Changes in PDB files used for clustering

Release 1.2 has 216 PDB files, release 1.3 has 216 PDB files, 215 of them are identical.

No equivalence class representatives have been replaced.

1 new structures in release 1.3: 4K50.

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 1.2 has 256 motif groups, release 1.3 has 256 motif groups, 252 of them are identical.

3 motif groups were updated, 1 groups are present only in release 1.2, 1 groups are only in release 1.3.

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_39895.535UNCG Hairpin motifs
2HL_18781.220Double sheared (tSH) with U-turn
3HL_91226.317Kissing Hairpin motif
4HL_97270.215T-loops with 1 bulged base
5HL_52574.215LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
6HL_74465.212tRNA Anti-Codon loop
7HL_48039.111MS2 virus RNA Hairpin
8HL_49036.211GNRA with one bulged base
9HL_46175.11016S helix 23 and 24 hairpin loops
10HL_17723.310LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
11HL_68081.310LSU Helix 20 Hairpin loop
12HL_80459.210
13HL_75759.210UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
14HL_56824.210LSU Helix 60A. LSU Helix 63A.
15HL_28436.39LSU Helix 96 (H96) Hairpin Loop
16HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
17HL_15603.18U1A protein-binding Hairpin Loop.
18HL_34027.285S Loop C - Upper part of Hairpin Loop.
19HL_82294.28SSU Helix 37 (h37) Hairpin loop.
20HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
21HL_24544.18LSU Helix 53 (H53) Hairpin Loop. T-loop like.
22HL_33402.27LSU Helix 13 (H13) Hairpin loop. GNRA-like.
23HL_39942.26LSU Helix 91 (H91) Hairpin Loop
24HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
25HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
26HL_70420.26LSU Helix 97 Hairpin loop
27HL_75579.26
28HL_87136.26LSU Helix 39A Hairpin loop
29HL_18156.26LSU Helix 72 (H72) Hairpin Loop
30HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
31HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
32HL_42677.16
33HL_41833.26LSU Helix 81 (H81) Hairpin Loop
34HL_46489.26LSU H89 Hairpin Loop
35HL_72273.15tRNA D-loop
36HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
37HL_88311.25LSU Helix 35 (H35) Hairpin Loop
38HL_45018.35Hairpin-Hairpin Interacting HL
39HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
40HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
41HL_12811.25LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
42HL_06643.25tRNA D-loop. Sec tRNA
43HL_57514.15Two base, cross-stacked hairpin loop
44HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
45HL_62228.24LSU Helix 35A (H35A) Hairpin Loop
46HL_47784.14SSU Central Pseudoknot (forms helix 2)
47HL_64543.14SSU Helix 31 (h31) Hairpin Loop
48HL_18798.14UNCG-like. cWW Closing pair.
49HL_62881.14RNase P Structured Hairpin Loop
50HL_61547.34
51HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
52HL_29831.14GNRA-like with bulged base.
53HL_98523.14GNRA-like. Closed by tSH UC.
54HL_19905.23LSU: Part of IL/3WJ between H55 and H56.
55HL_27429.33
56HL_25124.13tSW GA closed tetraloops
57HL_13707.23cSH AA Platform containing Hairpin Loop
58HL_54751.13
59HL_42687.23
60HL_19221.23
61HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
62HL_98833.13
63HL_58083.23
64HL_32644.13LSU Helix 69 (H69) Hairpin Loop
65HL_78361.13
66HL_41827.13
67HL_23182.13
68HL_74686.13SSU Central Pseudoknot (forms helix 2)
69HL_08382.23
70HL_42077.23LSU Helix 28 (H28) Hairpin Loop
71HL_82253.23
72HL_76036.33LSU Helix 8 (H8) Hairpin Loop
73HL_46794.23
74HL_80492.23tRNA D-loop
75HL_90579.23
76HL_16770.12
77HL_24711.12
78HL_49210.12
79HL_77555.12
80HL_42553.12
81HL_87554.12
82HL_60200.12
83HL_12595.12
84HL_23290.12
85HL_58687.12
86HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
87HL_57904.12
88HL_24473.32tRNA D-loop
89HL_94578.12
90HL_33451.12
91HL_06312.12
92HL_76766.12
93HL_64371.22
94HL_62967.12
95HL_81752.12
96HL_50312.12
97HL_57014.12
98HL_26057.12
99HL_03791.12
100HL_53753.12
101HL_38130.22
102HL_44467.12
103HL_99633.12
104HL_96915.12
105HL_45440.12
106HL_75575.12
107HL_05361.12
108HL_97512.12LSU Helix 8 (H8) Hairpin Loop
109HL_19399.12
110HL_68697.12
111HL_06122.12
112HL_65924.12
113HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
114HL_26495.12
115HL_67692.12
116HL_84353.12
117HL_67367.12
118HL_98577.12
119HL_17468.11
120HL_52393.11Double tSH (double sheared) with bulged base
121HL_59604.11
122HL_97499.11
123HL_63690.11
124HL_00721.11
125HL_26579.11
126HL_58601.11
127HL_88960.11
128HL_29084.11
129HL_62970.11
130HL_80746.11
131HL_97971.11
132HL_82243.11
133HL_10116.11Kink-turn-like Hairpin Loop
134HL_01418.11
135HL_24108.11
136HL_38898.11
137HL_81295.11UNCG-like. cWW Closing pair.
138HL_59610.11
139HL_55543.11
140HL_30128.11
141HL_48480.11
142HL_37962.11
143HL_65071.11
144HL_44522.11
145HL_66877.11cSH GU/cWS double platform, intercalation site
146HL_85753.11
147HL_62880.11
148HL_04194.11
149HL_78228.11
150HL_35200.11
151HL_69403.11GNRA-like
152HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
153HL_20028.11
154HL_59182.11
155HL_17008.11Nova-2 KH3 domain binding hairpin
156HL_93567.11
157HL_57217.11cHS platform Intercalation Site
158HL_35004.11
159HL_39422.11
160HL_66880.11
161HL_44390.11
162HL_67000.11
163HL_96192.11
164HL_75850.11
165HL_39486.11
166HL_82288.11
167HL_17537.11
168HL_16118.11
169HL_34375.11
170HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
171HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
172HL_57923.11
173HL_99779.11
174HL_20806.11
175HL_84289.11
176HL_27397.11
177HL_56809.11
178HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
179HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
180HL_33277.11
181HL_36842.11
182HL_85018.11
183HL_99584.11
184HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
185HL_07315.11
186HL_45411.11
187HL_19226.11
188HL_52109.11
189HL_95049.11Two base, cross-stacked hairpin loop
190HL_05113.11
191HL_34440.11
192HL_07915.11
193HL_63304.11
194HL_66467.11
195HL_19452.11tRNA D-loop
196HL_08203.11
197HL_33524.11tRNA T-loop distorted by RS binding
198HL_38138.11
199HL_33640.11
200HL_53789.11
201HL_78507.11
202HL_20914.11
203HL_45358.11Double hairpin loop based on GGA triple
204HL_42969.11
205HL_79902.11
206HL_30731.11
207HL_27819.11
208HL_00090.11
209HL_55272.11
210HL_47337.11
211HL_68733.11LSU Yeast Hairpin Loop
212HL_99207.11Tetrahymena LSU hairpin poorly modeled
213HL_98233.11
214HL_30008.11
215HL_65802.11
216HL_35865.11
217HL_24707.11
218HL_25195.11
219HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
220HL_60203.11
221HL_68435.11
222HL_84888.11T-loop like but without tWH UA
223HL_57843.11
224HL_68579.11
225HL_12706.11
226HL_67761.11
227HL_53015.11
228HL_78420.11
229HL_90102.11Kink-turn-like Hairpin Loop
230HL_93530.11
231HL_97784.11
232HL_73465.11
233HL_42345.11
234HL_55202.11U2B"-U2A" binding hairpin loop
235HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
236HL_56775.11
237HL_12984.11
238HL_25197.11
239HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
240HL_87223.11
241HL_58223.11
242HL_19132.11
243HL_91613.11
244HL_70912.11
245HL_13786.11
246HL_13105.11
247HL_25175.11
248HL_95716.11
249HL_71607.11
250HL_66900.11
251HL_31969.11
252HL_96994.11

Updated motif groups

#Motif idInstancesDescription
1HL_67042.7227GNRA Hairpin motifs
2HL_72498.863T-loops with two bulged bases
3HL_77235.34LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base

Removed motif groups

#Motif idInstancesDescription
1HL_06426.12tRNA D-loop

Added motif groups

#Motif idInstancesDescription
1HL_77692.11tRNA D-loop