Changes in PDB files used for clustering

Release 1.12 has 231 PDB files, release 1.13 has 231 PDB files, 230 of them are identical.

1 equivalence classes changed representatives: 3SD34LVZ.

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

Loading the Sankey diagram...

Changes in motif groups

Release 1.12 has 253 motif groups, release 1.13 has 253 motif groups, 251 of them are identical.

1 motif groups were updated, 1 groups are present only in release 1.12, 1 groups are only in release 1.13.

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_75759.411
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_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
17HL_15603.29U1A protein-binding Hairpin Loop.
18HL_80459.39
19HL_82294.38SSU Helix 37 (h37) Hairpin loop.
20HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
21HL_34027.285S Loop C - Upper part of Hairpin Loop.
22HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
23HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
24HL_42677.27
25HL_46489.26LSU H89 Hairpin Loop
26HL_39942.26LSU Helix 91 (H91) Hairpin Loop
27HL_06643.36tRNA D-loop. Sec tRNA
28HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
29HL_70420.26LSU Helix 97 Hairpin loop
30HL_57514.26Two base, cross-stacked hairpin loop
31HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
32HL_18156.26LSU Helix 72 (H72) Hairpin Loop
33HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
34HL_75579.26
35HL_87136.26LSU Helix 39A Hairpin loop
36HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
37HL_41833.26LSU Helix 81 (H81) Hairpin 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_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
42HL_88311.25LSU Helix 35 (H35) Hairpin Loop
43HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
44HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
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_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
49HL_11376.14LSU Helix 8 (H8) Hairpin Loop
50HL_98523.24GNRA-like. Closed by tSH UC.
51HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
52HL_47784.24SSU Central Pseudoknot (forms helix 2)
53HL_64543.24SSU Helix 31 (h31) Hairpin Loop
54HL_86115.14
55HL_62881.14RNase P Structured Hairpin Loop
56HL_29831.14GNRA-like with bulged base.
57HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
58HL_25124.24tSW GA closed tetraloops
59HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
60HL_35619.23
61HL_76766.43
62HL_68697.23
63HL_13707.23cSH AA Platform containing Hairpin Loop
64HL_78361.13
65HL_90579.33LSU Helix 69 (H69) Hairpin Loop
66HL_19221.23
67HL_41827.13
68HL_98833.33
69HL_76036.33LSU Helix 8 (H8) Hairpin Loop
70HL_58083.23
71HL_74686.13SSU Central Pseudoknot (forms helix 2)
72HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
73HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
74HL_08382.23
75HL_42077.23LSU Helix 28 (H28) Hairpin Loop
76HL_23182.13
77HL_80492.23tRNA D-loop
78HL_27429.33
79HL_06997.23
80HL_42553.12
81HL_64371.22
82HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
83HL_60200.12
84HL_24711.12
85HL_49210.12
86HL_33451.12
87HL_50312.12
88HL_74559.12Two base, cross-stacked hairpin loop
89HL_90542.12
90HL_63941.12
91HL_54751.22
92HL_91693.12
93HL_21675.32LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
94HL_23290.12
95HL_94578.12
96HL_32644.22LSU Helix 69 (H69) Hairpin Loop
97HL_44467.12
98HL_18587.12
99HL_62967.12
100HL_74505.12
101HL_24473.32tRNA D-loop
102HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
103HL_19399.12
104HL_93771.12tRNA T-loop distorted by RS binding
105HL_42094.12
106HL_99633.12
107HL_06122.12
108HL_65924.12
109HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
110HL_17790.12UNCG-like. cWW Closing pair.
111HL_05361.12
112HL_98577.12
113HL_21545.12LSU Helix 96 (H96) Hairpin Loop
114HL_84353.12
115HL_38130.22
116HL_26495.12
117HL_87554.12
118HL_86398.12
119HL_96915.12
120HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
121HL_16770.12
122HL_65249.12
123HL_19528.12
124HL_23129.12
125HL_91872.12
126HL_38898.11
127HL_59610.11
128HL_56775.11
129HL_28676.11
130HL_57217.11cHS platform Intercalation Site
131HL_39422.11
132HL_66880.11
133HL_67000.11
134HL_62970.11
135HL_76679.11
136HL_90102.11Kink-turn-like Hairpin Loop
137HL_97784.11
138HL_85018.11
139HL_99584.11
140HL_29196.11
141HL_17008.11Nova-2 KH3 domain binding hairpin
142HL_77692.11tRNA D-loop
143HL_30128.11
144HL_48480.11
145HL_20806.11
146HL_52540.11
147HL_84289.11
148HL_27397.11
149HL_44390.11
150HL_93263.11
151HL_62880.11
152HL_04194.11
153HL_93530.11
154HL_19452.11tRNA D-loop
155HL_08203.11
156HL_93567.11
157HL_99779.11
158HL_19226.11
159HL_95049.11Two base, cross-stacked hairpin loop
160HL_05113.11
161HL_34440.11
162HL_56809.11
163HL_95716.11
164HL_82243.11
165HL_10116.11Kink-turn-like Hairpin Loop
166HL_98233.11
167HL_30008.11
168HL_52116.11
169HL_57923.11
170HL_78507.11
171HL_45358.11Double hairpin loop based on GGA triple
172HL_42969.11
173HL_79902.11
174HL_30731.11
175HL_07915.11
176HL_00090.11
177HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
178HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
179HL_78228.11
180HL_97971.11
181HL_69403.11GNRA-like
182HL_46570.11
183HL_73465.11
184HL_42345.11
185HL_73972.11
186HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
187HL_45411.11
188HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
189HL_60203.11
190HL_68435.11
191HL_84888.11T-loop like but without tWH UA
192HL_57843.11
193HL_68579.11
194HL_12706.11
195HL_67761.11
196HL_63304.11
197HL_75850.11
198HL_35200.11
199HL_82288.11
200HL_83865.11
201HL_79038.11LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
202HL_96994.11
203HL_84768.11
204HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
205HL_53789.11
206HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
207HL_76585.11
208HL_87223.11
209HL_58223.11
210HL_19132.11
211HL_70912.11
212HL_13786.11
213HL_55272.11
214HL_47337.11
215HL_39486.11
216HL_36842.11
217HL_23195.11
218HL_01418.11
219HL_24108.11
220HL_55202.11U2B"-U2A" binding hairpin loop
221HL_38138.11
222HL_24707.11
223HL_25195.11
224HL_59604.11
225HL_97499.11
226HL_00721.11
227HL_26579.11
228HL_58601.11
229HL_88960.11
230HL_91613.11
231HL_53015.11
232HL_78420.11
233HL_33277.11
234HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
235HL_20028.11
236HL_59182.11
237HL_33640.11
238HL_65802.11
239HL_35865.11
240HL_25197.11
241HL_37962.11
242HL_65071.11
243HL_44522.11
244HL_66877.11cSH GU/cWS double platform, intercalation site
245HL_03785.11LSU Helix 8 (H8) Hairpin Loop
246HL_25175.11
247HL_68733.11LSU Yeast Hairpin Loop
248HL_66467.11
249HL_99207.11Tetrahymena LSU hairpin poorly modeled
250HL_17537.11
251HL_59225.11

Updated motif groups

#Motif idInstancesDescription
1HL_67042.12231GNRA Hairpin motifs

Removed motif groups

#Motif idInstancesDescription
1HL_27819.11

Added motif groups

#Motif idInstancesDescription
1HL_20920.11