Changes in PDB files used for clustering

Release 1.12 has 227 PDB files, release 1.13 has 227 PDB files, 226 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_48039.211MS2 virus RNA Hairpin
11HL_75759.411
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_17723.410LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
16HL_80459.39
17HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
18HL_15603.29U1A protein-binding Hairpin Loop.
19HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
20HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
21HL_82294.38SSU Helix 37 (h37) Hairpin loop.
22HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
23HL_34027.285S Loop C - Upper part of Hairpin Loop.
24HL_42677.27
25HL_75579.26
26HL_87136.26LSU Helix 39A Hairpin loop
27HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
28HL_41833.26LSU Helix 81 (H81) Hairpin Loop
29HL_06643.36tRNA D-loop. Sec tRNA
30HL_46489.26LSU H89 Hairpin Loop
31HL_39942.26LSU Helix 91 (H91) Hairpin Loop
32HL_57514.26Two base, cross-stacked hairpin loop
33HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
34HL_70420.26LSU Helix 97 Hairpin loop
35HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
36HL_18156.26LSU Helix 72 (H72) Hairpin Loop
37HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
38HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
39HL_72273.15tRNA D-loop
40HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
41HL_45018.35Hairpin-Hairpin Interacting HL
42HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
43HL_88311.25LSU Helix 35 (H35) Hairpin Loop
44HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
45HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
46HL_82538.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
47HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
48HL_62881.14RNase P Structured Hairpin Loop
49HL_29831.14GNRA-like with bulged base.
50HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
51HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
52HL_11376.14LSU Helix 8 (H8) Hairpin Loop
53HL_98523.24GNRA-like. Closed by tSH UC.
54HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
55HL_47784.24SSU Central Pseudoknot (forms helix 2)
56HL_64543.24SSU Helix 31 (h31) Hairpin Loop
57HL_86115.14
58HL_25124.24tSW GA closed tetraloops
59HL_58083.23
60HL_74686.13SSU Central Pseudoknot (forms helix 2)
61HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
62HL_27429.33
63HL_76766.43
64HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
65HL_08382.23
66HL_42077.23LSU Helix 28 (H28) Hairpin Loop
67HL_23182.13
68HL_80492.23tRNA D-loop
69HL_78361.13
70HL_06997.23
71HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
72HL_35619.23
73HL_68697.23
74HL_13707.23cSH AA Platform containing Hairpin Loop
75HL_19221.23
76HL_76036.33LSU Helix 8 (H8) Hairpin Loop
77HL_90579.33LSU Helix 69 (H69) Hairpin Loop
78HL_41827.13
79HL_98833.33
80HL_06122.12
81HL_65924.12
82HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
83HL_17790.12UNCG-like. cWW Closing pair.
84HL_64371.22
85HL_99633.12
86HL_84353.12
87HL_38130.22
88HL_26495.12
89HL_16770.12
90HL_65249.12
91HL_42553.12
92HL_86398.12
93HL_96915.12
94HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
95HL_33451.12
96HL_50312.12
97HL_21545.12LSU Helix 96 (H96) Hairpin Loop
98HL_87554.12
99HL_91872.12
100HL_24711.12
101HL_49210.12
102HL_32644.22LSU Helix 69 (H69) Hairpin Loop
103HL_19528.12
104HL_23129.12
105HL_60200.12
106HL_63941.12
107HL_54751.22
108HL_91693.12
109HL_21675.32LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
110HL_23290.12
111HL_94578.12
112HL_19399.12
113HL_98577.12
114HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
115HL_74559.12Two base, cross-stacked hairpin loop
116HL_90542.12
117HL_74505.12
118HL_24473.32tRNA D-loop
119HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
120HL_18587.12
121HL_62967.12
122HL_93771.12tRNA T-loop distorted by RS binding
123HL_42094.12
124HL_05361.12
125HL_84768.11
126HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
127HL_53789.11
128HL_25195.11
129HL_59604.11
130HL_97499.11
131HL_65071.11
132HL_39422.11
133HL_27397.11
134HL_07915.11
135HL_67761.11
136HL_63304.11
137HL_75850.11
138HL_35200.11
139HL_82288.11
140HL_83865.11
141HL_01418.11
142HL_24108.11
143HL_38138.11
144HL_24707.11
145HL_37962.11
146HL_84289.11
147HL_34440.11
148HL_12706.11
149HL_13786.11
150HL_55272.11
151HL_47337.11
152HL_39486.11
153HL_36842.11
154HL_23195.11
155HL_20028.11
156HL_59182.11
157HL_33640.11
158HL_65802.11
159HL_35865.11
160HL_25197.11
161HL_28676.11
162HL_57217.11cHS platform Intercalation Site
163HL_52540.11
164HL_05113.11
165HL_68579.11
166HL_70912.11
167HL_53015.11
168HL_78420.11
169HL_33277.11
170HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
171HL_59225.11
172HL_55202.11U2B"-U2A" binding hairpin loop
173HL_59610.11
174HL_56775.11
175HL_20806.11
176HL_95049.11Two base, cross-stacked hairpin loop
177HL_42969.11
178HL_79902.11
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_99584.11
186HL_29196.11
187HL_77692.11tRNA D-loop
188HL_30128.11
189HL_48480.11
190HL_99779.11
191HL_19226.11
192HL_68435.11
193HL_84888.11T-loop like but without tWH UA
194HL_57843.11
195HL_62970.11
196HL_76679.11
197HL_90102.11Kink-turn-like Hairpin Loop
198HL_97784.11
199HL_85018.11
200HL_08203.11
201HL_93567.11
202HL_78507.11
203HL_58223.11
204HL_19132.11
205HL_67000.11
206HL_62880.11
207HL_04194.11
208HL_93530.11
209HL_19452.11tRNA D-loop
210HL_30008.11
211HL_52116.11
212HL_45411.11
213HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
214HL_60203.11
215HL_26579.11
216HL_58601.11
217HL_88960.11
218HL_44390.11
219HL_93263.11
220HL_95716.11
221HL_82243.11
222HL_10116.11Kink-turn-like Hairpin Loop
223HL_73465.11
224HL_42345.11
225HL_73972.11
226HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
227HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
228HL_76585.11
229HL_87223.11
230HL_44522.11
231HL_66877.11cSH GU/cWS double platform, intercalation site
232HL_56809.11
233HL_00090.11
234HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
235HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
236HL_78228.11
237HL_97971.11
238HL_69403.11GNRA-like
239HL_46570.11
240HL_79038.11LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
241HL_96994.11

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