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_49036.312GNRA with one bulged base
9HL_27271.212LSU Helix 96 (H96) Hairpin Loop
10HL_48039.211MS2 virus RNA Hairpin
11HL_75759.411
12HL_46175.21016S helix 23 and 24 hairpin loops
13HL_56824.210LSU Helix 60A. LSU Helix 63A.
14HL_68081.310LSU Helix 20 Hairpin loop
15HL_17723.410LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
16HL_80459.39
17HL_15603.29U1A protein-binding Hairpin Loop.
18HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
19HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
20HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
21HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
22HL_34027.285S Loop C - Upper part of Hairpin Loop.
23HL_82294.38SSU Helix 37 (h37) Hairpin loop.
24HL_42677.27
25HL_06643.36tRNA D-loop. Sec tRNA
26HL_18156.26LSU Helix 72 (H72) Hairpin Loop
27HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
28HL_46489.26LSU H89 Hairpin Loop
29HL_70420.26LSU Helix 97 Hairpin loop
30HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
31HL_39942.26LSU Helix 91 (H91) Hairpin Loop
32HL_87136.26LSU Helix 39A Hairpin loop
33HL_57514.26Two base, cross-stacked hairpin loop
34HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
35HL_41833.26LSU Helix 81 (H81) Hairpin Loop
36HL_75579.26
37HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
38HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
39HL_82538.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
40HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
41HL_72273.15tRNA D-loop
42HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
43HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
44HL_45018.35Hairpin-Hairpin Interacting HL
45HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
46HL_88311.25LSU Helix 35 (H35) Hairpin Loop
47HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
48HL_64543.24SSU Helix 31 (h31) Hairpin Loop
49HL_86115.14
50HL_29831.14GNRA-like with bulged base.
51HL_62881.14RNase P Structured Hairpin Loop
52HL_47784.24SSU Central Pseudoknot (forms helix 2)
53HL_11376.14LSU Helix 8 (H8) Hairpin Loop
54HL_98523.24GNRA-like. Closed by tSH UC.
55HL_25124.24tSW GA closed tetraloops
56HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
57HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
58HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
59HL_35619.23
60HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
61HL_76036.33LSU Helix 8 (H8) Hairpin Loop
62HL_98833.33
63HL_06997.23
64HL_13707.23cSH AA Platform containing Hairpin Loop
65HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
66HL_08382.23
67HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
68HL_76766.43
69HL_90579.33LSU Helix 69 (H69) Hairpin Loop
70HL_41827.13
71HL_74686.13SSU Central Pseudoknot (forms helix 2)
72HL_80492.23tRNA D-loop
73HL_19221.23
74HL_42077.23LSU Helix 28 (H28) Hairpin Loop
75HL_58083.23
76HL_78361.13
77HL_23182.13
78HL_27429.33
79HL_68697.23
80HL_17790.12UNCG-like. cWW Closing pair.
81HL_96915.12
82HL_19528.12
83HL_23290.12
84HL_33451.12
85HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
86HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
87HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
88HL_18587.12
89HL_42553.12
90HL_65249.12
91HL_74505.12
92HL_86398.12
93HL_90542.12
94HL_93771.12tRNA T-loop distorted by RS binding
95HL_99633.12
96HL_24473.32tRNA D-loop
97HL_26495.12
98HL_49210.12
99HL_62967.12
100HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
101HL_74559.12Two base, cross-stacked hairpin loop
102HL_84353.12
103HL_94578.12
104HL_21545.12LSU Helix 96 (H96) Hairpin Loop
105HL_38130.22
106HL_54751.22
107HL_16770.12
108HL_21675.32LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
109HL_60200.12
110HL_65924.12
111HL_87554.12
112HL_91693.12
113HL_05361.12
114HL_23129.12
115HL_24711.12
116HL_32644.22LSU Helix 69 (H69) Hairpin Loop
117HL_50312.12
118HL_63941.12
119HL_91872.12
120HL_06122.12
121HL_19399.12
122HL_42094.12
123HL_64371.22
124HL_98577.12
125HL_19452.11tRNA D-loop
126HL_23195.11
127HL_25175.11
128HL_28676.11
129HL_39486.11
130HL_42345.11
131HL_45411.11
132HL_52540.11
133HL_56775.11
134HL_58601.11
135HL_66877.11cSH GU/cWS double platform, intercalation site
136HL_68733.11LSU Yeast Hairpin Loop
137HL_73972.11
138HL_78507.11
139HL_88960.11
140HL_93530.11
141HL_00090.11
142HL_12706.11
143HL_25195.11
144HL_29196.11
145HL_35865.11
146HL_48480.11
147HL_56809.11
148HL_59182.11
149HL_62880.11
150HL_65071.11
151HL_69403.11GNRA-like
152HL_76585.11
153HL_83865.11
154HL_90102.11Kink-turn-like Hairpin Loop
155HL_93567.11
156HL_96994.11
157HL_99207.11Tetrahymena LSU hairpin poorly modeled
158HL_01418.11
159HL_07915.11
160HL_24108.11
161HL_25197.11
162HL_33640.11
163HL_36842.11
164HL_53015.11
165HL_59225.11
166HL_67000.11
167HL_76679.11
168HL_79902.11
169HL_84289.11
170HL_13786.11
171HL_20806.11
172HL_30008.11
173HL_37962.11
174HL_46570.11
175HL_53789.11
176HL_57217.11cHS platform Intercalation Site
177HL_59604.11
178HL_67761.11
179HL_70912.11
180HL_97499.11
181HL_03785.11LSU Helix 8 (H8) Hairpin Loop
182HL_10116.11Kink-turn-like Hairpin Loop
183HL_19132.11
184HL_26579.11
185HL_30128.11
186HL_42969.11
187HL_47337.11
188HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
189HL_59610.11
190HL_62970.11
191HL_65802.11
192HL_77692.11tRNA D-loop
193HL_84768.11
194HL_87223.11
195HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
196HL_97784.11
197HL_04194.11
198HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
199HL_24707.11
200HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
201HL_38138.11
202HL_44390.11
203HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
204HL_55202.11U2B"-U2A" binding hairpin loop
205HL_57843.11
206HL_63304.11
207HL_68435.11
208HL_78228.11
209HL_82243.11
210HL_84888.11T-loop like but without tWH UA
211HL_95049.11Two base, cross-stacked hairpin loop
212HL_97971.11
213HL_17537.11
214HL_19226.11
215HL_27397.11
216HL_34440.11
217HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
218HL_44522.11
219HL_55272.11
220HL_60203.11
221HL_68579.11
222HL_82288.11
223HL_85018.11
224HL_95716.11
225HL_33277.11
226HL_35200.11
227HL_39422.11
228HL_52116.11
229HL_58223.11
230HL_66467.11
231HL_73465.11
232HL_75850.11
233HL_78420.11
234HL_93263.11

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