Changes in PDB files used for clustering

Release 1.2 has 211 PDB files, release 1.3 has 211 PDB files, 210 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_56824.210LSU Helix 60A. LSU Helix 63A.
10HL_68081.310LSU Helix 20 Hairpin loop
11HL_75759.210UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
12HL_17723.310LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
13HL_46175.11016S helix 23 and 24 hairpin loops
14HL_80459.210
15HL_28436.39LSU Helix 96 (H96) Hairpin Loop
16HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
17HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
18HL_15603.18U1A protein-binding Hairpin Loop.
19HL_24544.18LSU Helix 53 (H53) Hairpin Loop. T-loop like.
20HL_34027.285S Loop C - Upper part of Hairpin Loop.
21HL_82294.28SSU Helix 37 (h37) Hairpin loop.
22HL_33402.27LSU Helix 13 (H13) Hairpin loop. GNRA-like.
23HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
24HL_87136.26LSU Helix 39A Hairpin loop
25HL_41833.26LSU Helix 81 (H81) Hairpin Loop
26HL_70420.26LSU Helix 97 Hairpin loop
27HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
28HL_75579.26
29HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
30HL_18156.26LSU Helix 72 (H72) Hairpin Loop
31HL_42677.16
32HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
33HL_39942.26LSU Helix 91 (H91) Hairpin Loop
34HL_46489.26LSU H89 Hairpin Loop
35HL_06643.25tRNA D-loop. Sec tRNA
36HL_12811.25LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
37HL_45018.35Hairpin-Hairpin Interacting HL
38HL_57514.15Two base, cross-stacked hairpin loop
39HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
40HL_88311.25LSU Helix 35 (H35) Hairpin Loop
41HL_72273.15tRNA D-loop
42HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
43HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
44HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
45HL_18798.14UNCG-like. cWW Closing pair.
46HL_62228.24LSU Helix 35A (H35A) Hairpin Loop
47HL_64543.14SSU Helix 31 (h31) Hairpin Loop
48HL_98523.14GNRA-like. Closed by tSH UC.
49HL_47784.14SSU Central Pseudoknot (forms helix 2)
50HL_62881.14RNase P Structured Hairpin Loop
51HL_29831.14GNRA-like with bulged base.
52HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
53HL_61547.34
54HL_25124.13tSW GA closed tetraloops
55HL_27429.33
56HL_41827.13
57HL_46794.23
58HL_80492.23tRNA D-loop
59HL_23182.13
60HL_32644.13LSU Helix 69 (H69) Hairpin Loop
61HL_74686.13SSU Central Pseudoknot (forms helix 2)
62HL_19221.23
63HL_42077.23LSU Helix 28 (H28) Hairpin Loop
64HL_54751.13
65HL_78361.13
66HL_98833.13
67HL_08382.23
68HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
69HL_82253.23
70HL_13707.23cSH AA Platform containing Hairpin Loop
71HL_19905.23LSU: Part of IL/3WJ between H55 and H56.
72HL_58083.23
73HL_76036.33LSU Helix 8 (H8) Hairpin Loop
74HL_42687.23
75HL_90579.23
76HL_06312.12
77HL_38130.22
78HL_49210.12
79HL_53753.12
80HL_77555.12
81HL_12595.12
82HL_57014.12
83HL_58687.12
84HL_67367.12
85HL_96915.12
86HL_98577.12
87HL_16770.12
88HL_23290.12
89HL_67692.12
90HL_75575.12
91HL_84353.12
92HL_87554.12
93HL_50312.12
94HL_62967.12
95HL_65924.12
96HL_81752.12
97HL_03791.12
98HL_19399.12
99HL_24473.32tRNA D-loop
100HL_26057.12
101HL_33451.12
102HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
103HL_94578.12
104HL_99633.12
105HL_26495.12
106HL_42553.12
107HL_45440.12
108HL_57904.12
109HL_60200.12
110HL_97512.12LSU Helix 8 (H8) Hairpin Loop
111HL_05361.12
112HL_06122.12
113HL_24711.12
114HL_64371.22
115HL_68697.12
116HL_76766.12
117HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
118HL_20914.11
119HL_31969.11
120HL_42969.11
121HL_58601.11
122HL_67000.11
123HL_68733.11LSU Yeast Hairpin Loop
124HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
125HL_96192.11
126HL_00090.11
127HL_16118.11
128HL_19132.11
129HL_25175.11
130HL_27819.11
131HL_34375.11
132HL_38138.11
133HL_44390.11
134HL_47337.11
135HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
136HL_53789.11
137HL_62880.11
138HL_65071.11
139HL_69403.11GNRA-like
140HL_78228.11
141HL_80746.11
142HL_84289.11
143HL_87223.11
144HL_93530.11
145HL_01418.11
146HL_07315.11
147HL_12706.11
148HL_25195.11
149HL_33277.11
150HL_34440.11
151HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
152HL_44522.11
153HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
154HL_57217.11cHS platform Intercalation Site
155HL_59182.11
156HL_65802.11
157HL_81295.11UNCG-like. cWW Closing pair.
158HL_93567.11
159HL_96994.11
160HL_07915.11
161HL_17468.11
162HL_19226.11
163HL_24108.11
164HL_25197.11
165HL_29084.11
166HL_35004.11
167HL_39422.11
168HL_42345.11
169HL_55202.11U2B"-U2A" binding hairpin loop
170HL_59604.11
171HL_67761.11
172HL_70912.11
173HL_78420.11
174HL_84888.11T-loop like but without tWH UA
175HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
176HL_99207.11Tetrahymena LSU hairpin poorly modeled
177HL_12984.11
178HL_17537.11
179HL_35200.11
180HL_39486.11
181HL_45411.11
182HL_52109.11
183HL_55272.11
184HL_57843.11
185HL_59610.11
186HL_62970.11
187HL_71607.11
188HL_78507.11
189HL_82243.11
190HL_85018.11
191HL_97499.11
192HL_04194.11
193HL_10116.11Kink-turn-like Hairpin Loop
194HL_13105.11
195HL_19452.11tRNA D-loop
196HL_30008.11
197HL_33524.11tRNA T-loop distorted by RS binding
198HL_35865.11
199HL_52393.11Double tSH (double sheared) with bulged base
200HL_55543.11
201HL_63304.11
202HL_66467.11
203HL_68435.11
204HL_75850.11
205HL_88960.11
206HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
207HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
208HL_24707.11
209HL_26579.11
210HL_30128.11
211HL_33640.11
212HL_36842.11
213HL_48480.11
214HL_56775.11
215HL_60203.11
216HL_63690.11
217HL_66877.11cSH GU/cWS double platform, intercalation site
218HL_68579.11
219HL_79902.11
220HL_82288.11
221HL_85753.11
222HL_90102.11Kink-turn-like Hairpin Loop
223HL_95049.11Two base, cross-stacked hairpin loop
224HL_97784.11
225HL_13786.11
226HL_20806.11
227HL_27397.11
228HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
229HL_37962.11
230HL_53015.11
231HL_56809.11
232HL_58223.11
233HL_66900.11
234HL_73465.11
235HL_95716.11
236HL_97971.11

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