Changes in PDB files used for clustering

Release 1.9 has 225 PDB files, release 1.10 has 229 PDB files, 225 of them are identical.

No equivalence class representatives have been replaced.

4 new structures in release 1.10: 3WFS, 4M30, 4M4O, 4M6D.

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 1.9 has 253 motif groups, release 1.10 has 253 motif groups, 248 of them are identical.

4 motif groups were updated, 1 groups are present only in release 1.9, 1 groups are only in release 1.10.

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_67042.10229GNRA Hairpin motifs
2HL_39895.635UNCG Hairpin motifs
3HL_18781.420Double sheared (tSH) with U-turn
4HL_91226.317Kissing Hairpin motif
5HL_97270.315T-loops with 1 bulged base
6HL_52574.314LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
7HL_49036.312GNRA with one bulged base
8HL_48039.211MS2 virus RNA Hairpin
9HL_46175.21016S helix 23 and 24 hairpin loops
10HL_56824.210LSU Helix 60A. LSU Helix 63A.
11HL_17723.410LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
12HL_68081.310LSU Helix 20 Hairpin loop
13HL_75759.310LSU: Part of IL/3WJ between H55 and H56. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
14HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
15HL_80459.39
16HL_15603.18U1A protein-binding Hairpin Loop.
17HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
18HL_34027.285S Loop C - Upper part of Hairpin Loop.
19HL_82294.38SSU Helix 37 (h37) Hairpin loop.
20HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
21HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
22HL_42677.27
23HL_39942.26LSU Helix 91 (H91) Hairpin Loop
24HL_70420.26LSU Helix 97 Hairpin loop
25HL_57514.26Two base, cross-stacked hairpin loop
26HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
27HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
28HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
29HL_18156.26LSU Helix 72 (H72) Hairpin Loop
30HL_75579.26
31HL_87136.26LSU Helix 39A Hairpin loop
32HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
33HL_41833.26LSU Helix 81 (H81) Hairpin Loop
34HL_46489.26LSU H89 Hairpin Loop
35HL_72273.15tRNA D-loop
36HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
37HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
38HL_88311.25LSU Helix 35 (H35) Hairpin Loop
39HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
40HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
41HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
42HL_06643.25tRNA D-loop. Sec tRNA
43HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
44HL_45018.35Hairpin-Hairpin Interacting HL
45HL_82538.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
46HL_47784.24SSU Central Pseudoknot (forms helix 2)
47HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
48HL_64543.24SSU Helix 31 (h31) Hairpin Loop
49HL_62881.14RNase P Structured Hairpin Loop
50HL_25124.24tSW GA closed tetraloops
51HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
52HL_98523.24GNRA-like. Closed by tSH UC.
53HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
54HL_29831.14GNRA-like with bulged base.
55HL_11376.14LSU Helix 8 (H8) Hairpin Loop
56HL_90579.33LSU Helix 69 (H69) Hairpin Loop
57HL_19221.23
58HL_13707.23cSH AA Platform containing Hairpin Loop
59HL_76036.33LSU Helix 8 (H8) Hairpin Loop
60HL_98833.33
61HL_58083.23
62HL_74686.13SSU Central Pseudoknot (forms helix 2)
63HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
64HL_41827.13
65HL_80492.23tRNA D-loop
66HL_27429.33
67HL_06997.23
68HL_08382.23
69HL_42077.23LSU Helix 28 (H28) Hairpin Loop
70HL_23182.13
71HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
72HL_35619.23
73HL_68697.23
74HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
75HL_78361.13
76HL_24711.12
77HL_23290.12
78HL_94578.12
79HL_32644.22LSU Helix 69 (H69) Hairpin Loop
80HL_44467.12
81HL_18587.12
82HL_62967.12
83HL_91693.12
84HL_21675.32LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
85HL_24473.32tRNA D-loop
86HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
87HL_19399.12
88HL_42094.12
89HL_98577.12
90HL_21545.12LSU Helix 96 (H96) Hairpin Loop
91HL_99633.12
92HL_63941.12
93HL_54751.22
94HL_17790.12UNCG-like. cWW Closing pair.
95HL_05361.12
96HL_93771.12tRNA T-loop distorted by RS binding
97HL_74505.12
98HL_38130.22
99HL_26495.12
100HL_19528.12
101HL_87554.12
102HL_86398.12
103HL_96915.12
104HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
105HL_06122.12
106HL_65249.12
107HL_64371.22
108HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
109HL_23129.12
110HL_91872.12
111HL_84353.12
112HL_65924.12
113HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
114HL_42553.12
115HL_60200.12
116HL_16770.12
117HL_49210.12
118HL_33451.12
119HL_50312.12
120HL_74559.12Two base, cross-stacked hairpin loop
121HL_90542.12
122HL_77692.11tRNA D-loop
123HL_93567.11
124HL_99779.11
125HL_19226.11
126HL_45358.11Double hairpin loop based on GGA triple
127HL_42969.11
128HL_79902.11
129HL_30731.11
130HL_07915.11
131HL_95716.11
132HL_82243.11
133HL_10116.11Kink-turn-like Hairpin Loop
134HL_98233.11
135HL_30008.11
136HL_38898.11
137HL_59610.11
138HL_57923.11
139HL_78507.11
140HL_68435.11
141HL_84888.11T-loop like but without tWH UA
142HL_57843.11
143HL_68579.11
144HL_27819.11
145HL_00090.11
146HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
147HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
148HL_78228.11
149HL_97971.11
150HL_69403.11GNRA-like
151HL_46570.11
152HL_73465.11
153HL_42345.11
154HL_17008.11Nova-2 KH3 domain binding hairpin
155HL_52116.11
156HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
157HL_45411.11
158HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
159HL_60203.11
160HL_58223.11
161HL_19132.11
162HL_12706.11
163HL_67761.11
164HL_63304.11
165HL_75850.11
166HL_35200.11
167HL_82288.11
168HL_83865.11
169HL_79038.11LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
170HL_96994.11
171HL_73972.11
172HL_53789.11
173HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
174HL_76585.11
175HL_87223.11
176HL_26579.11
177HL_58601.11
178HL_88960.11
179HL_91613.11
180HL_70912.11
181HL_13786.11
182HL_55272.11
183HL_47337.11
184HL_39486.11
185HL_36842.11
186HL_23195.11
187HL_01418.11
188HL_24108.11
189HL_84768.11
190HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
191HL_24707.11
192HL_25195.11
193HL_59604.11
194HL_97499.11
195HL_00721.11
196HL_44522.11
197HL_66877.11cSH GU/cWS double platform, intercalation site
198HL_53015.11
199HL_78420.11
200HL_33277.11
201HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
202HL_20028.11
203HL_59182.11
204HL_38138.11
205HL_35865.11
206HL_25197.11
207HL_37962.11
208HL_65071.11
209HL_39422.11
210HL_66880.11
211HL_03785.11LSU Helix 8 (H8) Hairpin Loop
212HL_25175.11
213HL_68733.11LSU Yeast Hairpin Loop
214HL_66467.11
215HL_99207.11Tetrahymena LSU hairpin poorly modeled
216HL_17537.11
217HL_59225.11
218HL_33640.11
219HL_65802.11
220HL_28676.11
221HL_57217.11cHS platform Intercalation Site
222HL_52540.11
223HL_84289.11
224HL_27397.11
225HL_44390.11
226HL_67000.11
227HL_62970.11
228HL_76679.11
229HL_90102.11Kink-turn-like Hairpin Loop
230HL_97784.11
231HL_85018.11
232HL_99584.11
233HL_29196.11
234HL_55202.11U2B"-U2A" binding hairpin loop
235HL_56775.11
236HL_30128.11
237HL_48480.11
238HL_20806.11
239HL_95049.11Two base, cross-stacked hairpin loop
240HL_05113.11
241HL_34440.11
242HL_56809.11
243HL_93263.11
244HL_62880.11
245HL_04194.11
246HL_93530.11
247HL_19452.11tRNA D-loop
248HL_08203.11

Updated motif groups

#Motif idInstancesDescription
1HL_72498.1266T-loops with two bulged bases
2HL_74465.513tRNA Anti-Codon loop
3HL_27271.212LSU Helix 96 (H96) Hairpin Loop
4HL_76766.43

Removed motif groups

#Motif idInstancesDescription
1HL_42687.43

Added motif groups

#Motif idInstancesDescription
1HL_86115.14