Changes in PDB files used for clustering

Release 1.3 has 211 PDB files, release 1.4 has 211 PDB files, 211 of them are identical.

No equivalence class representatives have been replaced.

No new PDB files have been added.

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

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Changes in motif groups

Release 1.3 has 256 motif groups, release 1.4 has 256 motif groups, 256 of them are identical.

0 motif groups were updated, 0 groups are present only in release 1.3, 0 groups are only in release 1.4.

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_67042.7227GNRA Hairpin motifs
2HL_72498.863T-loops with two bulged bases
3HL_39895.535UNCG Hairpin motifs
4HL_18781.220Double sheared (tSH) with U-turn
5HL_91226.317Kissing Hairpin motif
6HL_97270.215T-loops with 1 bulged base
7HL_52574.215LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
8HL_74465.212tRNA Anti-Codon loop
9HL_48039.111MS2 virus RNA Hairpin
10HL_49036.211GNRA with one bulged base
11HL_17723.310LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
12HL_68081.310LSU Helix 20 Hairpin loop
13HL_80459.210
14HL_46175.11016S helix 23 and 24 hairpin loops
15HL_75759.210UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
16HL_56824.210LSU Helix 60A. LSU Helix 63A.
17HL_28436.39LSU Helix 96 (H96) Hairpin Loop
18HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
19HL_82294.28SSU Helix 37 (h37) Hairpin loop.
20HL_34027.285S Loop C - Upper part of Hairpin Loop.
21HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
22HL_24544.18LSU Helix 53 (H53) Hairpin Loop. T-loop like.
23HL_15603.18U1A protein-binding Hairpin Loop.
24HL_33402.27LSU Helix 13 (H13) Hairpin loop. GNRA-like.
25HL_42677.16
26HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
27HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
28HL_70420.26LSU Helix 97 Hairpin loop
29HL_75579.26
30HL_87136.26LSU Helix 39A Hairpin loop
31HL_18156.26LSU Helix 72 (H72) Hairpin Loop
32HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
33HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
34HL_41833.26LSU Helix 81 (H81) Hairpin Loop
35HL_46489.26LSU H89 Hairpin Loop
36HL_39942.26LSU Helix 91 (H91) Hairpin Loop
37HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
38HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
39HL_57514.15Two base, cross-stacked hairpin loop
40HL_72273.15tRNA D-loop
41HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
42HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
43HL_12811.25LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
44HL_06643.25tRNA D-loop. Sec tRNA
45HL_88311.25LSU Helix 35 (H35) Hairpin Loop
46HL_45018.35Hairpin-Hairpin Interacting HL
47HL_62228.24LSU Helix 35A (H35A) Hairpin Loop
48HL_62881.14RNase P Structured Hairpin Loop
49HL_18798.14UNCG-like. cWW Closing pair.
50HL_61547.34
51HL_29831.14GNRA-like with bulged base.
52HL_47784.14SSU Central Pseudoknot (forms helix 2)
53HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
54HL_64543.14SSU Helix 31 (h31) Hairpin Loop
55HL_98523.14GNRA-like. Closed by tSH UC.
56HL_77235.34LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
57HL_42687.23
58HL_32644.13LSU Helix 69 (H69) Hairpin Loop
59HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
60HL_41827.13
61HL_98833.13
62HL_19221.23
63HL_76036.33LSU Helix 8 (H8) Hairpin Loop
64HL_25124.13tSW GA closed tetraloops
65HL_08382.23
66HL_42077.23LSU Helix 28 (H28) Hairpin Loop
67HL_58083.23
68HL_74686.13SSU Central Pseudoknot (forms helix 2)
69HL_90579.23
70HL_23182.13
