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_15603.29U1A protein-binding Hairpin Loop.
5HL_39872.69LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
6HL_82538.57LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
7HL_42677.27
8HL_06643.36tRNA D-loop. Sec tRNA
9HL_20199.16SSU Central Pseudoknot (forms helix 2) | LSU Helix 69 (H69) Hairpin Loop | LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
10HL_72543.36LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
11HL_64543.46SSU Helix 31 (h31) Hairpin Loop
12HL_72273.15tRNA D-loop
13HL_08382.45
14HL_95720.15Double tSH (double sheared) with bulged base | LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
15HL_18587.34
16HL_66677.24
17HL_92706.14LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
18HL_62881.14RNase P Structured Hairpin Loop
19HL_79956.24GNRA-like with 5'-stacking of first unpaired base.
20HL_72846.14LSU Helix 69 (H69) Hairpin Loop
21HL_11376.14LSU Helix 8 (H8) Hairpin Loop
22HL_82418.24LSU Helix 8 (H8) Hairpin Loop
23HL_25124.24tSW GA closed tetraloops
24HL_19905.44LSU: Part of IL/3WJ between H55 and H56.
25HL_48116.34GNRA-like with 5'-stacking of first unpaired base.
26HL_61547.54LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
27HL_28339.23
28HL_76766.43
29HL_95969.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
30HL_41827.13
31HL_19221.23
32HL_42094.23
33HL_59516.13cHS GU/cWS Double Platform creates Intercalation site
34HL_80492.23tRNA D-loop
35HL_21419.23UNCG-like. cWW Closing pair. | UNCG-like. cWW Closing pair. | LSU: Part of IL/3WJ between H55 and H56.
36HL_78361.13
37HL_21545.23LSU Helix 96 (H96) Hairpin Loop
38HL_60200.23
39HL_65249.23
40HL_74307.13
41HL_84911.13
42HL_91142.13Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
43HL_27429.53
44HL_98833.33
45HL_06122.23
46HL_55684.13
47HL_58083.33
48HL_91693.23
49HL_01389.12
50HL_20004.12
51HL_41700.12
52HL_84172.12
53HL_86123.22SSU Helix 42 (h42) Hairpin Loop. T-loop like.
54HL_01766.12LSU Helix 35 (H35) Hairpin Loop from Yeast
55HL_26495.12
56HL_49210.12
57HL_77391.12
58HL_42077.32LSU Helix 28 (H28) Hairpin Loop
59HL_87554.12
60HL_24473.32tRNA D-loop
61HL_38130.22
62HL_54719.12Two base, cross-stacked hairpin loop
63HL_57263.12
64HL_64438.12Kink-turn-like Hairpin Loop
65HL_33451.12
66HL_46388.12
67HL_50312.12
68HL_15793.12UNCG-like. cWW Closing pair.
69HL_19399.12
70HL_24711.12
71HL_42436.12Kissing Hairpin from di-GMP-II riboswitch
72HL_50937.12
73HL_93771.12tRNA T-loop distorted by RS binding
74HL_98577.12
75HL_05361.12
76HL_34912.12
77HL_42553.12
78HL_51271.12
79HL_70383.12GNRA-like
80HL_27478.12
81HL_35652.12LSU Helix 84 (H84) Hairpin Loop. E.coli.
82HL_65924.12
83HL_14384.11
84HL_22461.11
85HL_25195.11
86HL_35865.11
87HL_44390.11
88HL_48480.11
89HL_52540.11
90HL_56775.11
91HL_58223.11
92HL_62564.11LSU Helix 28 (H28) Hairpin Loop | LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
93HL_79038.11LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
94HL_99207.11Tetrahymena LSU hairpin poorly modeled
95HL_08203.11
96HL_14524.11
97HL_19074.11
98HL_20028.11
99HL_22533.11
100HL_28776.11
101HL_36151.11SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
102HL_45411.11
103HL_53015.11
104HL_56809.11
105HL_59182.11
106HL_66877.11cSH GU/cWS double platform, intercalation site
107HL_72389.11
108HL_79902.11
109HL_84289.11
110HL_87223.11
111HL_93263.11
112HL_96515.11LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
113HL_99584.11
114HL_03785.11LSU Helix 8 (H8) Hairpin Loop
115HL_14536.11
116HL_19132.11
117HL_24108.11
118HL_26579.11
119HL_30008.11
120HL_37962.11
121HL_45740.11
122HL_49492.11Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
123HL_53789.11
124HL_57217.11cHS platform Intercalation Site
125HL_59225.11
126HL_63997.11
127HL_67000.11
128HL_77692.11tRNA D-loop
129HL_84720.11
130HL_93428.11
131HL_96994.11
132HL_99612.11
133HL_04305.11
134HL_10075.11
135HL_15291.11GNRA with one bulged base
136HL_20806.11
137HL_27236.11
138HL_30366.11LSU Helix 10 (H10) Hairpin E.coli
139HL_46055.11
140HL_50018.11
141HL_67761.11
142HL_78228.11
143HL_84768.11
144HL_88960.11
145HL_93530.11
146HL_97022.11
147HL_99779.11
148HL_04979.11LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
149HL_10116.11Kink-turn-like Hairpin Loop
150HL_19363.11
151HL_24707.11
152HL_38138.11
153HL_42345.11
154HL_55202.11U2B"-U2A" binding hairpin loop
155HL_57339.11
156HL_59610.11
157HL_68435.11
158HL_73972.11
159HL_82288.11
160HL_84888.11T-loop like but without tWH UA
161HL_89473.11
162HL_93567.11
163HL_97784.11
164HL_99932.11
165HL_05113.11
166HL_27397.11
167HL_33640.11
168HL_39422.11
169HL_46570.11
170HL_55272.11
171HL_57644.11
172HL_68579.11
173HL_78389.11
174HL_12706.11
175HL_17537.11
176HL_19452.11tRNA D-loop
177HL_21695.11UNCG-like. cWW Closing pair.
178HL_39846.11
179HL_47337.11
180HL_55450.11
181HL_57667.11
182HL_60203.11
183HL_65802.11
184HL_74451.11
185HL_78422.11SSU Central Pseudoknot (forms helix 2)
186HL_85018.11
187HL_95049.11Two base, cross-stacked hairpin loop
188HL_13786.11
189HL_21839.11
190HL_25175.11
191HL_52116.11
192HL_70912.11
193HL_75624.11
194HL_78507.11
195HL_83865.11
196HL_85044.11LSU Helix 10 (H10) Hairpin E.coli
197HL_98834.11

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_48039.412MS2 virus RNA Hairpin
15HL_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
16HL_34027.7115S Loop C - Upper part of Hairpin Loop.
17HL_80459.811
18HL_01926.811LSU Helix 71 (H71) Hairpin Loop.
19HL_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.
20HL_24544.611LSU Helix 53 (H53) Hairpin Loop. T-loop like.
21HL_46489.710LSU H89 Hairpin Loop
22HL_34108.710LSU Helix 37 (H37) Hairpin Loop.
23HL_70420.710LSU Helix 97 Hairpin loop
24HL_41833.710LSU Helix 81 (H81) Hairpin Loop
25HL_87136.710LSU Helix 39A Hairpin loop
26HL_18156.710LSU Helix 72 (H72) Hairpin Loop
27HL_75579.710
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_00311.27SSU Central Pseudoknot (forms helix 2)
33HL_66174.47cHS GU/cWS Double Platform creates Intercalation site
34HL_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
35HL_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.
36HL_99908.57LSU Helix 69 (H69) Hairpin Loop
37HL_45018.57Hairpin-Hairpin Interacting HL
38HL_62228.77LSU Helix 35A (H35A) Hairpin Loop
39HL_48254.56LSU Helix 84 (H84) Hairpin Loop.
40HL_12908.26LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
41HL_94364.25
42HL_39203.25
43HL_96915.45
44HL_86077.45GNRA with one bulged base | GNRA-like with bulged base.
45HL_43357.35SSU Central Pseudoknot (forms helix 2)
46HL_86115.35
47HL_89131.24
48HL_19033.24SSU Helix 43 (h43) Hairpin Loop E.coli | 16S helix 23 and 24 hairpin loops
49HL_13707.34cSH AA Platform containing Hairpin Loop
50HL_31147.24SSU Central Pseudoknot (forms helix 2)
51HL_01788.33LSU Yeast Hairpin Loop
52HL_23290.23
53HL_94578.32
54HL_64371.52SSU Central Pseudoknot (forms helix 2)

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_00415.15GNRA-like. Closed by tSH UC.
4HL_55035.15SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
5HL_72372.15
6HL_34954.14
7HL_23182.24
8HL_28422.24
9HL_18474.13LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
10HL_06997.23
11HL_15701.13
12HL_29892.12
13HL_49961.12
14HL_74026.12
15HL_92260.12
16HL_94212.1216S helix 23 and 24 hairpin loops
17HL_69907.12
18HL_82382.12
19HL_72489.12
20HL_84548.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
21HL_63001.11
22HL_87172.11
23HL_95822.11
24HL_04584.11
25HL_19673.11
26HL_50078.11
27HL_63323.11
28HL_75984.11
29HL_05350.11
30HL_50954.11
31HL_63642.11
32HL_76004.11
33HL_23628.11
34HL_38897.11S8 operon binding Hairpin Loop. T-loop like with purine stacking.
35HL_65107.11
36HL_79541.1116S helix 23 and 24 hairpin loops
37HL_92594.11
38HL_08388.11
39HL_24422.11
40HL_39035.11
41HL_58052.11
42HL_65428.11
43HL_81994.11
44HL_11337.11
45HL_25197.11
46HL_39943.11
47HL_61871.11
48HL_94639.11
49HL_25947.11
50HL_40070.11
51HL_62500.11
52HL_83263.11
53HL_94813.11
54HL_16822.11
55HL_40731.11
56HL_62880.11
57HL_94981.11

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_01475.14
5HL_57963.14GNRA-like. Closed by tSH UC.
6HL_90792.14
7HL_13352.14
8HL_85551.14
9HL_19066.14SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
10HL_57225.13
11HL_82098.1316S helix 23 and 24 hairpin loops
12HL_00394.12
13HL_72388.12LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
14HL_22952.12
15HL_43821.12
16HL_57621.12
17HL_23337.12
18HL_45343.12
19HL_05894.12
20HL_08494.12LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. | LSU Helix 80 (H80) P-site Hairpin Loop.
21HL_52338.12
22HL_84575.12
23HL_91125.12
24HL_53279.12
25HL_96309.12S8 operon binding Hairpin Loop. T-loop like with purine stacking.
26HL_19755.11
27HL_42161.11
28HL_87958.11
29HL_88259.11LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
30HL_03007.11
31HL_81815.11
32HL_89958.11LSU Helix 71 (H71) Hairpin Loop. | Double tSH (double sheared) with bulged base
33HL_04735.11
34HL_31261.11
35HL_45777.11
36HL_61400.11
37HL_33822.11
38HL_49013.11
39HL_64778.11
40HL_84030.11
41HL_36554.11
42HL_64859.11
43HL_38777.11
44HL_70061.11
45HL_91581.11
46HL_40222.11
47HL_56596.11
48HL_85802.11