Changes in PDB files used for clustering

Release 1.10 has 229 PDB files, release 1.11 has 229 PDB files, 229 of them are identical.

No equivalence class representatives have been replaced.

No new PDB files have been added.

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

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Changes in motif groups

Release 1.10 has 253 motif groups, release 1.11 has 253 motif groups, 253 of them are identical.

0 motif groups were updated, 0 groups are present only in release 1.10, 0 groups are only in release 1.11.

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_72498.1266T-loops with two bulged bases
3HL_39895.635UNCG Hairpin motifs
4HL_18781.420Double sheared (tSH) with U-turn
5HL_91226.317Kissing Hairpin motif
6HL_97270.315T-loops with 1 bulged base
7HL_52574.314LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
8HL_74465.513tRNA Anti-Codon loop
9HL_49036.312GNRA with one bulged base
10HL_27271.212LSU Helix 96 (H96) Hairpin Loop
11HL_48039.211MS2 virus RNA Hairpin
12HL_56824.210LSU Helix 60A. LSU Helix 63A.
13HL_17723.410LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
14HL_68081.310LSU Helix 20 Hairpin loop
15HL_46175.21016S helix 23 and 24 hairpin loops
16HL_75759.310LSU: Part of IL/3WJ between H55 and H56. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
17HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
18HL_80459.39
19HL_82294.38SSU Helix 37 (h37) Hairpin loop.
20HL_15603.18U1A protein-binding Hairpin Loop.
21HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
22HL_34027.285S Loop C - Upper part of Hairpin Loop.
23HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
24HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
25HL_42677.27
26HL_39942.26LSU Helix 91 (H91) Hairpin Loop
27HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
28HL_70420.26LSU Helix 97 Hairpin loop
29HL_57514.26Two base, cross-stacked hairpin loop
30HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
31HL_18156.26LSU Helix 72 (H72) Hairpin Loop
32HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
33HL_75579.26
34HL_87136.26LSU Helix 39A Hairpin loop
35HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
36HL_41833.26LSU Helix 81 (H81) Hairpin Loop
37HL_46489.26LSU H89 Hairpin Loop
38HL_45018.35Hairpin-Hairpin Interacting HL
39HL_06643.25tRNA D-loop. Sec tRNA
40HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
41HL_88311.25LSU Helix 35 (H35) Hairpin Loop
42HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
43HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
44HL_82538.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
45HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
46HL_72273.15tRNA D-loop
47HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
48HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
49HL_64543.24SSU Helix 31 (h31) Hairpin Loop
50HL_86115.14
51HL_62881.14RNase P Structured Hairpin Loop
52HL_29831.14GNRA-like with bulged base.
53HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
54HL_25124.24tSW GA closed tetraloops
55HL_47784.24SSU Central Pseudoknot (forms helix 2)
56HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
57HL_11376.14LSU Helix 8 (H8) Hairpin Loop
58HL_98523.24GNRA-like. Closed by tSH UC.
59HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
60HL_68697.23
61HL_13707.23cSH AA Platform containing Hairpin Loop
62HL_78361.13
63HL_19221.23
64HL_90579.33LSU Helix 69 (H69) Hairpin Loop
65HL_41827.13
66HL_98833.33
67HL_76036.33LSU Helix 8 (H8) Hairpin Loop
68HL_58083.23
69HL_74686.13SSU Central Pseudoknot (forms helix 2)
70HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
71HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
72HL_08382.23
73HL_42077.23LSU Helix 28 (H28) Hairpin Loop
74HL_23182.13
75HL_80492.23tRNA D-loop
76HL_27429.33
77HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
