Changes in PDB files used for clustering

Release 1.17 has 258 PDB files, release 1.18 has 263 PDB files, 254 of them are identical.

2 equivalence classes changed representatives: 4TUX4TV0, 4LCK4TZZ.

7 new structures in release 1.18: 4PDB, 4QJD, 4QJH, 4R0D, 4TZX, 4W21, 4W23.

Obsolete: 1VWW4W1Z, 1VX24W28.

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 1.17 has 323 motif groups, release 1.18 has 316 motif groups, 212 of them are identical.

54 motif groups were updated, 57 groups are present only in release 1.17, 50 groups are only in release 1.18.

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_91226.723Kissing Hairpin motif
2HL_27271.415LSU Helix 96 (H96) Hairpin Loop
3HL_17723.610LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
4HL_39872.69LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
5HL_15603.29U1A protein-binding Hairpin Loop.
6HL_82538.57LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
7HL_42677.27
8HL_06643.36tRNA D-loop. Sec tRNA
9HL_72543.36LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
10HL_20199.16SSU Central Pseudoknot (forms helix 2) | LSU Helix 69 (H69) Hairpin Loop | LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
11HL_64543.46SSU Helix 31 (h31) Hairpin Loop
12HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
13HL_72273.15tRNA D-loop
14HL_08382.45
15HL_25124.24tSW GA closed tetraloops
16HL_19905.44LSU: Part of IL/3WJ between H55 and H56.
17HL_48116.34GNRA-like with 5'-stacking of first unpaired base.
18HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
19HL_92706.14LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
20HL_18587.34
21HL_66677.24
22HL_62881.14RNase P Structured Hairpin Loop
23HL_79956.24GNRA-like with 5'-stacking of first unpaired base.
24HL_72846.14LSU Helix 69 (H69) Hairpin Loop
25HL_82418.24LSU Helix 8 (H8) Hairpin Loop
26HL_11376.14LSU Helix 8 (H8) Hairpin Loop
27HL_98833.33
28HL_27429.53
29HL_91693.23
30HL_06122.23
31HL_55684.13
32HL_58083.33
33HL_76766.43
34HL_95969.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
35HL_28339.23
36HL_41827.13
37HL_80492.23tRNA D-loop
38HL_19221.23
39HL_42094.23
40HL_59516.13cHS GU/cWS Double Platform creates Intercalation site
41HL_78361.13
42HL_21419.23UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
43HL_74307.13
44HL_84911.13
45HL_91142.13Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
46HL_21545.23LSU Helix 96 (H96) Hairpin Loop
47HL_60200.23
48HL_65249.23
49HL_70383.12GNRA-like
50HL_05361.12
51HL_34912.12
52HL_42553.12
53HL_51271.12
54HL_27478.12
55HL_35652.12LSU Helix 84 (H84) Hairpin Loop. E.coli.
56HL_65924.12
57HL_84172.12
58HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
59HL_01389.12
60HL_20004.12
61HL_41700.12
62HL_77391.12
63HL_01766.12LSU Helix 35 (H35) Hairpin Loop from Yeast
64HL_26495.12
65HL_49210.12
66HL_87554.12
67HL_42077.32LSU Helix 28 (H28) Hairpin Loop
68HL_24473.32tRNA D-loop
69HL_38130.22
70HL_54719.12Two base, cross-stacked hairpin loop
71HL_57263.12
72HL_64438.12Kink-turn-like Hairpin Loop
73HL_33451.12
74HL_46388.12
75HL_50312.12
76HL_93771.12tRNA T-loop distorted by RS binding
77HL_98577.12
78HL_15793.12UNCG-like. cWW Closing pair.
79HL_19399.12
80HL_24711.12
81HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
82HL_50937.12
83HL_74451.11
84HL_78422.11SSU Central Pseudoknot (forms helix 2)
85HL_85018.11
86HL_95049.11Two base, cross-stacked hairpin loop
87HL_12706.11
88HL_17537.11
89HL_19452.11tRNA D-loop
90HL_21695.11UNCG-like. cWW Closing pair.
91HL_39846.11
92HL_47337.11
93HL_55450.11
94HL_57667.11
95HL_60203.11
96HL_65802.11
97HL_70912.11
98HL_75624.11
99HL_78507.11
100HL_83865.11
101HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
102HL_98834.11
103HL_13786.11
104HL_21839.11
105HL_25175.11
106HL_52116.11
107HL_79038.11LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
108HL_99207.11Tetrahymena LSU hairpin poorly modeled
109HL_14384.11
110HL_22461.11
111HL_25195.11
112HL_35865.11
113HL_44390.11
114HL_48480.11
115HL_52540.11
116HL_56775.11
117HL_58223.11
118HL_62564.11LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
119HL_72389.11
120HL_79902.11
121HL_84289.11
122HL_87223.11
123HL_93263.11
124HL_96515.11LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
125HL_99584.11
126HL_08203.11
127HL_14524.11
128HL_19074.11
129HL_20028.11
130HL_22533.11
131HL_28776.11
132HL_36151.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
133HL_45411.11
134HL_53015.11
135HL_56809.11
136HL_59182.11
137HL_66877.11cSH GU/cWS double platform, intercalation site
138HL_77692.11tRNA D-loop
139HL_84720.11
140HL_93428.11
141HL_96994.11
142HL_99612.11
143HL_03785.11LSU Helix 8 (H8) Hairpin Loop
144HL_14536.11
145HL_19132.11
146HL_24108.11
147HL_26579.11
148HL_30008.11
149HL_37962.11
150HL_45740.11
151HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
152HL_53789.11
153HL_57217.11cHS platform Intercalation Site
154HL_59225.11
155HL_63997.11
156HL_67000.11
157HL_78228.11
158HL_84768.11
159HL_88960.11
160HL_93530.11
161HL_97022.11
162HL_99779.11
163HL_04305.11
164HL_10075.11
165HL_15291.11GNRA with one bulged base
166HL_20806.11
167HL_27236.11
168HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
169HL_46055.11
170HL_50018.11
171HL_67761.11
172HL_73972.11
173HL_82288.11
174HL_84888.11T-loop like but without tWH UA
175HL_89473.11
176HL_93567.11
177HL_97784.11
178HL_99932.11
179HL_04979.11LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
180HL_10116.11Kink-turn-like Hairpin Loop
181HL_19363.11
182HL_24707.11
183HL_38138.11
184HL_42345.11
185HL_55202.11U2B"-U2A" binding hairpin loop
186HL_57339.11
187HL_59610.11
188HL_68435.11
189HL_78389.11
190HL_05113.11
191HL_27397.11
192HL_33640.11
193HL_39422.11
194HL_46570.11
195HL_55272.11
196HL_57644.11
197HL_68579.11

Updated motif groups

#Motif idInstancesDescription
1HL_67042.17328GNRA Hairpin motifs
2HL_72498.1778T-loops with two bulged bases
3HL_39895.1146UNCG Hairpin motifs
4HL_18781.930Double sheared (tSH) with U-turn
5HL_97270.821T-loops with 1 bulged base
6HL_74411.318GNRA with one bulged base | GNRA-like with bulged base. | GNRA with one bulged base | GNRA Hairpin motifs | LSU Helix 11 (H11) Hairpin Loop. GNRA-like. | GNRA with one bulged base
7HL_74465.718tRNA Anti-Codon loop
8HL_46175.617SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops | 16S helix 23 and 24 hairpin loops
9HL_75759.916
10HL_33402.815LSU Helix 13 (H13) Hairpin loop. GNRA-like.
11HL_56824.714LSU Helix 60A. LSU Helix 63A.
12HL_68081.813LSU Helix 20 Hairpin loop
13HL_82294.613SSU Helix 37 (h37) Hairpin loop.
14HL_48507.312LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like. | GNRA with one bulged base
15HL_48039.412MS2 virus RNA Hairpin
16HL_11547.711LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop. | LSU Helix 80 (H80) P-site Hairpin Loop.
17HL_24544.611LSU Helix 53 (H53) Hairpin Loop. T-loop like.
18HL_34027.7115S Loop C - Upper part of Hairpin Loop.
19HL_80459.811
20HL_01926.811LSU Helix 71 (H71) Hairpin Loop.
21HL_70420.710LSU Helix 97 Hairpin loop
22HL_41833.710LSU Helix 81 (H81) Hairpin Loop
23HL_87136.710LSU Helix 39A Hairpin loop
24HL_18156.710LSU Helix 72 (H72) Hairpin Loop
25HL_75579.710
26HL_46489.710LSU H89 Hairpin Loop
27HL_34108.710LSU Helix 37 (H37) Hairpin Loop.
28HL_85534.69LSU Helix 65 (H65) Hairpin Loop. T-loop like.
29HL_11509.78LSU Helix 6 (H6) Hairpin Loop.
30HL_57087.28Two base, cross-stacked hairpin loop
31HL_88311.78LSU Helix 35 (H35) Hairpin Loop
32HL_27353.27UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
33HL_99908.57LSU Helix 69 (H69) Hairpin Loop
34HL_45018.57Hairpin-Hairpin Interacting HL
35HL_62228.77LSU Helix 35A (H35A) Hairpin Loop
36HL_00311.27SSU Central Pseudoknot (forms helix 2)
37HL_66174.47cHS GU/cWS Double Platform creates Intercalation site
38HL_19626.47LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
39HL_12908.26LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
40HL_48254.56LSU Helix 84 (H84) Hairpin Loop.
41HL_96915.45
42HL_86077.45GNRA with one bulged base | GNRA-like with bulged base.
43HL_43357.35SSU Central Pseudoknot (forms helix 2)
44HL_86115.35
45HL_94364.25
46HL_39203.25
47HL_13707.34cSH AA Platform containing Hairpin Loop
48HL_31147.24SSU Central Pseudoknot (forms helix 2)
49HL_89131.24
50HL_19033.24SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
51HL_23290.23
52HL_01788.33LSU Yeast Hairpin Loop
53HL_64371.52SSU Central Pseudoknot (forms helix 2)
54HL_94578.32

Removed motif groups

#Motif idInstancesDescription
1HL_37020.220LSU Helix 91 (H91) Hairpin Loop | LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like. | LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop.
2HL_89482.210LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop.
3HL_72372.15
4HL_00415.15GNRA-like. Closed by tSH UC.
5HL_55035.15SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
6HL_28422.24
7HL_34954.14
8HL_23182.24
9HL_15701.13
10HL_18474.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
11HL_06997.23
12HL_69907.12
13HL_82382.12
14HL_72489.12
15HL_84548.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
16HL_29892.12
17HL_49961.12
18HL_74026.12
19HL_92260.12
20HL_94212.1216S helix 23 and 24 hairpin loops
21HL_11337.11
22HL_25197.11
23HL_39943.11
24HL_61871.11
25HL_94639.11
26HL_25947.11
27HL_40070.11
28HL_62500.11
29HL_83263.11
30HL_94813.11
31HL_16822.11
32HL_40731.11
33HL_62880.11
34HL_94981.11
35HL_63001.11
36HL_87172.11
37HL_95822.11
38HL_04584.11
39HL_19673.11
40HL_50078.11
41HL_63323.11
42HL_75984.11
43HL_05350.11
44HL_50954.11
45HL_63642.11
46HL_76004.11
47HL_23628.11
48HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
49HL_65107.11
50HL_79541.1116S helix 23 and 24 hairpin loops
51HL_92594.11
52HL_08388.11
53HL_24422.11
54HL_39035.11
55HL_58052.11
56HL_65428.11
57HL_81994.11

Added motif groups

#Motif idInstancesDescription
1HL_71179.120LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop. | LSU Helix 91 (H91) Hairpin Loop | LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like. | LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop.
2HL_90506.19LSU Helix 91 (H91) Hairpin Loop | LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like. | LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop.
3HL_80263.15
4HL_90792.14
5HL_13352.14
6HL_85551.14
7HL_19066.14SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
8HL_01475.14
9HL_57963.14GNRA-like. Closed by tSH UC.
10HL_82098.1316S helix 23 and 24 hairpin loops
11HL_57225.13
12HL_05894.12
13HL_08494.12LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop.
14HL_52338.12
15HL_84575.12
16HL_91125.12
17HL_53279.12
18HL_96309.12S8 operon binding Hairpin Loop. T-loop like with purine stacking.
19HL_00394.12
20HL_72388.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
21HL_22952.12
22HL_43821.12
23HL_57621.12
24HL_23337.12
25HL_45343.12
26HL_04735.11
27HL_31261.11
28HL_45777.11
29HL_61400.11
30HL_33822.11
31HL_49013.11
32HL_64778.11
33HL_84030.11
34HL_36554.11
35HL_64859.11
36HL_38777.11
37HL_70061.11
38HL_91581.11
39HL_40222.11
40HL_56596.11
41HL_85802.11
42HL_19755.11
43HL_42161.11
44HL_87958.11
45HL_88259.11LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
46HL_03007.11
47HL_81815.11
48HL_89958.11LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base