1.17 | 1.18

Changes in PDB files used for clustering

Release 1.17 has 257 PDB files, release 1.18 has 262 PDB files, 253 of them are identical.

2 equivalence classes changed representatives: 4TUX → 4TV0, 4LCK → 4TZZ.

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

Obsolete: 1VWW → 4W1Z, 1VX2 → 4W28.

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 id	Instances	Description
1	HL_91226.7	23	Kissing Hairpin motif
2	HL_27271.4	15	LSU Helix 96 (H96) Hairpin Loop
3	HL_17723.6	10	LSU Helix 22 (H22) Hairpin Loop. Forms Pseudknot.
4	HL_15603.2	9	U1A protein-binding Hairpin Loop.
5	HL_39872.6	9	LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
6	HL_82538.5	7	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
7	HL_42677.2	7
8	HL_72543.3	6	LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
9	HL_20199.1	6	SSU Central Pseudoknot (forms helix 2) \| LSU Helix 69 (H69) Hairpin Loop \| LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
10	HL_06643.3	6	tRNA D-loop. Sec tRNA
11	HL_64543.4	6	SSU Helix 31 (h31) Hairpin Loop
12	HL_08382.4	5
13	HL_95720.1	5	Double tSH (double sheared) with bulged base \| LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
14	HL_72273.1	5	tRNA D-loop
15	HL_18587.3	4
16	HL_72846.1	4	LSU Helix 69 (H69) Hairpin Loop
17	HL_82418.2	4	LSU Helix 8 (H8) Hairpin Loop
18	HL_25124.2	4	tSW GA closed tetraloops
19	HL_92706.1	4	LSU Helix 28 (H28) Hairpin Loop \| LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
20	HL_48116.3	4	GNRA-like with 5'-stacking of first unpaired base.
21	HL_61547.5	4	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
22	HL_11376.1	4	LSU Helix 8 (H8) Hairpin Loop
23	HL_66677.2	4
24	HL_62881.1	4	RNase P Structured Hairpin Loop
25	HL_79956.2	4	GNRA-like with 5'-stacking of first unpaired base.
26	HL_19905.4	4	LSU: Part of IL/3WJ between H55 and H56.
27	HL_80492.2	3	tRNA D-loop
28	HL_06122.2	3
29	HL_42094.2	3
30	HL_59516.1	3	cHS GU/cWS Double Platform creates Intercalation site
31	HL_91142.1	3	Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
32	HL_78361.1	3
33	HL_84911.1	3
34	HL_98833.3	3
35	HL_21419.2	3	UNCG-like. cWW Closing pair. \| UNCG-like. cWW Closing pair. \| LSU: Part of IL/3WJ between H55 and H56.
36	HL_60200.2	3
37	HL_65249.2	3
38	HL_74307.1	3
39	HL_91693.2	3
40	HL_19221.2	3
41	HL_21545.2	3	LSU Helix 96 (H96) Hairpin Loop
42	HL_27429.5	3
43	HL_95969.1	3	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
44	HL_55684.1	3
45	HL_58083.3	3
46	HL_28339.2	3
47	HL_76766.4	3
48	HL_41827.1	3
49	HL_20004.1	2
50	HL_42077.3	2	LSU Helix 28 (H28) Hairpin Loop
51	HL_24473.3	2	tRNA D-loop
52	HL_38130.2	2
53	HL_54719.1	2	Two base, cross-stacked hairpin loop
54	HL_57263.1	2
55	HL_64438.1	2	Kink-turn-like Hairpin Loop
56	HL_93771.1	2	tRNA T-loop distorted by RS binding
57	HL_98577.1	2
58	HL_33451.1	2
59	HL_46388.1	2
60	HL_50312.1	2
61	HL_01389.1	2
62	HL_24711.1	2
63	HL_42436.1	2	Kissing Hairpin from di-GMP-II riboswitch
64	HL_50937.1	2
65	HL_01766.1	2	LSU Helix 35 (H35) Hairpin Loop from Yeast
66	HL_34912.1	2
67	HL_42553.1	2
68	HL_51271.1	2
69	HL_70383.1	2	GNRA-like
70	HL_86123.2	2	SSU Helix 42 (h42) Hairpin Loop. T-loop like.
71	HL_27478.1	2
72	HL_35652.1	2	LSU Helix 84 (H84) Hairpin Loop. E.coli.
73	HL_65924.1	2
74	HL_84172.1	2
75	HL_15793.1	2	UNCG-like. cWW Closing pair.
76	HL_19399.1	2
77	HL_41700.1	2
78	HL_87554.1	2
79	HL_26495.1	2
80	HL_49210.1	2
81	HL_77391.1	2
82	HL_05361.1	2
83	HL_24108.1	1
84	HL_26579.1	1
85	HL_30008.1	1
86	HL_37962.1	1
87	HL_45740.1	1
88	HL_49492.1	1	Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
89	HL_53789.1	1
90	HL_57217.1	1	cHS platform Intercalation Site
91	HL_59225.1	1
92	HL_63997.1	1
93	HL_67000.1	1
94	HL_77692.1	1	tRNA D-loop
95	HL_84768.1	1
96	HL_89473.1	1
97	HL_93567.1	1
98	HL_97784.1	1
99	HL_14384.1	1
100	HL_27236.1	1
101	HL_30366.1	1	LSU Helix 10 (H10) Hairpin E.coli
102	HL_46055.1	1
103	HL_50018.1	1
104	HL_67761.1	1
105	HL_78228.1	1
106	HL_82288.1	1
107	HL_84888.1	1	T-loop like but without tWH UA
108	HL_14524.1	1
109	HL_19074.1	1
110	HL_20806.1	1
111	HL_24707.1	1
112	HL_38138.1	1
113	HL_42345.1	1
114	HL_55202.1	1	U2B"-U2A" binding hairpin loop
115	HL_57339.1	1
116	HL_59610.1	1
117	HL_68435.1	1
118	HL_73972.1	1
119	HL_95049.1	1	Two base, cross-stacked hairpin loop
120	HL_14536.1	1
121	HL_19132.1	1
122	HL_27397.1	1
123	HL_33640.1	1
124	HL_39422.1	1
125	HL_46570.1	1
126	HL_55272.1	1
127	HL_57644.1	1
128	HL_68579.1	1
129	HL_78389.1	1
130	HL_85018.1	1
131	HL_98834.1	1
132	HL_10075.1	1
133	HL_15291.1	1	GNRA with one bulged base
134	HL_39846.1	1
135	HL_47337.1	1
136	HL_55450.1	1
137	HL_57667.1	1
138	HL_60203.1	1
139	HL_65802.1	1
140	HL_74451.1	1
141	HL_78422.1	1	SSU Central Pseudoknot (forms helix 2)
142	HL_83865.1	1
143	HL_99207.1	1	Tetrahymena LSU hairpin poorly modeled
144	HL_03785.1	1	LSU Helix 8 (H8) Hairpin Loop
145	HL_10116.1	1	Kink-turn-like Hairpin Loop
146	HL_19363.1	1
147	HL_21695.1	1	UNCG-like. cWW Closing pair.
148	HL_25175.1	1
149	HL_52116.1	1
150	HL_70912.1	1
151	HL_75624.1	1
152	HL_78507.1	1
153	HL_87223.1	1
154	HL_93263.1	1
155	HL_96515.1	1	LSU Helix 92 (H92) A-site Loop. GNRA-like with extra stacked base. \| LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
156	HL_99612.1	1
157	HL_04305.1	1
158	HL_22461.1	1
159	HL_25195.1	1
160	HL_35865.1	1
161	HL_44390.1	1
162	HL_48480.1	1
163	HL_52540.1	1
164	HL_56775.1	1
165	HL_58223.1	1
166	HL_62564.1	1	LSU Helix 28 (H28) Hairpin Loop \| LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
167	HL_79902.1	1
168	HL_84289.1	1
169	HL_93428.1	1
170	HL_96994.1	1
171	HL_99932.1	1
172	HL_04979.1	1	LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
173	HL_12706.1	1
174	HL_17537.1	1
175	HL_19452.1	1	tRNA D-loop
176	HL_22533.1	1
177	HL_28776.1	1
178	HL_36151.1	1	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
179	HL_45411.1	1
180	HL_53015.1	1
181	HL_56809.1	1
182	HL_59182.1	1
183	HL_66877.1	1	cSH GU/cWS double platform, intercalation site
184	HL_72389.1	1
185	HL_84720.1	1
186	HL_88960.1	1
187	HL_93530.1	1
188	HL_97022.1	1
189	HL_13786.1	1