78HL_35619.23
79HL_76766.43
80HL_06997.23
81HL_63941.12
82HL_24711.12
83HL_49210.12
84HL_33451.12
85HL_50312.12
86HL_60200.12
87HL_54751.22
88HL_91693.12
89HL_21675.32LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
90HL_23290.12
91HL_94578.12
92HL_32644.22LSU Helix 69 (H69) Hairpin Loop
93HL_74559.12Two base, cross-stacked hairpin loop
94HL_90542.12
95HL_93771.12tRNA T-loop distorted by RS binding
96HL_74505.12
97HL_24473.32tRNA D-loop
98HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
99HL_19399.12
100HL_44467.12
101HL_18587.12
102HL_62967.12
103HL_06122.12
104HL_42094.12
105HL_84353.12
106HL_65924.12
107HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
108HL_17790.12UNCG-like. cWW Closing pair.
109HL_05361.12
110HL_98577.12
111HL_21545.12LSU Helix 96 (H96) Hairpin Loop
112HL_99633.12
113HL_16770.12
114HL_38130.22
115HL_26495.12
116HL_65249.12
117HL_19528.12
118HL_87554.12
119HL_86398.12
120HL_96915.12
121HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
122HL_42553.12
123HL_64371.22
124HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
125HL_23129.12
126HL_91872.12
127HL_77692.11tRNA D-loop
128HL_30128.11
129HL_48480.11
130HL_20806.11
131HL_52540.11
132HL_84289.11
133HL_27397.11
134HL_44390.11
135HL_67000.11
136HL_62970.11
137HL_76679.11
138HL_90102.11Kink-turn-like Hairpin Loop
139HL_97784.11
140HL_85018.11
141HL_99584.11
142HL_29196.11
143HL_93567.11
144HL_99779.11
145HL_19226.11
146HL_95049.11Two base, cross-stacked hairpin loop
147HL_05113.11
148HL_34440.11
149HL_56809.11
150HL_93263.11
151HL_62880.11
152HL_04194.11
153HL_93530.11
154HL_19452.11tRNA D-loop
155HL_08203.11
156HL_52116.11
157HL_57923.11
158HL_78507.11
159HL_45358.11Double hairpin loop based on GGA triple
160HL_42969.11
161HL_79902.11
162HL_30731.11
163HL_07915.11
164HL_95716.11
165HL_82243.11
166HL_10116.11Kink-turn-like Hairpin Loop
167HL_98233.11
168HL_30008.11
169HL_73972.11
170HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
171HL_45411.11
172HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
173HL_60203.11
174HL_68435.11
175HL_84888.11T-loop like but without tWH UA
176HL_57843.11
177HL_68579.11
178HL_27819.11
179HL_00090.11
180HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
181HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
182HL_78228.11
183HL_97971.11
184HL_69403.11GNRA-like
185HL_46570.11
186HL_73465.11
187HL_42345.11
188HL_55202.11U2B"-U2A" binding hairpin loop
189HL_84768.11
190HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
191HL_53789.11
192HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
193HL_76585.11
194HL_87223.11
195HL_58223.11
196HL_19132.11
197HL_12706.11
198HL_67761.11
199HL_63304.11
200HL_75850.11
201HL_35200.11
202HL_82288.11
203HL_83865.11
204HL_79038.11LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
205HL_96994.11
206HL_38138.11
207HL_24707.11
208HL_25195.11
209HL_59604.11
210HL_97499.11
211HL_00721.11
212HL_26579.11
213HL_58601.11
214HL_88960.11
215HL_91613.11
216HL_70912.11
217HL_13786.11
218HL_55272.11
219HL_47337.11
220HL_39486.11
221HL_36842.11
222HL_23195.11
223HL_01418.11
224HL_24108.11
225HL_38898.11
226HL_33640.11
227HL_65802.11
228HL_35865.11
229HL_25197.11
230HL_37962.11
231HL_65071.11
232HL_44522.11
233HL_66877.11cSH GU/cWS double platform, intercalation site
234HL_53015.11
235HL_78420.11
236HL_33277.11
237HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
238HL_20028.11
239HL_59182.11
240HL_17008.11Nova-2 KH3 domain binding hairpin
241HL_59610.11
242HL_56775.11
243HL_28676.11
244HL_57217.11cHS platform Intercalation Site
245HL_39422.11
246HL_66880.11
247HL_03785.11LSU Helix 8 (H8) Hairpin Loop
248HL_25175.11
249HL_68733.11LSU Yeast Hairpin Loop
250HL_66467.11
251HL_99207.11Tetrahymena LSU hairpin poorly modeled
252HL_17537.11
253HL_59225.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription