Changes in PDB files used for clustering

Release 1.11 has 229 PDB files, release 1.12 has 231 PDB files, 229 of them are identical.

No equivalence class representatives have been replaced.

2 new structures in release 1.12: 4C4W, 4OO8.

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 1.11 has 253 motif groups, release 1.12 has 253 motif groups, 249 of them are identical.

4 motif groups were updated, 0 groups are present only in release 1.11, 0 groups are only in release 1.12.

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_72498.1266T-loops with two bulged bases
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_74465.513tRNA Anti-Codon loop
8HL_49036.312GNRA with one bulged base
9HL_27271.212LSU Helix 96 (H96) Hairpin Loop
10HL_48039.211MS2 virus RNA Hairpin
11HL_17723.410LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
12HL_68081.310LSU Helix 20 Hairpin loop
13HL_46175.21016S helix 23 and 24 hairpin loops
14HL_56824.210LSU Helix 60A. LSU Helix 63A.
15HL_80459.39
16HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
17HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
18HL_82294.38SSU Helix 37 (h37) Hairpin loop.
19HL_34027.285S Loop C - Upper part of 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_18156.26LSU Helix 72 (H72) Hairpin Loop
24HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
25HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
26HL_75579.26
27HL_87136.26LSU Helix 39A Hairpin loop
28HL_41833.26LSU Helix 81 (H81) Hairpin Loop
29HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
30HL_46489.26LSU H89 Hairpin Loop
31HL_39942.26LSU Helix 91 (H91) Hairpin Loop
32HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
33HL_70420.26LSU Helix 97 Hairpin loop
34HL_57514.26Two base, cross-stacked hairpin loop
35HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
36HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
37HL_72273.15tRNA D-loop
38HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
39HL_45018.35Hairpin-Hairpin Interacting HL
40HL_82538.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
41HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
42HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
43HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
44HL_88311.25LSU Helix 35 (H35) Hairpin Loop
45HL_86115.14
46HL_62881.14RNase P Structured Hairpin Loop
47HL_25124.24tSW GA closed tetraloops
48HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
49HL_29831.14GNRA-like with bulged base.
50HL_98523.24GNRA-like. Closed by tSH UC.
51HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
52HL_11376.14LSU Helix 8 (H8) Hairpin Loop
53HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
54HL_47784.24SSU Central Pseudoknot (forms helix 2)
55HL_64543.24SSU Helix 31 (h31) Hairpin Loop
56HL_13707.23cSH AA Platform containing Hairpin Loop
57HL_76036.33LSU Helix 8 (H8) Hairpin Loop
58HL_58083.23
59HL_74686.13SSU Central Pseudoknot (forms helix 2)
60HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
61HL_41827.13
62HL_98833.33
63HL_80492.23tRNA D-loop
64HL_27429.33
65HL_06997.23
66HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
67HL_42077.23LSU Helix 28 (H28) Hairpin Loop
68HL_23182.13
69HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
70HL_35619.23
71HL_76766.43
72HL_68697.23
73HL_08382.23
74HL_78361.13
75HL_90579.33LSU Helix 69 (H69) Hairpin Loop
76HL_19221.23
77HL_63941.12
78HL_54751.22
79HL_91693.12
80HL_42094.12
81HL_98577.12
82HL_21545.12LSU Helix 96 (H96) Hairpin Loop
83HL_99633.12
84HL_74505.12
85HL_17790.12UNCG-like. cWW Closing pair.
86HL_05361.12
87HL_93771.12tRNA T-loop distorted by RS binding
88HL_38130.22
89HL_26495.12
90HL_19528.12
91HL_87554.12
92HL_86398.12
93HL_96915.12
94HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
95HL_06122.12
96HL_65924.12
97HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
98HL_65249.12
99HL_64371.22
100HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
101HL_23129.12
102HL_91872.12
103HL_84353.12
104HL_42553.12
105HL_60200.12
106HL_16770.12
107HL_49210.12
108HL_33451.12
109HL_50312.12
110HL_74559.12Two base, cross-stacked hairpin loop
111HL_90542.12
112HL_23290.12
113HL_94578.12
114HL_32644.22LSU Helix 69 (H69) Hairpin Loop
115HL_44467.12
116HL_18587.12
117HL_62967.12
118HL_24711.12
119HL_21675.32LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
120HL_24473.32tRNA D-loop
121HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
122HL_19399.12
123HL_52116.11
124HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
125HL_45411.11
126HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
127HL_60203.11
128HL_68435.11
129HL_19132.11
130HL_12706.11
131HL_67761.11
132HL_63304.11
133HL_75850.11
134HL_35200.11
135HL_82288.11
136HL_83865.11
137HL_79038.11LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
138HL_96994.11
139HL_73972.11
140HL_53789.11
141HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
142HL_76585.11
143HL_87223.11
144HL_58223.11
145HL_58601.11
146HL_88960.11
147HL_91613.11
148HL_70912.11
149HL_13786.11
150HL_55272.11
151HL_47337.11
152HL_39486.11
153HL_36842.11
154HL_23195.11
155HL_01418.11
156HL_24108.11
157HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
158HL_24707.11
159HL_25195.11
160HL_59604.11
161HL_97499.11
162HL_00721.11
163HL_26579.11
164HL_66877.11cSH GU/cWS double platform, intercalation site
165HL_53015.11
166HL_78420.11
167HL_33277.11
168HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
169HL_20028.11
170HL_59182.11
171HL_84768.11
172HL_65802.11
173HL_35865.11
174HL_25197.11
175HL_37962.11
176HL_65071.11
177HL_44522.11
178HL_66880.11
179HL_03785.11LSU Helix 8 (H8) Hairpin Loop
180HL_25175.11
181HL_68733.11LSU Yeast Hairpin Loop
182HL_66467.11
183HL_99207.11Tetrahymena LSU hairpin poorly modeled
184HL_17537.11
185HL_59225.11
186HL_55202.11U2B"-U2A" binding hairpin loop
187HL_38138.11
188HL_33640.11
189HL_28676.11
190HL_57217.11cHS platform Intercalation Site
191HL_39422.11
192HL_84289.11
193HL_27397.11
194HL_44390.11
195HL_67000.11
196HL_62970.11
197HL_76679.11
198HL_90102.11Kink-turn-like Hairpin Loop
199HL_97784.11
200HL_85018.11
201HL_99584.11
202HL_29196.11
203HL_30128.11
204HL_48480.11
205HL_20806.11
206HL_52540.11
207HL_05113.11
208HL_34440.11
209HL_56809.11
210HL_93263.11
211HL_62880.11
212HL_04194.11
213HL_93530.11
214HL_19452.11tRNA D-loop
215HL_08203.11
216HL_38898.11
217HL_59610.11
218HL_56775.11
219HL_77692.11tRNA D-loop
220HL_93567.11
221HL_99779.11
222HL_19226.11
223HL_95049.11Two base, cross-stacked hairpin loop
224HL_42969.11
225HL_79902.11
226HL_30731.11
227HL_07915.11
228HL_95716.11
229HL_82243.11
230HL_10116.11Kink-turn-like Hairpin Loop
231HL_98233.11
232HL_30008.11
233HL_17008.11Nova-2 KH3 domain binding hairpin
234HL_57923.11
235HL_78507.11
236HL_45358.11Double hairpin loop based on GGA triple
237HL_84888.11T-loop like but without tWH UA
238HL_57843.11
239HL_68579.11
240HL_27819.11
241HL_00090.11
242HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
243HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
244HL_78228.11
245HL_97971.11
246HL_69403.11GNRA-like
247HL_46570.11
248HL_73465.11
249HL_42345.11

Updated motif groups

#Motif idInstancesDescription
1HL_67042.11231GNRA Hairpin motifs
2HL_75759.411
3HL_15603.29U1A protein-binding Hairpin Loop.
4HL_06643.36tRNA D-loop. Sec tRNA

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription