Changes in PDB files used for clustering

Release 1.1 has 208 PDB files, release 1.2 has 211 PDB files, 208 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_49036.211GNRA with one bulged base
7HL_48039.111MS2 virus RNA Hairpin
8HL_75759.210UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
9HL_56824.210LSU Helix 60A. LSU Helix 63A.
10HL_46175.11016S helix 23 and 24 hairpin loops
11HL_17723.310LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
12HL_68081.310LSU Helix 20 Hairpin loop
13HL_80459.210
14HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
15HL_28436.39LSU Helix 96 (H96) Hairpin Loop
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_46489.26LSU H89 Hairpin Loop
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_12811.25LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
35HL_06643.25tRNA D-loop. Sec tRNA
36HL_72273.15tRNA D-loop
37HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
38HL_88311.25LSU Helix 35 (H35) Hairpin Loop
39HL_45018.35Hairpin-Hairpin Interacting HL
40HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
41HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
42HL_57514.15Two base, cross-stacked hairpin loop
43HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
44HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
45HL_29831.14GNRA-like with bulged base.
46HL_98523.14GNRA-like. Closed by tSH UC.
47HL_62228.24LSU Helix 35A (H35A) Hairpin Loop
48HL_47784.14SSU Central Pseudoknot (forms helix 2)
49HL_64543.14SSU Helix 31 (h31) Hairpin Loop
50HL_18798.14UNCG-like. cWW Closing pair.
51HL_62881.14RNase P Structured Hairpin Loop
52HL_61547.34
53HL_08382.23
54HL_42077.23LSU Helix 28 (H28) Hairpin Loop
55HL_82253.23
56HL_80492.23tRNA D-loop
57HL_27429.33
58HL_78361.13
59HL_46794.23
60HL_19905.23LSU: Part of IL/3WJ between H55 and H56.
61HL_32644.13LSU Helix 69 (H69) Hairpin Loop
62HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
63HL_13707.23cSH AA Platform containing Hairpin Loop
64HL_54751.13
65HL_42687.23
66HL_19221.23
67HL_76036.33LSU Helix 8 (H8) Hairpin Loop
68HL_25124.13tSW GA closed tetraloops
69HL_98833.13
70HL_58083.23
71HL_74686.13SSU Central Pseudoknot (forms helix 2)
72HL_90579.23
73HL_41827.13
74HL_23182.13
75HL_65924.12
76HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
77HL_42553.12
78HL_76766.12
79HL_60200.12
80HL_06122.12
81HL_77555.12
82HL_58687.12
83HL_06312.12
84HL_26057.12
85HL_87554.12
86HL_84353.12
87HL_24711.12
88HL_49210.12
89HL_33451.12
90HL_50312.12
91HL_57014.12
92HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
93HL_62967.12
94HL_16770.12
95HL_12595.12
96HL_23290.12
97HL_94578.12
98HL_98577.12
99HL_57904.12
100HL_24473.32tRNA D-loop
101HL_97512.12LSU Helix 8 (H8) Hairpin Loop
102HL_19399.12
103HL_03791.12
104HL_99633.12
105HL_96915.12
106HL_45440.12
107HL_05361.12
108HL_67692.12
109HL_68697.12
110HL_81752.12
111HL_53753.12
112HL_38130.22
113HL_67367.12
114HL_64371.22
115HL_75575.12
116HL_26495.12
117HL_33524.11tRNA T-loop distorted by RS binding
118HL_65802.11
119HL_35865.11
120HL_25197.11
121HL_37962.11
122HL_68579.11
123HL_70912.11
124HL_62970.11
125HL_80746.11
126HL_97971.11
127HL_82243.11
128HL_10116.11Kink-turn-like Hairpin Loop
129HL_16118.11
130HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
131HL_56775.11
132HL_12984.11
133HL_57217.11cHS platform Intercalation Site
134HL_35004.11
135HL_42969.11
136HL_79902.11
137HL_29084.11
138HL_62880.11
139HL_04194.11
140HL_78228.11
141HL_35200.11
142HL_69403.11GNRA-like
143HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
144HL_30008.11
145HL_17468.11
146HL_52393.11Double tSH (double sheared) with bulged base
147HL_30128.11
148HL_48480.11
149HL_20806.11
150HL_95049.11Two base, cross-stacked hairpin loop
151HL_84888.11T-loop like but without tWH UA
152HL_57843.11
153HL_85753.11
154HL_96192.11
155HL_75850.11
156HL_39486.11
157HL_82288.11
158HL_17537.11
159HL_42345.11
160HL_81295.11UNCG-like. cWW Closing pair.
161HL_59610.11
162HL_55543.11
163HL_93567.11
164HL_19226.11
165HL_52109.11
166HL_68435.11
167HL_19132.11
168HL_44390.11
169HL_67000.11
170HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
171HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
172HL_33277.11
173HL_36842.11
174HL_85018.11
175HL_96994.11
176HL_55202.11U2B"-U2A" binding hairpin loop
177HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
178HL_45411.11
179HL_78507.11
180HL_20914.11
181HL_58223.11
182HL_58601.11
183HL_88960.11
184HL_56809.11
185HL_63304.11
186HL_66467.11
187HL_19452.11tRNA D-loop
188HL_24108.11
189HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
190HL_07315.11
191HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
192HL_60203.11
193HL_26579.11
194HL_66877.11cSH GU/cWS double platform, intercalation site
195HL_07915.11
196HL_00090.11
197HL_55272.11
198HL_47337.11
199HL_68733.11LSU Yeast Hairpin Loop
200HL_99207.11Tetrahymena LSU hairpin poorly modeled
201HL_73465.11
202HL_53789.11
203HL_25195.11
204HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
205HL_87223.11
206HL_44522.11
207HL_27397.11
208HL_27819.11
209HL_67761.11
210HL_53015.11
211HL_78420.11
212HL_90102.11Kink-turn-like Hairpin Loop
213HL_93530.11
214HL_97784.11
215HL_31969.11
216HL_38138.11
217HL_33640.11
218HL_24707.11
219HL_59604.11
220HL_97499.11
221HL_63690.11
222HL_65071.11
223HL_39422.11
224HL_84289.11
225HL_34440.11
226HL_12706.11
227HL_13786.11
228HL_13105.11
229HL_25175.11
230HL_95716.11
231HL_71607.11
232HL_66900.11
233HL_01418.11

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