71HL_82253.23
72HL_80492.23tRNA D-loop
73HL_27429.33
74HL_78361.13
75HL_46794.23
76HL_19905.23LSU: Part of IL/3WJ between H55 and H56.
77HL_54751.13
78HL_13707.23cSH AA Platform containing Hairpin Loop
79HL_53753.12
80HL_12595.12
81HL_23290.12
82HL_94578.12
83HL_98577.12
84HL_06122.12
85HL_57904.12
86HL_24473.32tRNA D-loop
87HL_97512.12LSU Helix 8 (H8) Hairpin Loop
88HL_19399.12
89HL_03791.12
90HL_99633.12
91HL_96915.12
92HL_45440.12
93HL_84353.12
94HL_65924.12
95HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
96HL_05361.12
97HL_67692.12
98HL_68697.12
99HL_16770.12
100HL_38130.22
101HL_67367.12
102HL_64371.22
103HL_75575.12
104HL_26495.12
105HL_24711.12
106HL_42553.12
107HL_76766.12
108HL_60200.12
109HL_81752.12
110HL_77555.12
111HL_58687.12
112HL_06312.12
113HL_26057.12
114HL_87554.12
115HL_49210.12
116HL_33451.12
117HL_50312.12
118HL_57014.12
119HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
120HL_62967.12
121HL_33524.11tRNA T-loop distorted by RS binding
122HL_93567.11
123HL_19226.11
124HL_52109.11
125HL_68435.11
126HL_19132.11
127HL_44390.11
128HL_67000.11
129HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
130HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
131HL_33277.11
132HL_36842.11
133HL_85018.11
134HL_96994.11
135HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
136HL_45411.11
137HL_78507.11
138HL_20914.11
139HL_58223.11
140HL_58601.11
141HL_88960.11
142HL_56809.11
143HL_63304.11
144HL_66467.11
145HL_19452.11tRNA D-loop
146HL_24108.11
147HL_38138.11
148HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
149HL_07315.11
150HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
151HL_60203.11
152HL_26579.11
153HL_66877.11cSH GU/cWS double platform, intercalation site
154HL_07915.11
155HL_00090.11
156HL_55272.11
157HL_47337.11
158HL_68733.11LSU Yeast Hairpin Loop
159HL_99207.11Tetrahymena LSU hairpin poorly modeled
160HL_73465.11
161HL_59182.11
162HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
163HL_53789.11
164HL_25195.11
165HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
166HL_87223.11
167HL_44522.11
168HL_27397.11
169HL_27819.11
170HL_67761.11
171HL_53015.11
172HL_78420.11
173HL_90102.11Kink-turn-like Hairpin Loop
174HL_93530.11
175HL_97784.11
176HL_31969.11
177HL_34375.11
178HL_55202.11U2B"-U2A" binding hairpin loop
179HL_56775.11
180HL_12984.11
181HL_33640.11
182HL_24707.11
183HL_59604.11
184HL_97499.11
185HL_63690.11
186HL_65071.11
187HL_39422.11
188HL_84289.11
189HL_34440.11
190HL_12706.11
191HL_13786.11
192HL_13105.11
193HL_25175.11
194HL_95716.11
195HL_71607.11
196HL_66900.11
197HL_01418.11
198HL_81295.11UNCG-like. cWW Closing pair.
199HL_59610.11
200HL_65802.11
201HL_35865.11
202HL_25197.11
203HL_37962.11
204HL_68579.11
205HL_70912.11
206HL_62970.11
207HL_80746.11
208HL_97971.11
209HL_82243.11
210HL_10116.11Kink-turn-like Hairpin Loop
211HL_16118.11
212HL_55543.11
213HL_77692.11tRNA D-loop
214HL_57217.11cHS platform Intercalation Site
215HL_35004.11
216HL_42969.11
217HL_79902.11
218HL_29084.11
219HL_62880.11
220HL_04194.11
221HL_78228.11
222HL_35200.11
223HL_69403.11GNRA-like
224HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
225HL_30008.11
226HL_17468.11
227HL_52393.11Double tSH (double sheared) with bulged base
228HL_30128.11
229HL_48480.11
230HL_20806.11
231HL_95049.11Two base, cross-stacked hairpin loop
232HL_84888.11T-loop like but without tWH UA
233HL_57843.11
234HL_85753.11
235HL_96192.11
236HL_75850.11
237HL_39486.11
238HL_82288.11
239HL_17537.11
240HL_42345.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription