Changes in PDB files used for clustering

Release 1.10 has 224 PDB files, release 1.11 has 224 PDB files, 224 of them are identical.

No equivalence class representatives have been replaced.

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

0 motif groups were updated, 0 groups are present only in release 1.10, 0 groups are only in release 1.11.

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_67042.10229GNRA Hairpin motifs
2HL_72498.1266T-loops with two bulged bases
3HL_39895.635UNCG Hairpin motifs
4HL_18781.420Double sheared (tSH) with U-turn
5HL_91226.317Kissing Hairpin motif
6HL_97270.315T-loops with 1 bulged base
7HL_52574.314LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base.
8HL_74465.513tRNA Anti-Codon loop
9HL_49036.312GNRA with one bulged base
10HL_27271.212LSU Helix 96 (H96) Hairpin Loop
11HL_48039.211MS2 virus RNA Hairpin
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_75759.310LSU: Part of IL/3WJ between H55 and H56. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
17HL_80459.39
18HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
19HL_15603.18U1A protein-binding Hairpin Loop.
20HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
21HL_34027.285S Loop C - Upper part of Hairpin Loop.
22HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
23HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
24HL_82294.38SSU Helix 37 (h37) Hairpin loop.
25HL_42677.27
26HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
27HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
28HL_46489.26LSU H89 Hairpin Loop
29HL_39942.26LSU Helix 91 (H91) Hairpin Loop
30HL_70420.26LSU Helix 97 Hairpin loop
31HL_57514.26Two base, cross-stacked hairpin loop
32HL_87136.26LSU Helix 39A Hairpin loop
33HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
34HL_41833.26LSU Helix 81 (H81) Hairpin Loop
35HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
36HL_75579.26
37HL_18156.26LSU Helix 72 (H72) Hairpin Loop
38HL_82538.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
39HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
40HL_72273.15tRNA D-loop
41HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
42HL_06643.25tRNA D-loop. Sec tRNA
43HL_45018.35Hairpin-Hairpin Interacting HL
44HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
45HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
46HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
47HL_88311.25LSU Helix 35 (H35) Hairpin Loop
48HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
49HL_86115.14
50HL_29831.14GNRA-like with bulged base.
51HL_62881.14RNase P Structured Hairpin Loop
52HL_11376.14LSU Helix 8 (H8) Hairpin Loop
53HL_47784.24SSU Central Pseudoknot (forms helix 2)
54HL_25124.24tSW GA closed tetraloops
55HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
56HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
57HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
58HL_98523.24GNRA-like. Closed by tSH UC.
59HL_64543.24SSU Helix 31 (h31) Hairpin Loop
60HL_13707.23cSH AA Platform containing Hairpin Loop
61HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
62HL_76036.33LSU Helix 8 (H8) Hairpin Loop
63HL_98833.33
64HL_08382.23
65HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
66HL_19221.23
67HL_41827.13
68HL_76766.43
69HL_90579.33LSU Helix 69 (H69) Hairpin Loop
70HL_74686.13SSU Central Pseudoknot (forms helix 2)
71HL_80492.23tRNA D-loop
72HL_23182.13
73HL_27429.33
74HL_42077.23LSU Helix 28 (H28) Hairpin Loop
75HL_58083.23
76HL_78361.13
77HL_06997.23
78HL_35619.23
79HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
80HL_68697.23
81HL_18587.12
82HL_33451.12
83HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
84HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
85HL_96915.12
86HL_24473.32tRNA D-loop
87HL_26495.12
88HL_42553.12
89HL_65249.12
90HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
91HL_21545.12LSU Helix 96 (H96) Hairpin Loop
92HL_49210.12
93HL_62967.12
94HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
95HL_74505.12
96HL_86398.12
97HL_90542.12
98HL_93771.12tRNA T-loop distorted by RS binding
99HL_99633.12
100HL_16770.12
101HL_21675.32LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
102HL_38130.22
103HL_54751.22
104HL_74559.12Two base, cross-stacked hairpin loop
105HL_84353.12
106HL_94578.12
107HL_05361.12
108HL_23129.12
109HL_24711.12
110HL_60200.12
111HL_65924.12
112HL_06122.12
113HL_19399.12
114HL_32644.22LSU Helix 69 (H69) Hairpin Loop
115HL_50312.12
116HL_63941.12
117HL_87554.12
118HL_91693.12
119HL_17790.12UNCG-like. cWW Closing pair.
120HL_42094.12
121HL_64371.22
122HL_91872.12
123HL_19528.12
124HL_23290.12
125HL_98577.12
126HL_01418.11
127HL_07915.11
128HL_24108.11
129HL_25197.11
130HL_29196.11
131HL_35865.11
132HL_48480.11
133HL_56809.11
134HL_59182.11
135HL_62880.11
136HL_65071.11
137HL_68733.11LSU Yeast Hairpin Loop
138HL_73972.11
139HL_78507.11
140HL_88960.11
141HL_93530.11
142HL_13786.11
143HL_20806.11
144HL_33640.11
145HL_36842.11
146HL_53015.11
147HL_59225.11
148HL_67000.11
149HL_69403.11GNRA-like
150HL_76585.11
151HL_83865.11
152HL_90102.11Kink-turn-like Hairpin Loop
153HL_93567.11
154HL_96994.11
155HL_99207.11Tetrahymena LSU hairpin poorly modeled
156HL_03785.11LSU Helix 8 (H8) Hairpin Loop
157HL_10116.11Kink-turn-like Hairpin Loop
158HL_19132.11
159HL_26579.11
160HL_30008.11
161HL_37962.11
162HL_46570.11
163HL_53789.11
164HL_57217.11cHS platform Intercalation Site
165HL_59604.11
166HL_76679.11
167HL_79902.11
168HL_84289.11
169HL_04194.11
170HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
171HL_24707.11
172HL_30128.11
173HL_42969.11
174HL_47337.11
175HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
176HL_59610.11
177HL_62970.11
178HL_65802.11
179HL_67761.11
180HL_70912.11
181HL_97499.11
182HL_17537.11
183HL_19226.11
184HL_27397.11
185HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
186HL_38138.11
187HL_44390.11
188HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
189HL_55202.11U2B"-U2A" binding hairpin loop
190HL_57843.11
191HL_63304.11
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_34440.11
198HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
199HL_44522.11
200HL_55272.11
201HL_60203.11
202HL_68435.11
203HL_78228.11
204HL_82243.11
205HL_84888.11T-loop like but without tWH UA
206HL_95049.11Two base, cross-stacked hairpin loop
207HL_97971.11
208HL_19452.11tRNA D-loop
209HL_23195.11
210HL_25175.11
211HL_27819.11
212HL_33277.11
213HL_35200.11
214HL_39422.11
215HL_52116.11
216HL_58223.11
217HL_66467.11
218HL_68579.11
219HL_82288.11
220HL_85018.11
221HL_95716.11
222HL_00090.11
223HL_12706.11
224HL_25195.11
225HL_28676.11
226HL_39486.11
227HL_42345.11
228HL_45411.11
229HL_52540.11
230HL_56775.11
231HL_58601.11
232HL_66877.11cSH GU/cWS double platform, intercalation site
233HL_73465.11
234HL_75850.11
235HL_78420.11
236HL_93263.11

Updated motif groups

#Motif idInstancesDescription

Removed motif groups

#Motif idInstancesDescription

Added motif groups

#Motif idInstancesDescription