Updated motif groups

#	Motif id	Instances	Description
1	HL_67042.17	328	GNRA Hairpin motifs
2	HL_72498.17	78	T-loops with two bulged bases
3	HL_39895.11	46	UNCG Hairpin motifs
4	HL_18781.9	30	Double sheared (tSH) with U-turn
5	HL_97270.8	21	T-loops with 1 bulged base
6	HL_74465.7	18	tRNA Anti-Codon loop
7	HL_74411.3	18	GNRA 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
8	HL_46175.6	17	SSU Helix 43 (h43) Hairpin Loop E.coli \| 16S helix 23 and 24 hairpin loops \| 16S helix 23 and 24 hairpin loops
9	HL_75759.9	16
10	HL_33402.8	15	LSU Helix 13 (H13) Hairpin loop. GNRA-like.
11	HL_56824.7	14	LSU Helix 60A. LSU Helix 63A.
12	HL_68081.8	13	LSU Helix 20 Hairpin loop
13	HL_82294.6	13	SSU Helix 37 (h37) Hairpin loop.
14	HL_48039.4	12	MS2 virus RNA Hairpin
15	HL_48507.3	12	LSU 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
16	HL_34027.7	11	5S Loop C - Upper part of Hairpin Loop.
17	HL_80459.8	11
18	HL_01926.8	11	LSU Helix 71 (H71) Hairpin Loop.
19	HL_11547.7	11	LSU 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.
20	HL_24544.6	11	LSU Helix 53 (H53) Hairpin Loop. T-loop like.
21	HL_87136.7	10	LSU Helix 39A Hairpin loop
22	HL_75579.7	10
23	HL_18156.7	10	LSU Helix 72 (H72) Hairpin Loop
24	HL_46489.7	10	LSU H89 Hairpin Loop
25	HL_34108.7	10	LSU Helix 37 (H37) Hairpin Loop.
26	HL_70420.7	10	LSU Helix 97 Hairpin loop
27	HL_41833.7	10	LSU Helix 81 (H81) Hairpin Loop
28	HL_85534.6	9	LSU Helix 65 (H65) Hairpin Loop. T-loop like.
29	HL_88311.7	8	LSU Helix 35 (H35) Hairpin Loop
30	HL_11509.7	8	LSU Helix 6 (H6) Hairpin Loop.
31	HL_57087.2	8	Two base, cross-stacked hairpin loop
32	HL_62228.7	7	LSU Helix 35A (H35A) Hairpin Loop
33	HL_45018.5	7	Hairpin-Hairpin Interacting HL
34	HL_66174.4	7	cHS GU/cWS Double Platform creates Intercalation site
35	HL_00311.2	7	SSU Central Pseudoknot (forms helix 2)
36	HL_19626.4	7	LSU 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
37	HL_99908.5	7	LSU Helix 69 (H69) Hairpin Loop
38	HL_27353.2	7	UNCG-like. cWW Closing pair. \| UNCG-like. cWW Closing pair. \| UNCG-like. cWW Closing pair. \| LSU: Part of IL/3WJ between H55 and H56.
39	HL_48254.5	6	LSU Helix 84 (H84) Hairpin Loop.
40	HL_12908.2	6	LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
41	HL_94364.2	5
42	HL_39203.2	5
43	HL_96915.4	5
44	HL_86077.4	5	GNRA with one bulged base \| GNRA-like with bulged base.
45	HL_86115.3	5
46	HL_43357.3	5	SSU Central Pseudoknot (forms helix 2)
47	HL_13707.3	4	cSH AA Platform containing Hairpin Loop
48	HL_31147.2	4	SSU Central Pseudoknot (forms helix 2)
49	HL_89131.2	4
50	HL_19033.2	4	SSU Helix 43 (h43) Hairpin Loop E.coli \| 16S helix 23 and 24 hairpin loops
51	HL_01788.3	3	LSU Yeast Hairpin Loop
52	HL_23290.2	3
53	HL_64371.5	2	SSU Central Pseudoknot (forms helix 2)
54	HL_94578.3	2

Removed motif groups

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

Added motif groups

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