IL_54307.127C-loop
3IL_73663.1151 or 2 bulged bases
4IL_48187.111Single sheared with bulged bases
5IL_99515.11123S H91 IL
6IL_68939.19Kink-turn from U4
7IL_76831.18REV element IL with syn G
8IL_40239.18Leadzyme Motif
9IL_82367.47
10IL_29610.16
11IL_59016.15
12IL_24476.15
13IL_78157.15
14IL_92936.15
15IL_93335.25
16IL_18947.14
17IL_69124.14
18IL_11167.34
19IL_49111.14tHS tHH bulge with S-turn
20IL_11594.14
21IL_92333.14
22IL_99434.13Single-Base Intercalation Site
23IL_30979.13
24IL_10804.13
25IL_13740.13
26IL_09390.12
27IL_47247.12
28IL_69009.12
29IL_89461.12
30IL_62718.12
31IL_19202.12
32IL_63741.12
33IL_91543.12
34IL_19889.12
35IL_75449.12
36IL_92123.12
37IL_67117.12
38IL_68736.12
39IL_02691.12
40IL_44742.12
41IL_57870.12
42IL_88684.12
43IL_17109.11
44IL_30650.11
45IL_10109.11H71 junction in 23S rRNA of T.th.
46IL_91513.11
47IL_31793.11Kink-turn from 16S H23
48IL_48650.11
49IL_38333.11
50IL_65978.11
51IL_24335.11
52IL_39165.11
53IL_50767.11
54IL_39230.11
55IL_67697.11
56IL_55167.11
57IL_14225.11
58IL_29877.11
59IL_99165.11

Added motif groups

#Motif idInstancesDescription
1IL_06390.125cWH basepair with syn base
2IL_73276.120C-loop
3IL_06429.11616S h19 IL and 23S H41 IL | 1 or 2 bulged bases
4IL_21304.111Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
5IL_46648.11123S H91 IL | Single-Base Intercalation Site
6IL_02809.18REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
7IL_89088.1616S h19 IL and 23S H41 IL
8IL_08926.1623S H91 IL
9IL_10007.16Single sheared with bulged bases
10IL_77263.15Kink-turn from U4
11IL_71288.15Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
12IL_07911.15
13IL_47758.14REV element IL with syn G | Tandem cWW pairs (Not AU or GC)
14IL_21333.14tSH-tHW-bulge
15IL_98556.14
16IL_53774.13Single sheared with bulged bases
17IL_71565.13
18IL_43946.13
19IL_45808.13
20IL_75447.13
21IL_01054.12
22IL_12068.12
23IL_31707.12Vitamin B12 aptamer
24IL_78674.12tHS tHH bulge with S-turn
25IL_12269.12
26IL_37406.12
27IL_48285.12Leadzyme Motif
28IL_65137.12Kink-turn like motif in Group I Intron
29IL_87548.12
30IL_43933.12
31IL_99575.12
32IL_21495.12
33IL_14023.12
34IL_74291.12
35IL_00998.12
36IL_16415.12SSU Helix 23 (h23) Kink-turn T. thermophilus
37IL_91026.12
38IL_11869.11
39IL_17603.11
40IL_31241.11
41IL_47457.11
42IL_58454.11
43IL_91379.11
44IL_18755.11
45IL_60643.11
46IL_95939.11
47IL_82601.11Tandem cWW water-inserted CU pairs
48IL_97191.11Sarcin-ricin motif with cWW UU instead of tSH basepair.
49IL_12507.11
50IL_41849.11
51IL_53423.11
52IL_07675.11tHS tHH bulge with S-turn
53IL_13682.11
54IL_21421.11
55IL_13942.11
56IL_56513.11
57IL_89794.11
58IL_23448.11
59IL_56779.11
60IL_90880.11
61IL_27243.11
62IL_57977.11