Changes in PDB files used for clustering

Release 1.12 has 226 PDB files, release 1.13 has 226 PDB files, 225 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

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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_27271.212LSU Helix 96 (H96) Hairpin Loop
9HL_49036.312GNRA with one bulged base
10HL_48039.211MS2 virus RNA Hairpin
11HL_75759.411
12HL_17723.410LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
13HL_68081.310LSU Helix 20 Hairpin loop
14HL_46175.21016S helix 23 and 24 hairpin loops
15HL_56824.210LSU Helix 60A. LSU Helix 63A.
16HL_15603.29U1A protein-binding Hairpin Loop.
17HL_80459.39
18HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
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_01926.36LSU Helix 71 (H71) Hairpin Loop.
26HL_70420.26LSU Helix 97 Hairpin loop
27HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
28HL_18156.26LSU Helix 72 (H72) Hairpin Loop
29HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
30HL_06643.36tRNA D-loop. Sec tRNA
31HL_75579.26
32HL_87136.26LSU Helix 39A Hairpin loop
33HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
34HL_41833.26LSU Helix 81 (H81) Hairpin Loop
35HL_46489.26LSU H89 Hairpin Loop
36HL_57514.26Two base, cross-stacked hairpin loop
37HL_39942.26LSU Helix 91 (H91) Hairpin Loop
38HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
39HL_88311.25LSU Helix 35 (H35) Hairpin Loop
40HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
41HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
42HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
43HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
44HL_72273.15tRNA D-loop
45HL_82538.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
46HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
47HL_45018.35Hairpin-Hairpin Interacting HL
48HL_86115.14
49HL_62881.14RNase P Structured Hairpin Loop
50HL_29831.14GNRA-like with bulged base.
51HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
52HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
53HL_11376.14LSU Helix 8 (H8) Hairpin Loop
54HL_98523.24GNRA-like. Closed by tSH UC.
55HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
56HL_47784.24SSU Central Pseudoknot (forms helix 2)
57HL_64543.24SSU Helix 31 (h31) Hairpin Loop
58HL_25124.24tSW GA closed tetraloops
59HL_13707.23cSH AA Platform containing Hairpin Loop
60HL_19221.23
61HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
62HL_41827.13
63HL_98833.33
64HL_74686.13SSU Central Pseudoknot (forms helix 2)
65HL_27429.33
66HL_76766.43
67HL_78361.13
68HL_58083.23
69HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
70HL_80492.23tRNA D-loop
71HL_68697.23
72HL_08382.23
73HL_42077.23LSU Helix 28 (H28) Hairpin Loop
74HL_23182.13
75HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
76HL_35619.23
77HL_90579.33LSU Helix 69 (H69) Hairpin Loop
78HL_06997.23
79HL_76036.33LSU Helix 8 (H8) Hairpin Loop
80HL_63941.12
81HL_54751.22
82HL_91693.12
83HL_21675.32LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
84HL_23290.12
85HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
86HL_64371.22
87HL_99633.12
88HL_74505.12
89HL_24473.32tRNA D-loop
90HL_42094.12
91HL_05361.12
92HL_93771.12tRNA T-loop distorted by RS binding
93HL_86398.12
94HL_96915.12
95HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
96HL_06122.12
97HL_65924.12
98HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
99HL_17790.12UNCG-like. cWW Closing pair.
100HL_26495.12
101HL_21545.12LSU Helix 96 (H96) Hairpin Loop
102HL_87554.12
103HL_91872.12
104HL_84353.12
105HL_38130.22
106HL_42553.12
107HL_50312.12
108HL_19528.12
109HL_23129.12
110HL_60200.12
111HL_16770.12
112HL_65249.12
113HL_33451.12
114HL_32644.22LSU Helix 69 (H69) Hairpin Loop
115HL_98577.12
116HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
117HL_74559.12Two base, cross-stacked hairpin loop
118HL_90542.12
119HL_19399.12
120HL_18587.12
121HL_62967.12
122HL_24711.12
123HL_49210.12
124HL_94578.12
125HL_45411.11
126HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
127HL_76585.11
128HL_87223.11
129HL_44522.11
130HL_27397.11
131HL_07915.11
132HL_67761.11
133HL_63304.11
134HL_75850.11
135HL_35200.11
136HL_82288.11
137HL_83865.11
138HL_59225.11
139HL_52116.11
140HL_59604.11
141HL_97499.11
142HL_65071.11
143HL_39422.11
144HL_84289.11
145HL_34440.11
146HL_12706.11
147HL_13786.11
148HL_55272.11
149HL_47337.11
150HL_39486.11
151HL_36842.11
152HL_23195.11
153HL_30008.11
154HL_73972.11
155HL_53789.11
156HL_25195.11
157HL_37962.11
158HL_68579.11
159HL_70912.11
160HL_53015.11
161HL_78420.11
162HL_33277.11
163HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
164HL_42345.11
165HL_84768.11
166HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
167HL_24707.11
168HL_28676.11
169HL_57217.11cHS platform Intercalation Site
170HL_52540.11
171HL_42969.11
172HL_79902.11
173HL_03785.11LSU Helix 8 (H8) Hairpin Loop
174HL_25175.11
175HL_68733.11LSU Yeast Hairpin Loop
176HL_66467.11
177HL_99207.11Tetrahymena LSU hairpin poorly modeled
178HL_17537.11
179HL_96994.11
180HL_38138.11
181HL_25197.11
182HL_20806.11
183HL_95049.11Two base, cross-stacked hairpin loop
184HL_84888.11T-loop like but without tWH UA
185HL_57843.11
186HL_62970.11
187HL_76679.11
188HL_90102.11Kink-turn-like Hairpin Loop
189HL_97784.11
190HL_85018.11
191HL_24108.11
192HL_33640.11
193HL_65802.11
194HL_35865.11
195HL_19226.11
196HL_68435.11
197HL_19132.11
198HL_67000.11
199HL_62880.11
200HL_04194.11
201HL_93530.11
202HL_19452.11tRNA D-loop
203HL_59182.11
204HL_55202.11U2B"-U2A" binding hairpin loop
205HL_59610.11
206HL_56775.11
207HL_30128.11
208HL_48480.11
209HL_78507.11
210HL_58223.11
211HL_58601.11
212HL_88960.11
213HL_44390.11
214HL_93263.11
215HL_95716.11
216HL_82243.11
217HL_10116.11Kink-turn-like Hairpin Loop
218HL_73465.11
219HL_77692.11tRNA D-loop
220HL_93567.11
221HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
222HL_60203.11
223HL_26579.11
224HL_66877.11cSH GU/cWS double platform, intercalation site
225HL_56809.11
226HL_00090.11
227HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
228HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
229HL_78228.11
230HL_97971.11
231HL_69403.11GNRA-like
232HL_46570.11
233HL_01418.11
234HL_29196.11

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