Changes in PDB files used for clustering

Release 1.1 has 213 PDB files, release 1.2 has 216 PDB files, 213 of them are identical.

No equivalence class representatives have been replaced.

3 new structures in release 1.2: 4JF2, 4JRC, 4JXZ.

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 1.1 has 254 motif groups, release 1.2 has 256 motif groups, 249 of them are identical.

4 motif groups were updated, 1 groups are present only in release 1.1, 3 groups are only in release 1.2.

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_18781.220Double sheared (tSH) with U-turn
2HL_91226.317Kissing Hairpin motif
3HL_97270.215T-loops with 1 bulged base
4HL_52574.215LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
5HL_74465.212tRNA Anti-Codon loop
6HL_48039.111MS2 virus RNA Hairpin
7HL_49036.211GNRA with one bulged base
8HL_17723.310LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
9HL_68081.310LSU Helix 20 Hairpin loop
10HL_80459.210
11HL_75759.210UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
12HL_56824.210LSU Helix 60A. LSU Helix 63A.
13HL_46175.11016S helix 23 and 24 hairpin loops
14HL_28436.39LSU Helix 96 (H96) Hairpin Loop
15HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
16HL_15603.18U1A protein-binding Hairpin Loop.
17HL_34027.285S Loop C - Upper part of Hairpin Loop.
18HL_82294.28SSU Helix 37 (h37) Hairpin loop.
19HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
20HL_24544.18LSU Helix 53 (H53) Hairpin Loop. T-loop like.
21HL_33402.27LSU Helix 13 (H13) Hairpin loop. GNRA-like.
22HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
23HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
24HL_70420.26LSU Helix 97 Hairpin loop
25HL_75579.26
26HL_87136.26LSU Helix 39A Hairpin loop
27HL_18156.26LSU Helix 72 (H72) Hairpin Loop
28HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
29HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
30HL_42677.16
31HL_41833.26LSU Helix 81 (H81) Hairpin Loop
32HL_46489.26LSU H89 Hairpin Loop
33HL_39942.26LSU Helix 91 (H91) Hairpin Loop
34HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
35HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
36HL_12811.25LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
37HL_06643.25tRNA D-loop. Sec tRNA
38HL_57514.15Two base, cross-stacked hairpin loop
39HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
40HL_72273.15tRNA D-loop
41HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
42HL_88311.25LSU Helix 35 (H35) Hairpin Loop
43HL_45018.35Hairpin-Hairpin Interacting HL
44HL_62228.24LSU Helix 35A (H35A) Hairpin Loop
45HL_47784.14SSU Central Pseudoknot (forms helix 2)
46HL_64543.14SSU Helix 31 (h31) Hairpin Loop
47HL_18798.14UNCG-like. cWW Closing pair.
48HL_62881.14RNase P Structured Hairpin Loop
49HL_61547.34
50HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
51HL_29831.14GNRA-like with bulged base.
52HL_98523.14GNRA-like. Closed by tSH UC.
53HL_27429.33
54HL_25124.13tSW GA closed tetraloops
55HL_13707.23cSH AA Platform containing Hairpin Loop
56HL_54751.13
57HL_42687.23
58HL_19221.23
59HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
60HL_98833.13
61HL_58083.23
62HL_32644.13LSU Helix 69 (H69) Hairpin Loop
63HL_78361.13
64HL_41827.13
65HL_23182.13
66HL_74686.13SSU Central Pseudoknot (forms helix 2)
67HL_08382.23
68HL_42077.23LSU Helix 28 (H28) Hairpin Loop
69HL_82253.23
70HL_76036.33LSU Helix 8 (H8) Hairpin Loop
71HL_46794.23
72HL_80492.23tRNA D-loop
73HL_90579.23
74HL_19905.23LSU: Part of IL/3WJ between H55 and H56.
75HL_16770.12
76HL_12595.12
77HL_23290.12
78HL_58687.12
79HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
80HL_57904.12
81HL_24473.32tRNA D-loop
82HL_94578.12
83HL_33451.12
84HL_06312.12
85HL_76766.12
86HL_64371.22
87HL_62967.12
88HL_50312.12
89HL_57014.12
90HL_26057.12
91HL_03791.12
92HL_81752.12
93HL_53753.12
94HL_38130.22
95HL_44467.12
96HL_99633.12
97HL_96915.12
98HL_45440.12
99HL_75575.12
100HL_05361.12
101HL_97512.12LSU Helix 8 (H8) Hairpin Loop
102HL_19399.12
103HL_68697.12
104HL_65924.12
105HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
106HL_26495.12
107HL_67692.12
108HL_06122.12
109HL_67367.12
110HL_98577.12
111HL_84353.12
112HL_24711.12
113HL_49210.12
114HL_77555.12
115HL_42553.12
116HL_87554.12
117HL_60200.12
118HL_81295.11UNCG-like. cWW Closing pair.
119HL_59610.11
120HL_55543.11
121HL_30128.11
122HL_48480.11
123HL_37962.11
124HL_65071.11
125HL_44522.11
126HL_66877.11cSH GU/cWS double platform, intercalation site
127HL_85753.11
128HL_62880.11
129HL_04194.11
130HL_78228.11
131HL_35200.11
132HL_69403.11GNRA-like
133HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
134HL_20028.11
135HL_38898.11
136HL_93567.11
137HL_57217.11cHS platform Intercalation Site
138HL_35004.11
139HL_39422.11
140HL_66880.11
141HL_44390.11
142HL_67000.11
143HL_96192.11
144HL_75850.11
145HL_39486.11
146HL_82288.11
147HL_17537.11
148HL_16118.11
149HL_17008.11Nova-2 KH3 domain binding hairpin
150HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
151HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
152HL_57923.11
153HL_99779.11
154HL_20806.11
155HL_84289.11
156HL_27397.11
157HL_56809.11
158HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
159HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
160HL_33277.11
161HL_36842.11
162HL_85018.11
163HL_99584.11
164HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
165HL_07315.11
166HL_45411.11
167HL_19226.11
168HL_52109.11
169HL_95049.11Two base, cross-stacked hairpin loop
170HL_05113.11
171HL_34440.11
172HL_07915.11
173HL_63304.11
174HL_66467.11
175HL_19452.11tRNA D-loop
176HL_08203.11
177HL_38138.11
178HL_33640.11
179HL_53789.11
180HL_78507.11
181HL_20914.11
182HL_45358.11Double hairpin loop based on GGA triple
183HL_42969.11
184HL_79902.11
185HL_30731.11
186HL_27819.11
187HL_00090.11
188HL_55272.11
189HL_47337.11
190HL_68733.11LSU Yeast Hairpin Loop
191HL_99207.11Tetrahymena LSU hairpin poorly modeled
192HL_98233.11
193HL_30008.11
194HL_33524.11tRNA T-loop distorted by RS binding
195HL_65802.11
196HL_35865.11
197HL_24707.11
198HL_25195.11
199HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
200HL_60203.11
201HL_68435.11
202HL_84888.11T-loop like but without tWH UA
203HL_57843.11
204HL_68579.11
205HL_12706.11
206HL_67761.11
207HL_53015.11
208HL_78420.11
209HL_90102.11Kink-turn-like Hairpin Loop
210HL_93530.11
211HL_97784.11
212HL_73465.11
213HL_42345.11
214HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
215HL_56775.11
216HL_12984.11
217HL_25197.11
218HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
219HL_87223.11
220HL_58223.11
221HL_19132.11
222HL_91613.11
223HL_70912.11
224HL_13786.11
225HL_13105.11
226HL_25175.11
227HL_95716.11
228HL_71607.11
229HL_66900.11
230HL_31969.11
231HL_96994.11
232HL_55202.11U2B"-U2A" binding hairpin loop
233HL_17468.11
234HL_52393.11Double tSH (double sheared) with bulged base
235HL_59604.11
236HL_97499.11
237HL_63690.11
238HL_00721.11
239HL_26579.11
240HL_58601.11
241HL_88960.11
242HL_29084.11
243HL_62970.11
244HL_80746.11
245HL_97971.11
246HL_82243.11
247HL_10116.11Kink-turn-like Hairpin Loop
248HL_01418.11
249HL_24108.11

Updated motif groups

#Motif idInstancesDescription
1HL_67042.6225GNRA Hairpin motifs
2HL_72498.764T-loops with two bulged bases
3HL_39895.535UNCG Hairpin motifs
4HL_77235.25LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base

Removed motif groups

#Motif idInstancesDescription
1HL_81661.11tRNA D-loop

Added motif groups

#Motif idInstancesDescription
1HL_06426.12tRNA D-loop
2HL_34375.11
3HL_59182.11