Changes in PDB files used for clustering

Release 1.7 has 213 PDB files, release 1.8 has 216 PDB files, 213 of them are identical.

No equivalence class representatives have been replaced.

3 new structures in release 1.8: 4L8H, 4MGM, 4MGN.

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 1.7 has 250 motif groups, release 1.8 has 254 motif groups, 232 of them are identical.

10 motif groups were updated, 8 groups are present only in release 1.7, 12 groups are only in release 1.8.

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_67042.9226GNRA Hairpin motifs
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_49036.312GNRA with one bulged base
8HL_48039.211MS2 virus RNA Hairpin
9HL_27271.110LSU Helix 96 (H96) Hairpin Loop
10HL_46175.21016S helix 23 and 24 hairpin loops
11HL_56824.210LSU Helix 60A. LSU Helix 63A.
12HL_68081.310LSU Helix 20 Hairpin loop
13HL_17723.410LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
14HL_75759.310LSU: Part of IL/3WJ between H55 and H56. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
15HL_80459.39
16HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
17HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
18HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
19HL_82294.38SSU Helix 37 (h37) Hairpin loop.
20HL_34027.285S Loop C - Upper part of Hairpin Loop.
21HL_15603.18U1A protein-binding Hairpin Loop.
22HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
23HL_46489.26LSU H89 Hairpin Loop
24HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
25HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
26HL_57514.26Two base, cross-stacked hairpin loop
27HL_18156.26LSU Helix 72 (H72) Hairpin Loop
28HL_39942.26LSU Helix 91 (H91) Hairpin Loop
29HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
30HL_41833.26LSU Helix 81 (H81) Hairpin Loop
31HL_70420.26LSU Helix 97 Hairpin loop
32HL_75579.26
33HL_87136.26LSU Helix 39A Hairpin loop
34HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
35HL_72273.15tRNA D-loop
36HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
37HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
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_06643.25tRNA D-loop. Sec tRNA
42HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
43HL_45018.35Hairpin-Hairpin Interacting HL
44HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
45HL_98523.24GNRA-like. Closed by tSH UC.
46HL_11376.14LSU Helix 8 (H8) Hairpin Loop
47HL_23971.14LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
48HL_47784.24SSU Central Pseudoknot (forms helix 2)
49HL_64543.24SSU Helix 31 (h31) Hairpin Loop
50HL_29831.14GNRA-like with bulged base.
51HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
52HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
53HL_62881.14RNase P Structured Hairpin Loop
54HL_19221.23
55HL_23182.13
56HL_76036.33LSU Helix 8 (H8) Hairpin Loop
57HL_25124.13tSW GA closed tetraloops
58HL_27429.33
59HL_80492.23tRNA D-loop
60HL_68697.23
61HL_58083.23
62HL_61547.43
63HL_78361.13
64HL_13707.23cSH AA Platform containing Hairpin Loop
65HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
66HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
67HL_41827.13
68HL_74686.13SSU Central Pseudoknot (forms helix 2)
69HL_08382.23
70HL_42077.23LSU Helix 28 (H28) Hairpin Loop
71HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
72HL_03791.12
73HL_16770.12
74HL_23129.12
75HL_62967.12
76HL_65924.12
77HL_84353.12
78HL_87554.12
79HL_91872.12
80HL_24711.12
81HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
82HL_98577.12
83HL_05361.12
84HL_19399.12
85HL_42553.12
86HL_49210.12
87HL_54751.22
88HL_60200.12
89HL_96915.12
90HL_06122.12
91HL_17790.12UNCG-like. cWW Closing pair.
92HL_23290.12
93HL_33451.12
94HL_64371.22
95HL_99633.12
96HL_19528.12
97HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
98HL_74559.12Two base, cross-stacked hairpin loop
99HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
100HL_93771.12tRNA T-loop distorted by RS binding
101HL_18587.12
102HL_38130.22
103HL_50312.12
104HL_86398.12
105HL_90542.12
106HL_94578.12
107HL_24473.32tRNA D-loop
108HL_26495.12
109HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
110HL_21545.12LSU Helix 96 (H96) Hairpin Loop
111HL_91693.12
112HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
113HL_24707.11
114HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
115HL_34440.11
116HL_39422.11
117HL_42345.11
118HL_48480.11
119HL_53015.11
120HL_59604.11
121HL_75850.11
122HL_79902.11
123HL_95716.11
124HL_04194.11
125HL_17537.11
126HL_19226.11
127HL_27397.11
128HL_33277.11
129HL_35200.11
130HL_39486.11
131HL_53789.11
132HL_57217.11cHS platform Intercalation Site
133HL_59610.11
134HL_62970.11
135HL_68435.11
136HL_84888.11T-loop like but without tWH UA
137HL_93530.11
138HL_23195.11
139HL_35865.11
140HL_46570.11
141HL_63304.11
142HL_66467.11
143HL_68579.11
144HL_73465.11
145HL_77692.11tRNA D-loop
146HL_85018.11
147HL_93567.11
148HL_99207.11Tetrahymena LSU hairpin poorly modeled
149HL_19452.11tRNA D-loop
150HL_25175.11
151HL_27819.11
152HL_36842.11
153HL_42969.11
154HL_47337.11
155HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
156HL_55202.11U2B"-U2A" binding hairpin loop
157HL_57843.11
158HL_60203.11
159HL_66877.11cSH GU/cWS double platform, intercalation site
160HL_73972.11
161HL_78228.11
162HL_82243.11
163HL_88960.11
164HL_93633.11
165HL_96994.11
166HL_00090.11
167HL_12706.11
168HL_25195.11
169HL_29196.11
170HL_33640.11
171HL_37962.11
172HL_44390.11
173HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
174HL_55272.11
175HL_68733.11LSU Yeast Hairpin Loop
176HL_82288.11
177HL_90102.11Kink-turn-like Hairpin Loop
178HL_01418.11
179HL_07915.11
180HL_24108.11
181HL_25197.11
182HL_44522.11
183HL_58223.11
184HL_65071.11
185HL_67000.11
186HL_69403.11GNRA-like
187HL_78420.11
188HL_97499.11
189HL_13786.11
190HL_20806.11
191HL_30008.11
192HL_38138.11
193HL_52540.11
194HL_56775.11
195HL_58601.11
196HL_62880.11
197HL_78507.11
198HL_83865.11
199HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
200HL_97784.11
201HL_03785.11LSU Helix 8 (H8) Hairpin Loop
202HL_10116.11Kink-turn-like Hairpin Loop
203HL_19132.11
204HL_26579.11
205HL_30128.11
206HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
207HL_45411.11
208HL_56809.11
209HL_59182.11
210HL_65802.11
211HL_67761.11
212HL_70912.11
213HL_84289.11
214HL_87223.11
215HL_95049.11Two base, cross-stacked hairpin loop
216HL_97971.11

Updated motif groups

#Motif idInstancesDescription
1HL_72498.1066T-loops with two bulged bases
2HL_74465.313tRNA Anti-Codon loop
3HL_42677.27
4HL_42687.43
5HL_06997.23
6HL_90579.33LSU Helix 69 (H69) Hairpin Loop
7HL_21675.23LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
8HL_98833.33
9HL_76766.32
10HL_32644.22LSU Helix 69 (H69) Hairpin Loop

Removed motif groups

#Motif idInstancesDescription
1HL_12595.23
2HL_53753.12
3HL_75575.12
4HL_81752.12
5HL_06312.12
6HL_26143.12
7HL_71607.11
8HL_07315.11

Added motif groups

#Motif idInstancesDescription
1HL_35619.13
2HL_63941.12
3HL_65249.12
4HL_74505.12
5HL_42094.12
6HL_59225.11
7HL_28676.11
8HL_76585.11
9HL_76679.11
10HL_84768.11
11HL_52116.11
12HL_98234.11LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking