Changes in PDB files used for clustering

Release 0.8 has 203 PDB files, release 1.0 has 206 PDB files, 203 of them are identical.

No equivalence class representatives have been replaced.

3 new structures in release 1.0: 3W3S, 4B5R, 4HXH.

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 0.8 has 246 motif groups, release 1.0 has 252 motif groups, 227 of them are identical.

9 motif groups were updated, 10 groups are present only in release 0.8, 16 groups are only in release 1.0.

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_39895.334UNCG Hairpin motifs
2HL_18781.121Double sheared (tSH) with U-turn
3HL_91226.217Kissing Hairpin motif
4HL_97270.115T-loops with 1 bulged base
5HL_52574.115LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
6HL_48039.111MS2 virus RNA Hairpin
7HL_80459.111
8HL_75759.110LSU: Part of IL/3WJ between H55 and H56.
9HL_56824.110LSU Helix 60A. LSU Helix 63A.
10HL_68081.210LSU Helix 20 Hairpin loop
11HL_46175.11016S helix 23 and 24 hairpin loops
12HL_49036.110GNRA with one bulged base
13HL_28436.29LSU Helix 96 (H96) Hairpin Loop
14HL_87844.19LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
15HL_82294.28SSU Helix 37 (h37) Hairpin loop.
16HL_15603.18U1A protein-binding Hairpin Loop.
17HL_11547.18LSU Helix 80 (H80) P-site Hairpin Loop.
18HL_24544.18LSU Helix 53 (H53) Hairpin Loop. T-loop like.
19HL_34027.175S Loop C - Upper part of Hairpin Loop.
20HL_33402.17LSU Helix 13 (H13) Hairpin loop. GNRA-like.
21HL_18156.16LSU Helix 72 (H72) Hairpin Loop
22HL_39872.16LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
23HL_42677.16
24HL_46489.16LSU H89 Hairpin Loop
25HL_87136.16LSU Helix 39A Hairpin loop
26HL_39942.16LSU Helix 91 (H91) Hairpin Loop
27HL_11509.16LSU Helix 6 (H6) Hairpin Loop.
28HL_75579.16
29HL_34108.16LSU Helix 37 (H37) Hairpin Loop.
30HL_41833.16LSU Helix 81 (H81) Hairpin Loop
31HL_70420.16LSU Helix 97 Hairpin loop
32HL_72543.15LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
33HL_45018.35Hairpin-Hairpin Interacting HL
34HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
35HL_88311.15LSU Helix 35 (H35) Hairpin Loop
36HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
37HL_12811.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
38HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
39HL_72273.15tRNA D-loop
40HL_29831.14GNRA-like with bulged base.
41HL_62228.14LSU Helix 35A (H35A) Hairpin Loop
42HL_64543.14SSU Helix 31 (h31) Hairpin Loop
43HL_48116.14GNRA-like with 5'-stacking of first unpaired base.
44HL_62881.14RNase P Structured Hairpin Loop
45HL_98523.14GNRA-like. Closed by tSH UC.
46HL_08382.23
47HL_13707.23cSH AA Platform containing Hairpin Loop
48HL_27429.23
49HL_54751.13
50HL_80492.23tRNA D-loop
51HL_25124.13tSW GA closed tetraloops
52HL_42687.23
53HL_46794.23
54HL_73023.13Two base, cross-stacked hairpin loop
55HL_90579.13
56HL_98833.13
57HL_23182.13
58HL_61547.23
59HL_78361.13
60HL_19221.23
61HL_41827.13
62HL_58083.23
63HL_32644.13LSU Helix 69 (H69) Hairpin Loop
64HL_42077.23LSU Helix 28 (H28) Hairpin Loop
65HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
66HL_82253.13
67HL_03791.12
68HL_24711.12
69HL_33451.12
70HL_49210.12
71HL_77555.12
72HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
73HL_98577.12
74HL_22614.12
75HL_49267.12
76HL_68697.12
77HL_81555.12
78HL_05361.12
79HL_57904.12
80HL_63823.12
81HL_75575.12
82HL_96915.12
83HL_05510.12
84HL_23290.12
85HL_38130.22
86HL_81752.12
87HL_84353.12
88HL_87554.12
89HL_99633.12
90HL_05797.12
91HL_16770.12
92HL_19399.12
93HL_67692.12
94HL_06122.12
95HL_12595.12
96HL_24473.32tRNA D-loop
97HL_26057.12
98HL_06312.12
99HL_19905.12
100HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
101HL_53753.12
102HL_65924.12
103HL_76105.12
104HL_94578.12
105HL_42553.12
106HL_57014.12
107HL_76766.12
108HL_20914.11
109HL_35865.11
110HL_57217.11cHS platform Intercalation Site
111HL_59610.11
112HL_63411.11
113HL_66467.11
114HL_68579.11
115HL_90365.115S rRNA Loop C from D.radiodurans
116HL_95716.11
117HL_04194.11
118HL_10116.11Kink-turn-like Hairpin Loop
119HL_13786.11
120HL_27819.11
121HL_33524.11tRNA T-loop distorted by RS binding
122HL_36842.11
123HL_55202.11U2B"-U2A" binding hairpin loop
124HL_57843.11
125HL_61061.11
126HL_63690.11
127HL_66877.11cSH GU/cWS double platform, intercalation site
128HL_78228.11
129HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
130HL_96192.11
131HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
132HL_19132.11
133HL_25175.11
134HL_33640.11
135HL_37962.11
136HL_42969.11
137HL_47337.11
138HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
139HL_55272.11
140HL_66900.11
141HL_68733.11LSU Yeast Hairpin Loop
142HL_81661.11tRNA D-loop
143HL_84289.11
144HL_87223.11
145HL_99207.11Tetrahymena LSU hairpin poorly modeled
146HL_15771.11
147HL_25195.11
148HL_44390.11
149HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
150HL_55543.11
151HL_67000.11
152HL_69403.11GNRA-like
153HL_78420.11
154HL_93206.11
155HL_00090.11
156HL_23522.11
157HL_25197.11
158HL_30128.11
159HL_38138.11
160HL_44522.11
161HL_56775.11
162HL_58223.11
163HL_62880.11
164HL_65071.11
165HL_78507.11
166HL_81780.11
167HL_84888.11T-loop like but without tWH UA
168HL_93567.11
169HL_97499.11
170HL_00238.11
171HL_17468.11
172HL_19452.11tRNA D-loop
173HL_34440.11
174HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
175HL_53015.11
176HL_56809.11
177HL_58601.11
178HL_65802.11
179HL_67761.11
180HL_70912.11
181HL_75850.11
182HL_82243.11
183HL_85018.11
184HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
185HL_97784.11
186HL_02479.11
187HL_12706.11
188HL_17537.11
189HL_26579.11
190HL_33277.11
191HL_35004.11
192HL_39422.11
193HL_45411.11
194HL_48480.11
195HL_58786.11
196HL_62970.11
197HL_71607.11
198HL_79902.11
199HL_88960.11
200HL_97971.11
201HL_03431.11
202HL_07315.11
203HL_18011.11
204HL_20806.11
205HL_24707.11
206HL_27397.11
207HL_35200.11
208HL_39486.11
209HL_53789.11
210HL_59604.11
211HL_63304.11
212HL_68435.11
213HL_82288.11
214HL_85753.11
215HL_90102.11Kink-turn-like Hairpin Loop
216HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.

Updated motif groups

#Motif idInstancesDescription
1HL_67042.4225GNRA Hairpin motifs
2HL_72498.563T-loops with two bulged bases
3HL_74465.212tRNA Anti-Codon loop
4HL_17723.210LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
5HL_01926.26LSU Helix 71 (H71) Hairpin Loop.
6HL_95423.25UNCG-like. cWW Closing pair.
7HL_06643.25tRNA D-loop. Sec tRNA
8HL_76036.23LSU Helix 8 (H8) Hairpin Loop
9HL_64371.22

Removed motif groups

#Motif idInstancesDescription
1HL_19261.15SSU Central Pseudoknot (forms helix 2)
2HL_53664.13Double tSH (double sheared) with bulged base
3HL_20739.13
4HL_46981.12
5HL_70106.12LSU Helix 10 (H10) Hairpin E.coli
6HL_70459.12
7HL_14013.12
8HL_93015.12
9HL_27831.11
10HL_01987.11

Added motif groups

#Motif idInstancesDescription
1HL_47784.14SSU Central Pseudoknot (forms helix 2)
2HL_77235.14LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
3HL_74686.13SSU Central Pseudoknot (forms helix 2)
4HL_62967.12
5HL_67367.12
6HL_85138.11LSU Helix 8 (H8) Hairpin Loop
7HL_52393.11Double tSH (double sheared) with bulged base
8HL_60203.11
9HL_12984.11
10HL_13105.11
11HL_19226.11
12HL_29084.11
13HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
14HL_80746.11
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