Changes in PDB files used for clustering

Release 1.1 has 208 PDB files, release 1.9 has 220 PDB files, 204 of them are identical.

2 equivalence classes changed representatives: 2XZM4BPP, 3NPB4KQY.

14 new structures in release 1.9: 4BW0, 4C7O, 4C9D, 4JF2, 4JRC, 4K27, 4K50, 4KJI, 4L8H, 4L8R, 4LCK, 4LGT, 4MGM, 4MGN.

Obsolete: 2XZM4V5O, 3NPB4KQY, 4HXH4L8R.

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 1.1 has 254 motif groups, release 1.9 has 253 motif groups, 186 of them are identical.

29 motif groups were updated, 39 groups are present only in release 1.1, 38 groups are only in release 1.9.

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_91226.317Kissing Hairpin motif
2HL_56824.210LSU Helix 60A. LSU Helix 63A.
3HL_68081.310LSU Helix 20 Hairpin loop
4HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
5HL_15603.18U1A protein-binding Hairpin Loop.
6HL_34027.285S Loop C - Upper part of Hairpin Loop.
7HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
8HL_39942.26LSU Helix 91 (H91) Hairpin Loop
9HL_75579.26
10HL_41833.26LSU Helix 81 (H81) Hairpin Loop
11HL_70420.26LSU Helix 97 Hairpin loop
12HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
13HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
14HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
15HL_46489.26LSU H89 Hairpin Loop
16HL_87136.26LSU Helix 39A Hairpin loop
17HL_18156.26LSU Helix 72 (H72) Hairpin Loop
18HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
19HL_06643.25tRNA D-loop. Sec tRNA
20HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
21HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
22HL_88311.25LSU Helix 35 (H35) Hairpin Loop
23HL_45018.35Hairpin-Hairpin Interacting HL
24HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
25HL_72273.15tRNA D-loop
26HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
27HL_62881.14RNase P Structured Hairpin Loop
28HL_29831.14GNRA-like with bulged base.
29HL_61547.34
30HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
31HL_13707.23cSH AA Platform containing Hairpin Loop
32HL_19221.23
33HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
34HL_27429.33
35HL_41827.13
36HL_98833.13
37HL_08382.23
38HL_76036.33LSU Helix 8 (H8) Hairpin Loop
39HL_80492.23tRNA D-loop
40HL_42077.23LSU Helix 28 (H28) Hairpin Loop
41HL_23182.13
42HL_78361.13
43HL_42687.23
44HL_58083.23
45HL_74686.13SSU Central Pseudoknot (forms helix 2)
46HL_24473.32tRNA D-loop
47HL_84353.12
48HL_98577.12
49HL_33451.12
50HL_62967.12
51HL_19399.12
52HL_24711.12
53HL_38130.22
54HL_49210.12
55HL_76766.12
56HL_96915.12
57HL_99633.12
58HL_16770.12
59HL_60200.12
60HL_64371.22
61HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
62HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
63HL_50312.12
64HL_05361.12
65HL_23290.12
66HL_26495.12
67HL_42553.12
68HL_06122.12
69HL_65924.12
70HL_87554.12
71HL_94578.12
72HL_27397.11
73HL_33277.11
74HL_36842.11
75HL_42969.11
76HL_55202.11U2B"-U2A" binding hairpin loop
77HL_58223.11
78HL_68733.11LSU Yeast Hairpin Loop
79HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
80HL_07915.11
81HL_13786.11
82HL_19226.11
83HL_24707.11
84HL_37962.11
85HL_44390.11
86HL_48480.11
87HL_55272.11
88HL_58601.11
89HL_66467.11
90HL_69403.11GNRA-like
91HL_75850.11
92HL_79902.11
93HL_84888.11T-loop like but without tWH UA
94HL_95049.11Two base, cross-stacked hairpin loop
95HL_00090.11
96HL_27819.11
97HL_33640.11
98HL_44522.11
99HL_56775.11
100HL_59604.11
101HL_62970.11
102HL_66877.11cSH GU/cWS double platform, intercalation site
103HL_85018.11
104HL_88960.11
105HL_95716.11
106HL_99207.11Tetrahymena LSU hairpin poorly modeled
107HL_01418.11
108HL_10116.11Kink-turn-like Hairpin Loop
109HL_16118.11
110HL_19452.11tRNA D-loop
111HL_25175.11
112HL_38138.11
113HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
114HL_56809.11
115HL_59610.11
116HL_63304.11
117HL_67000.11
118HL_70912.11
119HL_80746.11
120HL_90102.11Kink-turn-like Hairpin Loop
121HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
122HL_20806.11
123HL_25195.11
124HL_30008.11
125HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
126HL_42345.11
127HL_45411.11
128HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
129HL_67761.11
130HL_78228.11
131HL_81661.11tRNA D-loop
132HL_96994.11
133HL_04194.11
134HL_17537.11
135HL_25197.11
136HL_30128.11
137HL_34440.11
138HL_39422.11
139HL_57217.11cHS platform Intercalation Site
140HL_60203.11
141HL_65071.11
142HL_82243.11
143HL_93530.11
144HL_97499.11
145HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
146HL_35200.11
147HL_39486.11
148HL_47337.11
149HL_53015.11
150HL_57843.11
151HL_65802.11
152HL_68435.11
153HL_73465.11
154HL_78420.11
155HL_82288.11
156HL_87223.11
157HL_93567.11
158HL_97784.11
159HL_12706.11
160HL_19132.11
161HL_24108.11
162HL_26579.11
163HL_31969.11
164HL_35865.11
165HL_53789.11
166HL_62880.11
167HL_68579.11
168HL_78507.11
169HL_84289.11
170HL_97971.11

Updated motif groups

#Motif idInstancesDescription
1HL_97270.315T-loops with 1 bulged base
2HL_52574.314LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
3HL_49036.312GNRA with one bulged base
4HL_48039.211MS2 virus RNA Hairpin
5HL_46175.21016S helix 23 and 24 hairpin loops
6HL_17723.410LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
7HL_75759.310LSU: Part of IL/3WJ between H55 and H56. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
8HL_80459.39
9HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
10HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
11HL_82294.38SSU Helix 37 (h37) Hairpin loop.
12HL_42677.27
13HL_57514.26Two base, cross-stacked hairpin loop
14HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
15HL_98523.24GNRA-like. Closed by tSH UC.
16HL_64543.24SSU Helix 31 (h31) Hairpin Loop
17HL_47784.24SSU Central Pseudoknot (forms helix 2)
18HL_25124.24tSW GA closed tetraloops
19HL_68697.23
20HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
21HL_90579.33LSU Helix 69 (H69) Hairpin Loop
22HL_32644.22LSU Helix 69 (H69) Hairpin Loop
23HL_54751.22

Removed motif groups

#Motif idInstancesDescription
1HL_28436.39LSU Helix 96 (H96) Hairpin Loop
2HL_77235.14LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
3HL_18798.14UNCG-like. cWW Closing pair.
4HL_46794.23
5HL_82253.23
6HL_57904.12
7HL_45440.12
8HL_58687.12
9HL_77555.12
10HL_97512.12LSU Helix 8 (H8) Hairpin Loop
11HL_03791.12
12HL_81752.12
13HL_06312.12
14HL_26057.12
15HL_67367.12
16HL_53753.12
17HL_67692.12
18HL_12595.12
19HL_57014.12
20HL_75575.12
21HL_13105.11
22HL_35004.11
23HL_96192.11
24HL_17468.11
25HL_63690.11
26HL_81295.11UNCG-like. cWW Closing pair.
27HL_20914.11
28HL_52109.11
29HL_66900.11
30HL_52393.11Double tSH (double sheared) with bulged base
31HL_07315.11
32HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
33HL_29084.11
34HL_55543.11
35HL_71607.11
36HL_85753.11
37HL_12984.11
38HL_33524.11tRNA T-loop distorted by RS binding
39HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli

Added motif groups

#Motif idInstancesDescription
1HL_27271.110LSU Helix 96 (H96) Hairpin Loop
2HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
3HL_11376.14LSU Helix 8 (H8) Hairpin Loop
4HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
5HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
6HL_35619.23
7HL_06997.23
8HL_19528.12
9HL_63941.12
10HL_21545.12LSU Helix 96 (H96) Hairpin Loop
11HL_65249.12
12HL_21675.32LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
13HL_42094.12
14HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
15HL_86398.12
16HL_23129.12
17HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
18HL_90542.12
19HL_91693.12
20HL_74505.12
21HL_91872.12
22HL_17790.12UNCG-like. cWW Closing pair.
23HL_74559.12Two base, cross-stacked hairpin loop
24HL_18587.12
25HL_93771.12tRNA T-loop distorted by RS binding
26HL_83865.11
27HL_84768.11
28HL_03785.11LSU Helix 8 (H8) Hairpin Loop
29HL_46570.11
30HL_23195.11
31HL_52116.11
32HL_73972.11
33HL_52540.11
34HL_28676.11
35HL_93263.11
36HL_29196.11
37HL_59182.11
38HL_76585.11
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