Changes in PDB files used for clustering

Release 1.14 has 236 PDB files, release 1.15 has 245 PDB files, 236 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_06643.36tRNA D-loop. Sec tRNA
9HL_62228.46LSU Helix 35A (H35A) Hairpin Loop
10HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
11HL_72273.15tRNA D-loop
12HL_86077.15GNRA with one bulged base | GNRA-like with bulged base.
13HL_78731.25LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
14HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
15HL_45018.35Hairpin-Hairpin Interacting HL
16HL_11376.14LSU Helix 8 (H8) Hairpin Loop
17HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
18HL_82418.14LSU Helix 8 (H8) Hairpin Loop
19HL_86115.14
20HL_25124.24tSW GA closed tetraloops
21HL_62881.14RNase P Structured Hairpin Loop
22HL_98523.24GNRA-like. Closed by tSH UC.
23HL_48116.34GNRA-like with 5'-stacking of first unpaired base.
24HL_78361.13
25HL_19221.23
26HL_13707.23cSH AA Platform containing Hairpin Loop
27HL_21545.23LSU Helix 96 (H96) Hairpin Loop
28HL_91693.23
29HL_06997.23
30HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
31HL_27429.43
32HL_35619.33
33HL_41827.13
34HL_76766.43
35HL_64371.33SSU Central Pseudoknot (forms helix 2)
36HL_80492.23tRNA D-loop
37HL_98833.33
38HL_24473.32tRNA D-loop
39HL_26495.12
40HL_49210.12
41HL_65924.12
42HL_05361.12
43HL_33451.12
44HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
45HL_93771.12tRNA T-loop distorted by RS binding
46HL_42553.12
47HL_53745.12
48HL_78660.12
49HL_94309.12GNRA with one bulged base
50HL_24711.12
51HL_38964.12LSU Helix 84 (H84) Hairpin Loop. E.coli.
52HL_91872.12
53HL_94578.12
54HL_19399.12
55HL_23129.12
56HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
57HL_92635.12
58HL_44467.12
59HL_50312.12
60HL_98577.12
61HL_19528.12
62HL_23290.12
63HL_42077.32LSU Helix 28 (H28) Hairpin Loop
64HL_87554.12
65HL_38130.22
66HL_42094.12
67HL_05113.11
68HL_19132.11
69HL_20806.11
70HL_30731.11
71HL_38138.11
72HL_42345.11
73HL_45358.11Double hairpin loop based on GGA triple
74HL_53015.11
75HL_57217.11cHS platform Intercalation Site
76HL_60203.11
77HL_69403.11GNRA-like
78HL_82288.11
79HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
80HL_93567.11
81HL_96994.11
82HL_99584.11
83HL_12706.11
84HL_20920.11
85HL_26579.11
86HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
87HL_45411.11
88HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
89HL_53116.11
90HL_70912.11
91HL_78507.11
92HL_85982.11
93HL_91613.11
94HL_97022.11
95HL_99612.11
96HL_19226.11
97HL_24707.11
98HL_27236.11
99HL_33640.11
100HL_38898.11
101HL_46055.11
102HL_49998.11
103HL_57923.11
104HL_66877.11cSH GU/cWS double platform, intercalation site
105HL_82622.11SSU Central Pseudoknot (forms helix 2)
106HL_97784.11
107HL_99779.11
108HL_13786.11
109HL_19363.11
110HL_23080.11
111HL_27397.11
112HL_46570.11
113HL_50018.11
114HL_53789.11
115HL_58223.11
116HL_62880.11
117HL_66880.11
118HL_73465.11
119HL_83865.11
120HL_98233.11
121HL_99932.11
122HL_00721.11
123HL_08203.11
124HL_39422.11
125HL_44390.11
126HL_47337.11
127HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
128HL_55202.11U2B"-U2A" binding hairpin loop
129HL_59182.11
130HL_67000.11
131HL_73972.11
132HL_79038.11LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
133HL_84289.11
134HL_95049.11Two base, cross-stacked hairpin loop
135HL_01418.11
136HL_10075.11
137HL_17008.11Nova-2 KH3 domain binding hairpin
138HL_19452.11tRNA D-loop
139HL_23195.11
140HL_25175.11
141HL_29196.11
142HL_35865.11
143HL_55272.11
144HL_59225.11
145HL_63997.11
146HL_67761.11
147HL_79902.11
148HL_84768.11
149HL_87223.11
150HL_93263.11
151HL_95716.11
152HL_03785.11LSU Helix 8 (H8) Hairpin Loop
153HL_10116.11Kink-turn-like Hairpin Loop
154HL_17537.11
155HL_25195.11
156HL_30008.11
157HL_37962.11
158HL_44522.11
159HL_52116.11
160HL_56775.11
161HL_59610.11
162HL_68435.11
163HL_77692.11tRNA D-loop
164HL_84888.11T-loop like but without tWH UA
165HL_93428.11
166HL_04305.11
167HL_10894.11
168HL_20028.11
169HL_24108.11
170HL_25197.11
171HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
172HL_48480.11
173HL_52540.11
174HL_56809.11
175HL_59982.11
176HL_65802.11
177HL_68579.11
178HL_78228.11
179HL_82243.11
180HL_85018.11
181HL_88960.11
182HL_93530.11
183HL_96012.11
184HL_99207.11Tetrahymena LSU hairpin poorly modeled

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_49036.513LSU Helix 11 (H11) Hairpin Loop. GNRA-like. | GNRA with one bulged base
10HL_46175.413SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops | 16S helix 23 and 24 hairpin loops
11HL_75759.612
12HL_56824.412LSU Helix 60A. LSU Helix 63A.
13HL_33402.511LSU Helix 13 (H13) Hairpin loop. GNRA-like.
14HL_68081.511LSU Helix 20 Hairpin loop
15HL_82294.411SSU Helix 37 (h37) Hairpin loop.
16HL_80459.510
17HL_34027.495S Loop C - Upper part of Hairpin Loop.
18HL_11547.48LSU Helix 80 (H80) P-site Hairpin Loop.
19HL_46489.48LSU H89 Hairpin Loop
20HL_75579.48
21HL_87136.48LSU Helix 39A Hairpin loop
22HL_18156.48LSU Helix 72 (H72) Hairpin Loop
23HL_34108.48LSU Helix 37 (H37) Hairpin Loop.
24HL_39872.48LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
25HL_70420.48LSU Helix 97 Hairpin loop
26HL_01926.58LSU Helix 71 (H71) Hairpin Loop.
27HL_39942.48LSU Helix 91 (H91) Hairpin Loop
28HL_41833.48LSU Helix 81 (H81) Hairpin Loop
29HL_88311.47LSU Helix 35 (H35) Hairpin Loop
30HL_85534.37LSU Helix 65 (H65) Hairpin Loop. T-loop like.
31HL_11509.47LSU Helix 6 (H6) 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_08382.45
36HL_99908.25LSU Helix 69 (H69) Hairpin Loop
37HL_64543.35SSU Helix 31 (h31) Hairpin Loop
38HL_48254.34LSU Helix 84 (H84) Hairpin Loop.
39HL_79956.24GNRA-like with 5'-stacking of first unpaired base.
40HL_19905.44LSU: Part of IL/3WJ between H55 and H56.
41HL_23182.24
42HL_65249.23
43HL_18587.23
44HL_54751.33
45HL_96915.23
46HL_06122.23
47HL_58083.33
48HL_99633.23
49HL_60200.23
50HL_74559.23Two base, cross-stacked hairpin loop
51HL_86398.23

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_84258.13LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
5HL_68697.33
6HL_16643.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
7HL_16728.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
8HL_17790.12UNCG-like. cWW Closing pair.
9HL_81510.12LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
10HL_46903.12
11HL_50461.12
12HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
13HL_86889.12SSU Central Pseudoknot (forms helix 2)
14HL_74505.12
15HL_90542.12
16HL_62967.12
17HL_95756.12
18HL_62970.11
19HL_78420.11
20HL_97499.11
21HL_63304.11
22HL_65071.11
23HL_00090.11
24HL_04194.11
25HL_68733.11LSU Yeast Hairpin Loop
26HL_90102.11Kink-turn-like Hairpin Loop
27HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
28HL_57843.11
29HL_75850.11

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_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
4HL_25878.15UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
5HL_92706.14LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
6HL_91142.13Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
7HL_19033.13SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
8HL_33223.13SSU Central Pseudoknot (forms helix 2)
9HL_55684.13
10HL_66677.13
11HL_84911.13
12HL_95969.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
13HL_74307.13
14HL_27478.12
15HL_64438.12Kink-turn-like Hairpin Loop
16HL_28339.12
17HL_64803.12
18HL_50937.12
19HL_65386.12UNCG-like. cWW Closing pair.
20HL_84172.12
21HL_20004.12
22HL_94189.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
23HL_01788.12LSU Yeast Hairpin Loop
24HL_34912.12
25HL_84967.12
26HL_09641.12SSU Central Pseudoknot (forms helix 2)
27HL_41700.12
28HL_14536.11
29HL_44485.1116S helix 23 and 24 hairpin loops
30HL_75984.11
31HL_45740.11
32HL_78389.11
33HL_34491.11
34HL_84720.11
35HL_21695.11UNCG-like. cWW Closing pair.
36HL_57667.11
37HL_70872.11
38HL_95079.11
39HL_04979.11LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
40HL_22461.11
41HL_39846.11
42HL_62564.11LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
43HL_72389.11
44HL_22533.11
45HL_64102.11LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
46HL_11337.11
47HL_42255.11
48HL_64209.11UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
49HL_75624.11
50HL_90541.11LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base