Changes in PDB files used for clustering

Release 1.14 has 230 PDB files, release 1.15 has 239 PDB files, 230 of them are identical.

No equivalence class representatives have been replaced.

9 new structures in release 1.15: 4CUV, 4CUX, 4KR2, 4L81, 4O26, 4P5J, 4P8Z, 4P9R, 4PQV.

No equivalence class representatives have been obsoleted.

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 1.14 has 264 motif groups, release 1.15 has 285 motif groups, 184 of them are identical.

51 motif groups were updated, 29 groups are present only in release 1.14, 50 groups are only in release 1.15.

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
1HL_48039.211MS2 virus RNA Hairpin
2HL_17723.510LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
3HL_15603.29U1A protein-binding Hairpin Loop.
4HL_24544.38LSU Helix 53 (H53) Hairpin Loop. T-loop like.
5HL_42677.27
6HL_89236.16LSU Helix 69 (H69) Hairpin Loop
7HL_57514.26Two base, cross-stacked hairpin loop
8HL_62228.46LSU Helix 35A (H35A) Hairpin Loop
9HL_06643.36tRNA D-loop. Sec tRNA
10HL_86077.15GNRA with one bulged base | GNRA-like with bulged base.
11HL_45018.35Hairpin-Hairpin Interacting HL
12HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
13HL_72273.15tRNA D-loop
14HL_78731.25LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
15HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
16HL_98523.24GNRA-like. Closed by tSH UC.
17HL_48116.34GNRA-like with 5'-stacking of first unpaired base.
18HL_82418.14LSU Helix 8 (H8) Hairpin Loop
19HL_11376.14LSU Helix 8 (H8) Hairpin Loop
20HL_86115.14
21HL_25124.24tSW GA closed tetraloops
22HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
23HL_62881.14RNase P Structured Hairpin Loop
24HL_64371.33SSU Central Pseudoknot (forms helix 2)
25HL_91693.23
26HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
27HL_78361.13
28HL_19221.23
29HL_21545.23LSU Helix 96 (H96) Hairpin Loop
30HL_35619.33
31HL_41827.13
32HL_98833.33
33HL_27429.43
34HL_13707.23cSH AA Platform containing Hairpin Loop
35HL_06997.23
36HL_76766.43
37HL_80492.23tRNA D-loop
38HL_19528.12
39HL_24473.32tRNA D-loop
40HL_26495.12
41HL_33451.12
42HL_42553.12
43HL_93771.12tRNA T-loop distorted by RS binding
44HL_38964.12LSU Helix 84 (H84) Hairpin Loop. E.coli.
45HL_50312.12
46HL_94309.12GNRA with one bulged base
47HL_91872.12
48HL_94578.12
49HL_98577.12
50HL_24711.12
51HL_65924.12
52HL_92635.12
53HL_23129.12
54HL_42077.32LSU Helix 28 (H28) Hairpin Loop
55HL_49210.12
56HL_78660.12
57HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
58HL_05361.12
59HL_42094.12
60HL_19399.12
61HL_23290.12
62HL_38130.22
63HL_53745.12
64HL_87554.12
65HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
66HL_10075.11
67HL_17537.11
68HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
69HL_47337.11
70HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
71HL_55202.11U2B"-U2A" binding hairpin loop
72HL_59225.11
73HL_63997.11
74HL_68435.11
75HL_77692.11tRNA D-loop
76HL_82243.11
77HL_85018.11
78HL_97784.11
79HL_10116.11Kink-turn-like Hairpin Loop
80HL_20806.11
81HL_26579.11
82HL_33640.11
83HL_55272.11
84HL_59610.11
85HL_68579.11
86HL_78228.11
87HL_82288.11
88HL_85982.11
89HL_01418.11
90HL_10894.11
91HL_19132.11
92HL_20920.11
93HL_24707.11
94HL_27236.11
95HL_39422.11
96HL_44390.11
97HL_52116.11
98HL_56775.11
99HL_59982.11
100HL_65802.11
101HL_69403.11GNRA-like
102HL_03785.11LSU Helix 8 (H8) Hairpin Loop
103HL_27397.11
104HL_44522.11
105HL_48480.11
106HL_52540.11
107HL_56809.11
108HL_60203.11
109HL_70912.11
110HL_78507.11
111HL_82622.11SSU Central Pseudoknot (forms helix 2)
112HL_95049.11Two base, cross-stacked hairpin loop
113HL_04305.11
114HL_12706.11
115HL_19226.11
116HL_35865.11
117HL_53015.11
118HL_57217.11cHS platform Intercalation Site
119HL_83865.11
120HL_93263.11
121HL_95716.11
122HL_99207.11Tetrahymena LSU hairpin poorly modeled
123HL_19363.11
124HL_23195.11
125HL_25175.11
126HL_29196.11
127HL_37962.11
128HL_45411.11
129HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
130HL_53116.11
131HL_66877.11cSH GU/cWS double platform, intercalation site
132HL_73465.11
133HL_84289.11
134HL_87223.11
135HL_93428.11
136HL_99612.11
137HL_13786.11
138HL_25195.11
139HL_30008.11
140HL_42345.11
141HL_46055.11
142HL_49998.11
143HL_58223.11
144HL_62880.11
145HL_67000.11
146HL_73972.11
147HL_79902.11
148HL_84768.11
149HL_93530.11
150HL_96994.11
151HL_99932.11
152HL_19452.11tRNA D-loop
153HL_24108.11
154HL_25197.11
155HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
156HL_38138.11
157HL_46570.11
158HL_50018.11
159HL_53789.11
160HL_59182.11
161HL_67761.11
162HL_84888.11T-loop like but without tWH UA
163HL_88960.11
164HL_93567.11
165HL_97022.11

Updated motif groups

#Motif idInstancesDescription
1HL_67042.14270GNRA Hairpin motifs
2HL_72498.1471T-loops with two bulged bases
3HL_39895.838UNCG Hairpin motifs
4HL_18781.624Double sheared (tSH) with U-turn
5HL_91226.520Kissing Hairpin motif
6HL_97270.517T-loops with 1 bulged base
7HL_74465.616tRNA Anti-Codon loop
8HL_27271.314LSU Helix 96 (H96) Hairpin Loop
9HL_46175.413SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops | 16S helix 23 and 24 hairpin loops
10HL_49036.513LSU Helix 11 (H11) Hairpin Loop. GNRA-like. | GNRA with one bulged base
11HL_56824.412LSU Helix 60A. LSU Helix 63A.
12HL_75759.612
13HL_82294.411SSU Helix 37 (h37) Hairpin loop.
14HL_33402.511LSU Helix 13 (H13) Hairpin loop. GNRA-like.
15HL_68081.511LSU Helix 20 Hairpin loop
16HL_80459.510
17HL_34027.495S Loop C - Upper part of Hairpin Loop.
18HL_01926.58LSU Helix 71 (H71) Hairpin Loop.
19HL_39942.48LSU Helix 91 (H91) Hairpin Loop
20HL_41833.48LSU Helix 81 (H81) Hairpin Loop
21HL_46489.48LSU H89 Hairpin Loop
22HL_75579.48
23HL_87136.48LSU Helix 39A Hairpin loop
24HL_11547.48LSU Helix 80 (H80) P-site Hairpin Loop.
25HL_18156.48LSU Helix 72 (H72) Hairpin Loop
26HL_34108.48LSU Helix 37 (H37) Hairpin Loop.
27HL_39872.48LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
28HL_70420.48LSU Helix 97 Hairpin loop
29HL_85534.37LSU Helix 65 (H65) Hairpin Loop. T-loop like.
30HL_11509.47LSU Helix 6 (H6) Hairpin Loop.
31HL_88311.47LSU Helix 35 (H35) Hairpin Loop
32HL_72543.36LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
33HL_82538.36LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
34HL_31318.26SSU Central Pseudoknot (forms helix 2)
35HL_99908.25LSU Helix 69 (H69) Hairpin Loop
36HL_08382.45
37HL_64543.35SSU Helix 31 (h31) Hairpin Loop
38HL_19905.44LSU: Part of IL/3WJ between H55 and H56.
39HL_23182.24
40HL_48254.34LSU Helix 84 (H84) Hairpin Loop.
41HL_79956.24GNRA-like with 5'-stacking of first unpaired base.
42HL_58083.33
43HL_99633.23
44HL_06122.23
45HL_60200.23
46HL_74559.23Two base, cross-stacked hairpin loop
47HL_86398.23
48HL_65249.23
49HL_18587.23
50HL_54751.33
51HL_96915.23

Removed motif groups

#Motif idInstancesDescription
1HL_52574.415LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
2HL_87844.38LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
3HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
4HL_68697.33
5HL_16643.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
6HL_84258.13LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
7HL_74505.12
8HL_90542.12
9HL_62967.12
10HL_95756.12
11HL_16728.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
12HL_81510.12LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
13HL_17790.12UNCG-like. cWW Closing pair.
14HL_46903.12
15HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
16HL_86889.12SSU Central Pseudoknot (forms helix 2)
17HL_50461.12
18HL_00090.11
19HL_68733.11LSU Yeast Hairpin Loop
20HL_90102.11Kink-turn-like Hairpin Loop
21HL_04194.11
22HL_57843.11
23HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
24HL_75850.11
25HL_62970.11
26HL_78420.11
27HL_97499.11
28HL_63304.11
29HL_65071.11

Added motif groups

#Motif idInstancesDescription
1HL_92565.116LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
2HL_89482.110LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop.
3HL_25878.15UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
4HL_19626.15LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
5HL_92706.14LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
6HL_95969.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
7HL_74307.13
8HL_91142.13Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
9HL_19033.13SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
10HL_33223.13SSU Central Pseudoknot (forms helix 2)
11HL_55684.13
12HL_66677.13
13HL_84911.13
14HL_34912.12
15HL_84967.12
16HL_01788.12LSU Yeast Hairpin Loop
17HL_41700.12
18HL_09641.12SSU Central Pseudoknot (forms helix 2)
19HL_64438.12Kink-turn-like Hairpin Loop
20HL_27478.12
21HL_64803.12
22HL_28339.12
23HL_50937.12
24HL_65386.12UNCG-like. cWW Closing pair.
25HL_84172.12
26HL_94189.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
27HL_20004.12
28HL_21695.11UNCG-like. cWW Closing pair.
29HL_62564.11LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
30HL_72389.11
31HL_22461.11
32HL_39846.11
33HL_64102.11LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
34HL_04979.11LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
35HL_22533.11
36HL_64209.11UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
37HL_75624.11
38HL_90541.11LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
39HL_44485.1116S helix 23 and 24 hairpin loops
40HL_75984.11
41HL_11337.11
42HL_45740.11
43HL_78389.11
44HL_14536.11
45HL_84720.11
46HL_34491.11
47HL_57667.11
48HL_70872.11
49HL_95079.11
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