Changes in PDB files used for clustering

Release 0.4 has 196 PDB files, release 0.5 has 202 PDB files, 196 of them are identical.

No equivalence class representatives have been replaced.

6 new structures in release 0.5: 4AY2, 4FNJ, 4FRG, 4FRN, 4GMA, 4GXY.

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 0.4 has 245 motif groups, release 0.5 has 247 motif groups, 230 of them are identical.

7 motif groups were updated, 8 groups are present only in release 0.4, 10 groups are only in release 0.5.

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_18781.121Double sheared (tSH) with U-turn
2HL_97270.115T-loops with 1 bulged base
3HL_52574.115LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
4HL_80459.111
5HL_74465.111tRNA Anti-Codon loop
6HL_48039.111MS2 virus RNA Hairpin
7HL_75759.110LSU: Part of IL/3WJ between H55 and H56.
8HL_49036.110GNRA with one bulged base
9HL_56824.110LSU Helix 60A. LSU Helix 63A.
10HL_46175.11016S helix 23 and 24 hairpin loops
11HL_87844.19LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
12HL_17723.19LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
13HL_24544.18LSU Helix 53 (H53) Hairpin Loop. T-loop like.
14HL_15603.18U1A protein-binding Hairpin Loop.
15HL_11547.18LSU Helix 80 (H80) P-site Hairpin Loop.
16HL_01926.17LSU Helix 71 (H71) Hairpin Loop.
17HL_34027.175S Loop C - Upper part of Hairpin Loop.
18HL_33402.17LSU Helix 13 (H13) Hairpin loop. GNRA-like.
19HL_41833.16LSU Helix 81 (H81) Hairpin Loop
20HL_42677.16
21HL_75579.16
22HL_11509.16LSU Helix 6 (H6) Hairpin Loop.
23HL_46489.16LSU H89 Hairpin Loop
24HL_39942.16LSU Helix 91 (H91) Hairpin Loop
25HL_70420.16LSU Helix 97 Hairpin loop
26HL_39872.16LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
27HL_34108.16LSU Helix 37 (H37) Hairpin Loop.
28HL_18156.16LSU Helix 72 (H72) Hairpin Loop
29HL_87136.16LSU Helix 39A Hairpin loop
30HL_12811.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
31HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
32HL_72273.15tRNA D-loop
33HL_72543.15LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
34HL_88311.15LSU Helix 35 (H35) Hairpin Loop
35HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
36HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
37HL_19261.15SSU Central Pseudoknot (forms helix 2)
38HL_06643.15tRNA D-loop. Sec tRNA
39HL_62881.14RNase P Structured Hairpin Loop
40HL_98523.14GNRA-like. Closed by tSH UC.
41HL_48116.14GNRA-like with 5'-stacking of first unpaired base.
42HL_08382.14
43HL_29831.14GNRA-like with bulged base.
44HL_45018.24
45HL_95423.14UNCG-like. cWW Closing pair.
46HL_62228.14LSU Helix 35A (H35A) Hairpin Loop
47HL_64543.14SSU Helix 31 (h31) Hairpin Loop
48HL_41827.13
49HL_76036.13LSU Helix 8 (H8) Hairpin Loop
50HL_90579.13
51HL_78361.13
52HL_42077.23LSU Helix 28 (H28) Hairpin Loop
53HL_23182.13
54HL_46794.23
55HL_80492.23tRNA D-loop
56HL_27429.23
57HL_20739.13
58HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
59HL_13707.23cSH AA Platform containing Hairpin Loop
60HL_19221.23
61HL_32644.13LSU Helix 69 (H69) Hairpin Loop
62HL_42687.23
63HL_53664.13Double tSH (double sheared) with bulged base
64HL_58083.23
65HL_82253.13
66HL_73023.13Two base, cross-stacked hairpin loop
67HL_54751.13
68HL_98833.13
69HL_64371.13
70HL_27658.13
71HL_25124.13tSW GA closed tetraloops
72HL_10832.12
73HL_27809.12
74HL_57904.12
75HL_20857.12
76HL_63823.12
77HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
78HL_61547.12
79HL_05510.12
80HL_65924.12
81HL_49210.12
82HL_42553.12
83HL_57014.12
84HL_06122.12
85HL_23290.12
86HL_19905.12
87HL_33451.12
88HL_05797.12
89HL_76105.12
90HL_76766.12
91HL_24711.12
92HL_24473.32tRNA D-loop
93HL_88640.12
94HL_14013.12
95HL_26057.12
96HL_87554.12
97HL_99633.12
98HL_96915.12
99HL_16770.12
100HL_94578.12
101HL_19399.12
102HL_67692.12
103HL_98577.12
104HL_56859.12
105HL_70459.12
106HL_70106.12LSU Helix 10 (H10) Hairpin E.coli
107HL_49267.12
108HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
109HL_38130.22
110HL_03791.12
111HL_39922.11
112HL_35865.11
113HL_24707.11
114HL_53789.11
115HL_25195.11
116HL_03431.11
117HL_00238.11
118HL_44522.11
119HL_84289.11
120HL_88960.11
121HL_56809.11
122HL_00090.11
123HL_55272.11
124HL_97971.11
125HL_99207.11Tetrahymena LSU hairpin poorly modeled
126HL_38138.11
127HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
128HL_65802.11
129HL_25197.11
130HL_58786.11
131HL_59604.11
132HL_97499.11
133HL_35004.11
134HL_93206.11
135HL_39422.11
136HL_66877.11cSH GU/cWS double platform, intercalation site
137HL_27819.11
138HL_67761.11
139HL_53015.11
140HL_78228.11
141HL_35200.11
142HL_97784.11
143HL_33524.11tRNA T-loop distorted by RS binding
144HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
145HL_27831.11
146HL_37962.11
147HL_81780.11
148HL_90365.115S rRNA Loop C from D.radiodurans
149HL_05113.11
150HL_77981.11
151HL_27397.11
152HL_12706.11
153HL_13786.11
154HL_04194.11
155HL_75850.11
156HL_39486.11
157HL_66900.11
158HL_56775.11
159HL_33640.11
160HL_79390.11
161HL_10842.11
162HL_57217.11cHS platform Intercalation Site
163HL_42969.11
164HL_76027.11
165HL_34440.11
166HL_70912.11
167HL_62970.11
168HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
169HL_33277.11
170HL_10116.11Kink-turn-like Hairpin Loop
171HL_60420.11
172HL_59610.11
173HL_23522.11
174HL_30128.11
175HL_48480.11
176HL_20806.11
177HL_20914.11
178HL_15771.11
179HL_84888.11T-loop like but without tWH UA
180HL_88921.11
181HL_68579.11
182HL_62880.11
183HL_66467.11
184HL_55543.11
185HL_81661.11tRNA D-loop
186HL_93567.11
187HL_99779.11
188HL_63411.11
189HL_68435.11
190HL_85753.11
191HL_96192.11
192HL_47337.11
193HL_68733.11LSU Yeast Hairpin Loop
194HL_69403.11GNRA-like
195HL_55202.11U2B"-U2A" binding hairpin loop
196HL_17468.11
197HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
198HL_45411.11
199HL_78507.11
200HL_87223.11
201HL_65071.11
202HL_58223.11
203HL_58601.11
204HL_79902.11
205HL_67000.11
206HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
207HL_78420.11
208HL_90102.11Kink-turn-like Hairpin Loop
209HL_82288.11
210HL_20252.11
211HL_07315.11
212HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
213HL_63690.11
214HL_02479.11
215HL_61061.11
216HL_26579.11
217HL_57843.11
218HL_44390.11
219HL_63304.11
220HL_25175.11
221HL_95716.11
222HL_36842.11

Updated motif groups

#Motif idInstancesDescription
1HL_67042.2222
2HL_72498.362
3HL_39895.234
4HL_91226.217Kissing Hairpin motif
5HL_68081.210LSU Helix 20 Hairpin loop
6HL_28436.29LSU Helix 96 (H96) Hairpin Loop
7HL_82294.28SSU Helix 37 (h37) Hairpin loop.

Removed motif groups

#Motif idInstancesDescription
1HL_76014.12
2HL_81241.12
3HL_85369.12
4HL_08091.12
5HL_16860.11
6HL_58149.11
7HL_66090.11
8HL_03805.11

Added motif groups