Changes in PDB files used for clustering

Release 1.4 has 216 PDB files, release 1.5 has 217 PDB files, 214 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_06643.25tRNA D-loop. Sec tRNA
27HL_78731.15LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
28HL_72273.15tRNA D-loop
29HL_85534.15LSU Helix 65 (H65) Hairpin Loop. T-loop like.
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_76036.33LSU Helix 8 (H8) Hairpin Loop
36HL_08382.23
37HL_90579.23
38HL_25124.13tSW GA closed tetraloops
39HL_41827.13
40HL_19221.23
41HL_27429.33
42HL_78361.13
43HL_74686.13SSU Central Pseudoknot (forms helix 2)
44HL_80492.23tRNA D-loop
45HL_32644.13LSU Helix 69 (H69) Hairpin Loop
46HL_48254.13LSU Helix 84 (H84) Hairpin Loop.
47HL_13707.23cSH AA Platform containing Hairpin Loop
48HL_42077.23LSU Helix 28 (H28) Hairpin Loop
49HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
50HL_65924.12
51HL_03791.12
52HL_81752.12
53HL_49210.12
54HL_05361.12
55HL_64371.22
56HL_44467.12
57HL_24711.12
58HL_23290.12
59HL_60200.12
60HL_06122.12
61HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
62HL_24473.32tRNA D-loop
63HL_26495.12
64HL_06312.12
65HL_84353.12
66HL_42553.12
67HL_50312.12
68HL_62967.12
69HL_16770.12
70HL_38130.22
71HL_33451.12
72HL_53753.12
73HL_75575.12
74HL_94578.12
75HL_19399.12
76HL_98577.12
77HL_87554.12
78HL_99633.12
79HL_96915.12
80HL_38898.11
81HL_38138.11
82HL_30128.11
83HL_57923.11
84HL_94697.11LSU Helix 84 (H84) Hairpin Loop. E.coli.
85HL_60203.11
86HL_26579.11
87HL_58601.11
88HL_88960.11
89HL_67000.11
90HL_10378.11Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
91HL_47337.11
92HL_68733.11LSU Yeast Hairpin Loop
93HL_93530.11
94HL_10116.11Kink-turn-like Hairpin Loop
95HL_20028.11
96HL_17008.11Nova-2 KH3 domain binding hairpin
97HL_77692.11tRNA D-loop
98HL_35865.11
99HL_93567.11
100HL_45411.11
101HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
102HL_87223.11
103HL_44522.11
104HL_66877.11cSH GU/cWS double platform, intercalation site
105HL_44390.11
106HL_63304.11
107HL_78420.11
108HL_90102.11Kink-turn-like Hairpin Loop
109HL_71607.11
110HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
111HL_99584.11
112HL_56775.11
113HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
114HL_07315.11
115HL_59604.11
116HL_97499.11
117HL_00721.11
118HL_39422.11
119HL_66880.11
120HL_56809.11
121HL_55272.11
122HL_25175.11
123HL_95716.11
124HL_82243.11
125HL_17537.11
126HL_08203.11
127HL_65802.11
128HL_53789.11
129HL_25195.11
130HL_37962.11
131HL_65071.11
132HL_84289.11
133HL_27397.11
134HL_07915.11
135HL_00090.11
136HL_53015.11
137HL_97971.11
138HL_69403.11GNRA-like
139HL_85018.11
140HL_30008.11
141HL_33640.11
142HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
143HL_57217.11cHS platform Intercalation Site
144HL_95049.11Two base, cross-stacked hairpin loop
145HL_05113.11
146HL_34440.11
147HL_27819.11
148HL_67761.11
149HL_04194.11
150HL_78228.11
151HL_35200.11
152HL_82288.11
153HL_19452.11tRNA D-loop
154HL_42345.11
155HL_20806.11
156HL_45358.11Double hairpin loop based on GGA triple
157HL_42969.11
158HL_79902.11
159HL_30731.11
160HL_12706.11
161HL_13786.11
162HL_75850.11
163HL_39486.11
164HL_36842.11
165HL_98233.11
166HL_96994.11
167HL_59610.11
168HL_24707.11
169HL_48480.11
170HL_19226.11
171HL_68435.11
172HL_84888.11T-loop like but without tWH UA
173HL_57843.11
174HL_68579.11
175HL_70912.11
176HL_62970.11
177HL_50059.11LSU Helix 35 (H35) Hairpin Loop from Yeast
178HL_33277.11
179HL_99207.11Tetrahymena LSU hairpin poorly modeled
180HL_73465.11
181HL_24108.11
182HL_55202.11U2B"-U2A" binding hairpin loop
183HL_25197.11
184HL_99779.11
185HL_78507.11
186HL_58223.11
187HL_19132.11
188HL_91613.11
189HL_62880.11
190HL_66467.11
191HL_97784.11
192HL_01418.11
193HL_59182.11

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_75759.310LSU: Part of IL/3WJ between H55 and H56. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
10HL_46175.21016S helix 23 and 24 hairpin loops
11HL_80459.39
12HL_24544.28LSU Helix 53 (H53) Hairpin Loop. T-loop like.
13HL_33402.38LSU Helix 13 (H13) Hairpin loop. GNRA-like.
14HL_82294.38SSU Helix 37 (h37) Hairpin loop.
15HL_57514.26Two base, cross-stacked hairpin loop
16HL_62228.35LSU Helix 35A (H35A) Hairpin Loop
17HL_98523.24GNRA-like. Closed by tSH UC.
18HL_47784.24SSU Central Pseudoknot (forms helix 2)
19HL_64543.24SSU Helix 31 (h31) Hairpin Loop
20HL_19905.33LSU: Part of IL/3WJ between H55 and H56.
21HL_68697.23
22HL_76766.23
23HL_42687.33
24HL_61547.43
25HL_12595.23
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_82253.23
6HL_46794.23
7HL_67692.12
8HL_57014.12
9HL_77555.12
10HL_97512.12LSU Helix 8 (H8) Hairpin Loop
11HL_57904.12
12HL_58687.12
13HL_45440.12
14HL_26057.12
15HL_67367.12
16HL_12984.11
17HL_29084.11
18HL_52393.11Double tSH (double sheared) with bulged base
19HL_94145.11SSU Helix 43 (h43) Hairpin Loop E.coli
20HL_13105.11
21HL_31969.11
22HL_55543.11
23HL_96192.11
24HL_16118.11
25HL_33524.11tRNA T-loop distorted by RS binding
26HL_17468.11
27HL_34375.11
28HL_80746.11
29HL_35004.11
30HL_81295.11UNCG-like. cWW Closing pair.
31HL_20914.11
32HL_63690.11
33HL_66900.11
34HL_83053.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
35HL_52109.11
36HL_85753.11

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_11376.14LSU Helix 8 (H8) Hairpin Loop
4HL_23971.14LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
5HL_55718.14UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
6HL_33875.13SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
7HL_21675.13LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
8HL_06997.12
9HL_65347.12SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
10HL_91872.12
11HL_66948.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
12HL_17790.12UNCG-like. cWW Closing pair.
13HL_26143.12
14HL_93771.12tRNA T-loop distorted by RS binding
15HL_18587.12
16HL_74559.12Two base, cross-stacked hairpin loop
17HL_19528.12
18HL_21545.12LSU Helix 96 (H96) Hairpin Loop
19HL_86398.12
20HL_90542.12
21HL_23129.12
22HL_91693.12
23HL_23195.11
24HL_93633.11
25HL_73972.11
26HL_83865.11
27HL_46570.11
28HL_52540.11
29HL_03785.11LSU Helix 8 (H8) Hairpin Loop