Changes in PDB files used for clustering

Release 1.4 has 211 PDB files, release 1.5 has 212 PDB files, 209 of them are identical.

1 equivalence classes changed representatives: 2XZM4BPP.

2 new structures in release 1.5: 4L8R, 4LCK.

Obsolete: 2XZM4V5O, 4HXH4L8R.

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 1.4 has 256 motif groups, release 1.5 has 249 motif groups, 193 of them are identical.

27 motif groups were updated, 36 groups are present only in release 1.4, 29 groups are only in release 1.5.

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_91226.317Kissing Hairpin motif
2HL_74465.212tRNA Anti-Codon loop
3HL_56824.210LSU Helix 60A. LSU Helix 63A.
4HL_17723.310LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
5HL_68081.310LSU Helix 20 Hairpin loop
6HL_87844.29LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
7HL_11547.28LSU Helix 80 (H80) P-site Hairpin Loop.
8HL_15603.18U1A protein-binding Hairpin Loop.
9HL_34027.285S Loop C - Upper part of Hairpin Loop.
10HL_42677.16
11HL_18156.26LSU Helix 72 (H72) Hairpin Loop
12HL_41833.26LSU Helix 81 (H81) Hairpin Loop
13HL_11509.26LSU Helix 6 (H6) Hairpin Loop.
14HL_34108.26LSU Helix 37 (H37) Hairpin Loop.
15HL_87136.26LSU Helix 39A Hairpin loop
16HL_46489.26LSU H89 Hairpin Loop
17HL_39942.26LSU Helix 91 (H91) Hairpin Loop
18HL_75579.26
19HL_70420.26LSU Helix 97 Hairpin loop
20HL_01926.36LSU Helix 71 (H71) Hairpin Loop.
21HL_39872.26LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
22HL_72543.25LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
23HL_45018.35Hairpin-Hairpin Interacting HL
24HL_88311.25LSU Helix 35 (H35) Hairpin Loop
25HL_66174.15cHS GU/cWS Double Platform creates Intercalation site
26HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
27HL_72273.15tRNA D-loop
28HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
29HL_06643.25tRNA D-loop. Sec tRNA
30HL_48116.24GNRA-like with 5'-stacking of first unpaired base.
31HL_29831.14GNRA-like with bulged base.
32HL_62881.14RNase P Structured Hairpin Loop
33HL_23182.13
34HL_58083.23
35HL_27429.33
36HL_08382.23
37HL_41827.13
38HL_19221.23
39HL_32644.13LSU Helix 69 (H69) Hairpin Loop
40HL_25124.13tSW GA closed tetraloops
41HL_74686.13SSU Central Pseudoknot (forms helix 2)
42HL_80492.23tRNA D-loop
43HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
44HL_76036.33LSU Helix 8 (H8) Hairpin Loop
45HL_90579.23
46HL_78361.13
47HL_13707.23cSH AA Platform containing Hairpin Loop
48HL_42077.23LSU Helix 28 (H28) Hairpin Loop
49HL_05361.12
50HL_03791.12
51HL_65924.12
52HL_06312.12
53HL_98577.12
54HL_60200.12
55HL_81752.12
56HL_49210.12
57HL_50312.12
58HL_24711.12
59HL_23290.12
60HL_26495.12
61HL_42553.12
62HL_62967.12
63HL_06122.12
64HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
65HL_24473.32tRNA D-loop
66HL_33451.12
67HL_19399.12
68HL_64371.22
69HL_84353.12
70HL_99633.12
71HL_96915.12
72HL_16770.12
73HL_38130.22
74HL_94578.12
75HL_87554.12
76HL_53753.12
77HL_75575.12
78HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
79HL_38138.11
80HL_93567.11
81HL_37962.11
82HL_95049.11Two base, cross-stacked hairpin loop
83HL_84888.11T-loop like but without tWH UA
84HL_57843.11
85HL_44390.11
86HL_55272.11
87HL_25175.11
88HL_95716.11
89HL_82243.11
90HL_17537.11
91HL_24108.11
92HL_55202.11U2B"-U2A" binding hairpin loop
93HL_77692.11tRNA D-loop
94HL_35865.11
95HL_07315.11
96HL_25195.11
97HL_57217.11cHS platform Intercalation Site
98HL_68435.11
99HL_19132.11
100HL_56809.11
101HL_00090.11
102HL_53015.11
103HL_97971.11
104HL_69403.11GNRA-like
105HL_85018.11
106HL_59182.11
107HL_56775.11
108HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
109HL_53789.11
110HL_20806.11
111HL_58223.11
112HL_58601.11
113HL_88960.11
114HL_07915.11
115HL_67761.11
116HL_04194.11
117HL_78228.11
118HL_35200.11
119HL_82288.11
120HL_19452.11tRNA D-loop
121HL_65802.11
122HL_19226.11
123HL_26579.11
124HL_66877.11cSH GU/cWS double platform, intercalation site
125HL_27819.11
126HL_13786.11
127HL_75850.11
128HL_39486.11
129HL_36842.11
130HL_73465.11
131HL_33640.11
132HL_78507.11
133HL_44522.11
134HL_27397.11
135HL_12706.11
136HL_62970.11
137HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
138HL_33277.11
139HL_99207.11Tetrahymena LSU hairpin poorly modeled
140HL_01418.11
141HL_24707.11
142HL_48480.11
143HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
144HL_60203.11
145HL_39422.11
146HL_84289.11
147HL_34440.11
148HL_70912.11
149HL_62880.11
150HL_66467.11
151HL_97784.11
152HL_30008.11
153HL_59610.11
154HL_25197.11
155HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
156HL_87223.11
157HL_68579.11
158HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
159HL_47337.11
160HL_68733.11LSU Yeast Hairpin Loop
161HL_93530.11
162HL_10116.11Kink-turn-like Hairpin Loop
163HL_42345.11
164HL_30128.11
165HL_45411.11
166HL_59604.11
167HL_97499.11
168HL_65071.11
169HL_42969.11
170HL_79902.11
171HL_67000.11
172HL_63304.11
173HL_78420.11
174HL_90102.11Kink-turn-like Hairpin Loop
175HL_71607.11
176HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
177HL_96994.11

Updated motif groups

#Motif idInstancesDescription
1HL_67042.8226GNRA Hairpin motifs
2HL_72498.964T-loops with two bulged bases
3HL_39895.635UNCG Hairpin motifs
4HL_18781.320Double sheared (tSH) with U-turn
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_46175.21016S helix 23 and 24 hairpin loops
10HL_75759.310LSU: Part of IL/3WJ between H55 and H56. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
11HL_80459.39
12HL_82294.38SSU Helix 37 (h37) Hairpin loop.
13HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
14HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
15HL_57514.26Two base, cross-stacked hairpin loop
16HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
17HL_47784.24SSU Central Pseudoknot (forms helix 2)
18HL_64543.24SSU Helix 31 (h31) Hairpin Loop
19HL_98523.24GNRA-like. Closed by tSH UC.
20HL_12595.23
21HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
22HL_68697.23
23HL_76766.23
24HL_42687.33
25HL_61547.43
26HL_98833.22
27HL_54751.22

Removed motif groups

#Motif idInstancesDescription
1HL_28436.39LSU Helix 96 (H96) Hairpin Loop
2HL_12811.25LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
3HL_77235.34LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
4HL_18798.14UNCG-like. cWW Closing pair.
5HL_46794.23
6HL_82253.23
7HL_26057.12
8HL_67367.12
9HL_67692.12
10HL_57014.12
11HL_77555.12
12HL_97512.12LSU Helix 8 (H8) Hairpin Loop
13HL_57904.12
14HL_58687.12
15HL_45440.12
16HL_66900.11
17HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
18HL_52109.11
19HL_85753.11
20HL_12984.11
21HL_29084.11
22HL_52393.11Double tSH (double sheared) with bulged base
23HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
24HL_13105.11
25HL_31969.11
26HL_55543.11
27HL_96192.11
28HL_16118.11
29HL_33524.11tRNA T-loop distorted by RS binding
30HL_17468.11
31HL_34375.11
32HL_80746.11
33HL_35004.11
34HL_81295.11UNCG-like. cWW Closing pair.
35HL_20914.11
36HL_63690.11

Added motif groups

#Motif idInstancesDescription
1HL_27271.110LSU Helix 96 (H96) Hairpin Loop
2HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
3HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
4HL_11376.14LSU Helix 8 (H8) Hairpin Loop
5HL_23971.14LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
6HL_21675.13LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
7HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
8HL_90542.12
9HL_23129.12
10HL_91693.12
11HL_06997.12
12HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
13HL_91872.12
14HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
15HL_17790.12UNCG-like. cWW Closing pair.
16HL_26143.12
17HL_93771.12tRNA T-loop distorted by RS binding
18HL_18587.12
19HL_74559.12Two base, cross-stacked hairpin loop
20HL_19528.12
21HL_21545.12LSU Helix 96 (H96) Hairpin Loop
22HL_86398.12
23HL_52540.11
24HL_03785.11LSU Helix 8 (H8) Hairpin Loop
25HL_23195.11
26HL_93633.11
27HL_73972.11
28HL_83865.11
29HL_46570.11