1.0 | 1.10

Changes in PDB files used for clustering

Release 1.0 has 211 PDB files, release 1.10 has 229 PDB files, 205 of them are identical.

4 equivalence classes changed representatives: 3ZD3 → 3ZP8, 2XZM → 4BPP, 2ZJR → 4IOA, 3NPB → 4KQY.

20 new structures in release 1.10: 3WFS, 4BW0, 4C7O, 4C9D, 4ILL, 4ILM, 4JF2, 4JRC, 4K27, 4K50, 4KJI, 4L8H, 4L8R, 4LCK, 4LGT, 4M30, 4M4O, 4M6D, 4MGM, 4MGN.

Obsolete: 2XZM → 4V5O, 3NPB → 4KQY, 3ZD3 → 3ZP8, 4HXH → 4L8R.

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 1.0 has 252 motif groups, release 1.10 has 253 motif groups, 145 of them are identical.

50 motif groups were updated, 57 groups are present only in release 1.0, 58 groups are only in release 1.10.

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_15603.1	8	U1A protein-binding Hairpin Loop.
2	HL_85534.1	5	LSU Helix 65 (H65) Hairpin Loop. T-loop like.
3	HL_45018.3	5	Hairpin-Hairpin Interacting HL
4	HL_72273.1	5	tRNA D-loop
5	HL_66174.1	5	cHS GU/cWS Double Platform creates Intercalation site
6	HL_78731.1	5	LSU Helix 7 (H7) Hairpin Loop. Forms Pseudo-knot
7	HL_06643.2	5	tRNA D-loop. Sec tRNA
8	HL_29831.1	4	GNRA-like with bulged base.
9	HL_62881.1	4	RNase P Structured Hairpin Loop
10	HL_08382.2	3
11	HL_41827.1	3
12	HL_23182.1	3
13	HL_78361.1	3
14	HL_58083.2	3
15	HL_19221.2	3
16	HL_80492.2	3	tRNA D-loop
17	HL_48254.1	3	LSU Helix 84 (H84) Hairpin Loop.
18	HL_13707.2	3	cSH AA Platform containing Hairpin Loop
19	HL_42077.2	3	LSU Helix 28 (H28) Hairpin Loop
20	HL_98833.1	3
21	HL_74686.1	3	SSU Central Pseudoknot (forms helix 2)
22	HL_65924.1	2
23	HL_23290.1	2
24	HL_98577.1	2
25	HL_42436.1	2	Kissing Hairpin from di-GMP-II riboswitch
26	HL_44467.1	2
27	HL_24473.3	2	tRNA D-loop
28	HL_19399.1	2
29	HL_38130.2	2
30	HL_05361.1	2
31	HL_64371.2	2
32	HL_63823.1	2
33	HL_86123.2	2	SSU Helix 42 (h42) Hairpin Loop. T-loop like.
34	HL_24711.1	2
35	HL_62967.1	2
36	HL_06122.1	2
37	HL_42553.1	2
38	HL_84353.1	2
39	HL_33451.1	2
40	HL_87554.1	2
41	HL_99633.1	2
42	HL_96915.1	2
43	HL_16770.1	2
44	HL_49210.1	2
45	HL_94578.1	2
46	HL_38138.1	1
47	HL_38897.1	1	S8 operon binding Hairpin Loop. T-loop like with purine stacking.
48	HL_24707.1	1
49	HL_57923.1	1
50	HL_30366.1	1	LSU Helix 10 (H10) Hairpin E.coli
51	HL_19226.1	1
52	HL_58223.1	1
53	HL_88960.1	1
54	HL_55272.1	1
55	HL_78420.1	1
56	HL_90102.1	1	Kink-turn-like Hairpin Loop
57	HL_69403.1	1	GNRA-like
58	HL_85018.1	1
59	HL_33640.1	1
60	HL_25197.1	1
61	HL_45411.1	1
62	HL_59604.1	1
63	HL_26579.1	1
64	HL_58601.1	1
65	HL_66877.1	1	cSH GU/cWS double platform, intercalation site
66	HL_44390.1	1
67	HL_00090.1	1
68	HL_53015.1	1
69	HL_25175.1	1
70	HL_95716.1	1
71	HL_82288.1	1
72	HL_19452.1	1	tRNA D-loop
73	HL_55202.1	1	U2B"-U2A" binding hairpin loop
74	HL_56775.1	1
75	HL_30128.1	1
76	HL_20806.1	1
77	HL_60203.1	1
78	HL_44522.1	1
79	HL_66880.1	1
80	HL_56809.1	1
81	HL_67761.1	1
82	HL_80746.1	1
83	HL_97971.1	1
84	HL_36842.1	1
85	HL_98233.1	1
86	HL_38898.1	1
87	HL_93567.1	1
88	HL_25195.1	1
89	HL_78507.1	1
90	HL_87223.1	1
91	HL_39422.1	1
92	HL_84289.1	1
93	HL_27397.1	1
94	HL_27819.1	1
95	HL_13786.1	1
96	HL_04194.1	1
97	HL_78228.1	1
98	HL_35200.1	1
99	HL_99207.1	1	Tetrahymena LSU hairpin poorly modeled
100	HL_17008.1	1	Nova-2 KH3 domain binding hairpin
101	HL_65802.1	1
102	HL_53789.1	1
103	HL_94697.1	1	LSU Helix 84 (H84) Hairpin Loop. E.coli.
104	HL_00721.1	1
105	HL_34440.1	1
106	HL_12706.1	1
107	HL_62970.1	1
108	HL_75850.1	1
109	HL_39486.1	1
110	HL_97784.1	1
111	HL_59610.1	1
112	HL_97499.1	1
113	HL_65071.1	1
114	HL_05113.1	1
115	HL_79902.1	1
116	HL_30731.1	1
117	HL_70912.1	1
118	HL_62880.1	1
119	HL_50059.1	1	LSU Helix 35 (H35) Hairpin Loop from Yeast
120	HL_33277.1	1
121	HL_10116.1	1	Kink-turn-like Hairpin Loop
122	HL_35865.1	1
123	HL_85044.1	1	LSU Helix 10 (H10) Hairpin E.coli
124	HL_48480.1	1
125	HL_37962.1	1
126	HL_45358.1	1	Double hairpin loop based on GGA triple
127	HL_42969.1	1
128	HL_57843.1	1
129	HL_68579.1	1
130	HL_10378.1	1	Double 5'-stacked purine Hairpin Loop from Eukaryal LSU
131	HL_66467.1	1
132	HL_49492.1	1	Forms 7-BP PseudoKnot. Has embedded sarcin-like motif
133	HL_81661.1	1	tRNA D-loop
134	HL_99779.1	1
135	HL_57217.1	1	cHS platform Intercalation Site
136	HL_68435.1	1
137	HL_84888.1	1	T-loop like but without tWH UA
138	HL_19132.1	1
139	HL_91613.1	1
140	HL_67000.1	1
141	HL_63304.1	1
142	HL_47337.1	1
143	HL_68733.1	1	LSU Yeast Hairpin Loop
144	HL_82243.1	1
145	HL_17537.1	1

Updated motif groups

#	Motif id	Instances	Description
1	HL_91226.3	17	Kissing Hairpin motif
2	HL_48039.2	11	MS2 virus RNA Hairpin
3	HL_56824.2	10	LSU Helix 60A. LSU Helix 63A.
4	HL_46175.2	10	16S helix 23 and 24 hairpin loops
5	HL_68081.3	10	LSU Helix 20 Hairpin loop
6	HL_87844.2	9	LSU Helix 11 (H11) Hairpin Loop. GNRA-like.
7	HL_24544.2	8	LSU Helix 53 (H53) Hairpin Loop. T-loop like.
8	HL_11547.2	8	LSU Helix 80 (H80) P-site Hairpin Loop.
9	HL_82294.3	8	SSU Helix 37 (h37) Hairpin loop.
10	HL_34027.2	8	5S Loop C - Upper part of Hairpin Loop.
11	HL_42677.2	7
12	HL_87136.2	6	LSU Helix 39A Hairpin loop
13	HL_39942.2	6	LSU Helix 91 (H91) Hairpin Loop
14	HL_11509.2	6	LSU Helix 6 (H6) Hairpin Loop.
15	HL_70420.2	6	LSU Helix 97 Hairpin loop
16	HL_39872.2	6	LSU Helix 99A (H99A) Hairpin Loop. Closed by cSW AA.
17	HL_75579.2	6
18	HL_01926.3	6	LSU Helix 71 (H71) Hairpin Loop.
19	HL_18156.2	6	LSU Helix 72 (H72) Hairpin Loop
20	HL_41833.2	6	LSU Helix 81 (H81) Hairpin Loop
21	HL_34108.2	6	LSU Helix 37 (H37) Hairpin Loop.
22	HL_46489.2	6	LSU H89 Hairpin Loop
23	HL_72543.2	5	LSU Helix 43 (H43) Hairpin Loop. T-loop Like.
24	HL_88311.2	5	LSU Helix 35 (H35) Hairpin Loop
25	HL_47784.2	4	SSU Central Pseudoknot (forms helix 2)
26	HL_25124.2	4	tSW GA closed tetraloops
27	HL_64543.2	4	SSU Helix 31 (h31) Hairpin Loop
28	HL_98523.2	4	GNRA-like. Closed by tSH UC.
29	HL_48116.2	4	GNRA-like with 5'-stacking of first unpaired base.
30	HL_68697.2	3
31	HL_76036.3	3	LSU Helix 8 (H8) Hairpin Loop
32	HL_27429.3	3
33	HL_32644.2	2	LSU Helix 69 (H69) Hairpin Loop
34	HL_54751.2	2

Removed motif groups

#	Motif id	Instances	Description
1	HL_80459.1	11
2	HL_28436.2	9	LSU Helix 96 (H96) Hairpin Loop
3	HL_12811.1	5	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
4	HL_62228.1	4	LSU Helix 35A (H35A) Hairpin Loop
5	HL_77235.1	4	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
6	HL_90579.1	3
7	HL_42687.2	3
8	HL_46794.2	3
9	HL_73023.1	3	Two base, cross-stacked hairpin loop
10	HL_05510.1	2
11	HL_77555.1	2
12	HL_05797.1	2
13	HL_57014.1	2
14	HL_67367.1	2
15	HL_06312.1	2
16	HL_57904.1	2
17	HL_67692.1	2
18	HL_81555.1	2
19	HL_81752.1	2
20	HL_12595.1	2
21	HL_22614.1	2
22	HL_49267.1	2
23	HL_75575.1	2
24	HL_26057.1	2
25	HL_76105.1	2
26	HL_53753.1	2
27	HL_03791.1	2
28	HL_15771.1	1
29	HL_29084.1	1
30	HL_55543.1	1
31	HL_66900.1	1
32	HL_90365.1	1	5S rRNA Loop C from D.radiodurans
33	HL_17468.1	1
34	HL_33524.1	1	tRNA T-loop distorted by RS binding
35	HL_18011.1	1
36	HL_35004.1	1
37	HL_93206.1	1
38	HL_07315.1	1
39	HL_20914.1	1
40	HL_58786.1	1
41	HL_71607.1	1
42	HL_94145.1	1	SSU Helix 43 (h43) Hairpin Loop E.coli
43	HL_61061.1	1
44	HL_81780.1	1
45	HL_96192.1	1
46	HL_00238.1	1
47	HL_23522.1	1
48	HL_83053.1	1	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
49	HL_02479.1	1
50	HL_12984.1	1
51	HL_52393.1	1	Double tSH (double sheared) with bulged base
52	HL_63411.1	1
53	HL_85138.1	1	LSU Helix 8 (H8) Hairpin Loop
54	HL_03431.1	1
55	HL_13105.1	1
56	HL_63690.1	1
57	HL_85753.1	1

Added motif groups

#	Motif id	Instances	Description
1	HL_27271.2	12	LSU Helix 96 (H96) Hairpin Loop
2	HL_80459.3	9
3	HL_57514.2	6	Two base, cross-stacked hairpin loop
4	HL_62228.3	5	LSU Helix 35A (H35A) Hairpin Loop
5	HL_95720.1	5	Double tSH (double sheared) with bulged base \| LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
6	HL_82538.1	5	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
7	HL_11376.1	4	LSU Helix 8 (H8) Hairpin Loop
8	HL_86115.1	4
9	HL_35619.2	3
10	HL_90579.3	3	LSU Helix 69 (H69) Hairpin Loop
11	HL_06997.2	3
12	HL_33875.1	3	SSU Helix 43 (h43) Hairpin Loop from T.th. T-loop like.
13	HL_42094.1	2
14	HL_93771.1	2	tRNA T-loop distorted by RS binding
15	HL_18587.1	2
16	HL_26495.1	2
17	HL_60200.1	2
18	HL_74505.1	2
19	HL_86398.1	2
20	HL_19528.1	2
21	HL_90542.1	2
22	HL_50312.1	2
23	HL_63941.1	2
24	HL_21545.1	2	LSU Helix 96 (H96) Hairpin Loop
25	HL_65249.1	2
26	HL_91693.1	2
27	HL_21675.3	2	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
28	HL_65347.1	2	SSU Helix 43 (h43) Hairpin Loop E.coli \| 16S helix 23 and 24 hairpin loops
29	HL_91872.1	2
30	HL_23129.1	2
31	HL_66948.1	2	LSU Helix 71 (H71) Hairpin Loop. \| Double tSH (double sheared) with bulged base
32	HL_08203.1	1
33	HL_23195.1	1
34	HL_59182.1	1
35	HL_73465.1	1
36	HL_84768.1	1
37	HL_93530.1	1
38	HL_24108.1	1
39	HL_59225.1	1
40	HL_73972.1	1
41	HL_42345.1	1
42	HL_95049.1	1	Two base, cross-stacked hairpin loop
43	HL_46570.1	1
44	HL_76585.1	1
45	HL_20028.1	1
46	HL_28676.1	1
47	HL_79038.1	1	LSU Helix 12 (H12) Hairpin Loop. GNRA-like with altered stacking
48	HL_96994.1	1
49	HL_01418.1	1
50	HL_29196.1	1
51	HL_52116.1	1
52	HL_99584.1	1
53	HL_03785.1	1	LSU Helix 8 (H8) Hairpin Loop
54	HL_30008.1	1
55	HL_52540.1	1
56	HL_83865.1	1
57	HL_93263.1	1
58	HL_07915.1	1