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

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_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_46175.21016S helix 23 and 24 hairpin loops
14HL_56824.210LSU Helix 60A. LSU Helix 63A.
15HL_68081.310LSU Helix 20 Hairpin loop
16HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
17HL_80459.39
18HL_15603.29U1A protein-binding Hairpin Loop.
19HL_82294.38SSU Helix 37 (h37) Hairpin loop.
20HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
21HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
22HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
23HL_34027.285S Loop C - Upper part of Hairpin Loop.
24HL_42677.27
25HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
26HL_41833.26LSU Helix 81 (H81) Hairpin Loop
27HL_75579.26
28HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
29HL_06643.36tRNA D-loop. Sec tRNA
30HL_18156.26LSU Helix 72 (H72) Hairpin Loop
31HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
32HL_46489.26LSU H89 Hairpin Loop
33HL_70420.26LSU Helix 97 Hairpin loop
34HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
35HL_39942.26LSU Helix 91 (H91) Hairpin Loop
36HL_87136.26LSU Helix 39A Hairpin loop
37HL_57514.26Two base, cross-stacked hairpin loop
38HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
39HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
40HL_45018.35Hairpin-Hairpin Interacting HL
41HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
42HL_88311.25LSU Helix 35 (H35) Hairpin Loop
43HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
44HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
45HL_82538.15LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
46HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
47HL_72273.15tRNA D-loop
48HL_47784.24SSU Central Pseudoknot (forms helix 2)
49HL_11376.14LSU Helix 8 (H8) Hairpin Loop
50HL_98523.24GNRA-like. Closed by tSH UC.
51HL_25124.24tSW GA closed tetraloops
52HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
53HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
54HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
55HL_64543.24SSU Helix 31 (h31) Hairpin Loop
56HL_86115.14
57HL_29831.14GNRA-like with bulged base.
58HL_62881.14RNase P Structured Hairpin Loop
59HL_19221.23
60HL_42077.23LSU Helix 28 (H28) Hairpin Loop
61HL_58083.23
62HL_78361.13
63HL_23182.13
64HL_27429.33
65HL_68697.23
66HL_35619.23
67HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
68HL_76036.33LSU Helix 8 (H8) Hairpin Loop
69HL_98833.33
70HL_06997.23
71HL_13707.23cSH AA Platform containing Hairpin Loop
72HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
73HL_08382.23
74HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
75HL_76766.43
76HL_90579.33LSU Helix 69 (H69) Hairpin Loop
77HL_41827.13
78HL_74686.13SSU Central Pseudoknot (forms helix 2)
79HL_80492.23tRNA D-loop
80HL_16770.12
81HL_21675.32LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
82HL_60200.12
83HL_65924.12
84HL_87554.12
85HL_91693.12
86HL_05361.12
87HL_23129.12
88HL_24711.12
89HL_32644.22LSU Helix 69 (H69) Hairpin Loop
90HL_50312.12
91HL_63941.12
92HL_91872.12
93HL_06122.12
94HL_19399.12
95HL_42094.12
96HL_64371.22
97HL_98577.12
98HL_17790.12UNCG-like. cWW Closing pair.
99HL_96915.12
100HL_19528.12
101HL_23290.12
102HL_33451.12
103HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
104HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
105HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
106HL_18587.12
107HL_42553.12
108HL_65249.12
109HL_74505.12
110HL_86398.12
111HL_90542.12
112HL_93771.12tRNA T-loop distorted by RS binding
113HL_99633.12
114HL_24473.32tRNA D-loop
115HL_26495.12
116HL_49210.12
117HL_62967.12
118HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
119HL_74559.12Two base, cross-stacked hairpin loop
120HL_84353.12
121HL_94578.12
122HL_21545.12LSU Helix 96 (H96) Hairpin Loop
123HL_38130.22
124HL_54751.22
125HL_04194.11
126HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
127HL_24707.11
128HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
129HL_38138.11
130HL_44390.11
131HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
132HL_55202.11U2B"-U2A" binding hairpin loop
133HL_57843.11
134HL_63304.11
135HL_68435.11
136HL_78228.11
137HL_82243.11
138HL_84888.11T-loop like but without tWH UA
139HL_95049.11Two base, cross-stacked hairpin loop
140HL_97971.11
141HL_17537.11
142HL_19226.11
143HL_27397.11
144HL_34440.11
145HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
146HL_44522.11
147HL_55272.11
148HL_60203.11
149HL_68579.11
150HL_82288.11
151HL_85018.11
152HL_95716.11
153HL_33277.11
154HL_35200.11
155HL_39422.11
156HL_52116.11
157HL_58223.11
158HL_66467.11
159HL_73465.11
160HL_75850.11
161HL_78420.11
162HL_93263.11
163HL_19452.11tRNA D-loop
164HL_23195.11
165HL_25175.11
166HL_28676.11
167HL_39486.11
168HL_42345.11
169HL_45411.11
170HL_52540.11
171HL_56775.11
172HL_58601.11
173HL_66877.11cSH GU/cWS double platform, intercalation site
174HL_68733.11LSU Yeast Hairpin Loop
175HL_73972.11
176HL_78507.11
177HL_88960.11
178HL_93530.11
179HL_00090.11
180HL_12706.11
181HL_25195.11
182HL_29196.11
183HL_35865.11
184HL_48480.11
185HL_56809.11
186HL_59182.11
187HL_62880.11
188HL_65071.11
189HL_69403.11GNRA-like
190HL_76585.11
191HL_83865.11
192HL_90102.11Kink-turn-like Hairpin Loop
193HL_93567.11
194HL_96994.11
195HL_99207.11Tetrahymena LSU hairpin poorly modeled
196HL_01418.11
197HL_07915.11
198HL_24108.11
199HL_25197.11
200HL_33640.11
201HL_36842.11
202HL_53015.11
203HL_59225.11
204HL_67000.11
205HL_76679.11
206HL_79902.11
207HL_84289.11
208HL_13786.11
209HL_20806.11
210HL_30008.11
211HL_37962.11
212HL_46570.11
213HL_53789.11
214HL_57217.11cHS platform Intercalation Site
215HL_59604.11
216HL_67761.11
217HL_70912.11
218HL_97499.11
219HL_03785.11LSU Helix 8 (H8) Hairpin Loop
220HL_10116.11Kink-turn-like Hairpin Loop
221HL_19132.11
222HL_26579.11
223HL_30128.11
224HL_42969.11
225HL_47337.11
226HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
227HL_59610.11
228HL_62970.11
229HL_65802.11
230HL_77692.11tRNA D-loop
231HL_84768.11
232HL_87223.11
233HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
234HL_97784.11

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