0.6 | 0.7

Changes in PDB files used for clustering

Release 0.6 has 185 PDB files, release 0.7 has 192 PDB files, 181 of them are identical.

1 equivalence classes changed representatives: 3UXR → 3V2F.

10 new structures in release 0.7: 3SYW, 3SZX, 3TZR, 3U4M, 3V7E, 4AOB, 4E48, 4E5C, 4ERD, 4EYA.

Obsolete: 3UXR → 4V8A.

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 0.6 has 260 motif groups, release 0.7 has 263 motif groups, 142 of them are identical.

59 motif groups were updated, 59 groups are present only in release 0.6, 62 groups are only in release 0.7.

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	IL_92484.1	5
2	IL_82188.1	5	LSU H68 IL from H.m.
3	IL_01239.1	5
4	IL_28572.1	4	16S h18 kink-turn like motif
5	IL_31066.2	4	SSU Helix 44 (h44) extension
6	IL_22732.1	4	tSH-inserted-tHS
7	IL_98421.1	3
8	IL_95150.2	3
9	IL_52173.1	3
10	IL_37053.1	3	Kink-turn from 23S H58
11	IL_89028.1	3	Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
12	IL_15840.1	3
13	IL_62499.2	3
14	IL_30840.1	3
15	IL_79955.2	3	SSU Helix (23) h23 IL1
16	IL_34363.1	3	Kink-turn from 23S H42
17	IL_95652.2	3	SSU Helix 27 (h27) IL Sarcin-Ricin motif
18	IL_82563.1	3	Thi-box riboswitch T-loop
19	IL_80093.1	2
20	IL_87173.1	2
21	IL_25271.1	2	SSU Helix 8 (h8) IL E.c. and Yeast
22	IL_92459.1	2
23	IL_50521.1	2
24	IL_55287.1	2
25	IL_09882.1	2
26	IL_46435.1	2
27	IL_23414.1	2
28	IL_52940.1	2
29	IL_97833.1	2
30	IL_28942.1	2
31	IL_25174.1	2
32	IL_37197.1	2
33	IL_81441.1	2
34	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
35	IL_45794.1	2
36	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
37	IL_90057.1	2
38	IL_74876.1	2
39	IL_16166.1	2
40	IL_98566.1	2
41	IL_12211.1	2
42	IL_16330.1	2
43	IL_40892.1	2
44	IL_70280.1	2	Double sheared with wobble cWW.
45	IL_40845.1	1
46	IL_31006.1	1	tSH-tHW-L-bif-cWW
47	IL_52509.1	1
48	IL_37715.1	1
49	IL_12233.1	1
50	IL_75328.1	1
51	IL_81398.1	1
52	IL_05221.1	1
53	IL_26971.1	1
54	IL_07375.1	1
55	IL_41139.1	1
56	IL_85805.1	1
57	IL_03110.1	1
58	IL_68827.1	1	Reverse Kink-Turn
59	IL_26868.1	1
60	IL_53988.1	1
61	IL_25739.1	1	M-Box Riboswitch
62	IL_65788.1	1
63	IL_55934.1	1	kink-turn-like
64	IL_26241.1	1
65	IL_82113.1	1
66	IL_53323.1	1
67	IL_59529.1	1
68	IL_02957.1	1
69	IL_96260.1	1
70	IL_63952.1	1
71	IL_83250.1	1	16S h40 3WJ T.th.
72	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
73	IL_11302.1	1
74	IL_52958.1	1
75	IL_20775.1	1	tSH-inserted
76	IL_32080.1	1
77	IL_75688.1	1	Part of Helix 71 (H71) junction in 23S of D.r.
78	IL_61730.1	1
79	IL_25082.1	1
80	IL_98924.1	1
81	IL_25181.1	1
82	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
83	IL_91089.1	1
84	IL_39324.1	1
85	IL_80505.1	1
86	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
87	IL_55649.1	1
88	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
89	IL_78809.1	1
90	IL_75415.1	1	Pseudo-knot forming internal loop
91	IL_24143.1	1	Yeast 18S
92	IL_71685.1	1	Sarcin-like with an intercalated basepair
93	IL_15205.1	1
94	IL_92280.1	1
95	IL_41791.1	1
96	IL_86059.1	1
97	IL_82650.1	1
98	IL_88403.1	1
99	IL_02690.1	1
100	IL_54576.1	1
101	IL_03741.1	1
102	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
103	IL_23639.1	1	tWH-tHS-L-cWW
104	IL_30390.1	1
105	IL_43316.1	1
106	IL_25307.1	1
107	IL_06468.1	1	16S h40 3WJ E.c.
108	IL_05462.1	1
109	IL_97073.1	1
110	IL_12486.1	1
111	IL_61723.1	1
112	IL_91078.1	1
113	IL_76486.1	1	Sarcin-ricin motif with syn G
114	IL_37990.1	1
115	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
116	IL_85510.1	1
117	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
118	IL_52752.1	1
119	IL_22858.1	1
120	IL_47687.1	1
121	IL_80652.1	1
122	IL_62352.1	1
123	IL_54450.1	1
124	IL_29949.1	1
125	IL_77014.1	1
126	IL_67735.1	1
127	IL_97842.1	1
128	IL_88367.1	1
129	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
130	IL_88865.1	1
131	IL_02835.1	1
132	IL_76263.1	1
133	IL_83920.1	1
134	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
135	IL_22579.1	1
136	IL_41009.1	1
137	IL_71942.1	1
138	IL_06306.1	1
139	IL_37347.1	1
140	IL_46306.1	1
141	IL_91904.1	1
142	IL_40527.1	1	Kink-turn

Updated motif groups

#	Motif id	Instances	Description
1	IL_97217.2	234
2	IL_47174.2	200	16S h34 ILa : Part of larger motif
3	IL_39199.2	55	Hoogsteen-edge Platform, Single bulged base
4	IL_41766.2	49	Tandem cWW pairs (Not AU or GC)
5	IL_56465.2	45	Single, unpaired intercalated base, consensus A
6	IL_44540.2	43	Sugar-edge, 1-base platform, consensus tHS
7	IL_87904.2	31	Triple sheared
8	IL_13959.2	24	Double Sheared (tSH-tHS)
9	IL_93424.2	22	tSH-inserted-tHW
10	IL_32390.2	21	16S h19 IL and 23S H41 IL
11	IL_65553.2	21	Kink-turn
12	IL_55938.2	19	LSU Helix 89 (H89) IL2. cSH Platform.
13	IL_92027.2	17	16S h21 S8 binding site
14	IL_85647.2	16	Sarcin-ricin parent motif with 15 Nts
15	IL_31555.2	15	16S decoding site
16	IL_24982.3	15	SSU helix 20 (h20) IL. Prokaryal 5S Loop E Sub-motif
17	IL_49493.2	14	Sarcin-ricin Parent Motif - bacterial LSU H95 IL
18	IL_94430.2	14	16S h32-h33-h34 3WJ
19	IL_40090.2	11	16S h34 ILa : Part of larger motif
20	IL_27618.2	11	23S H73 ILa : Part of larger Motif
21	IL_24546.2	10	23S H41 IL and 16S h18 IL : Has large bulge on one side
22	IL_58291.2	9	Recurrent Sub-motif found in junctions
23	IL_47444.2	9	SRP Loop E-like motif
24	IL_92114.2	9	GAAA loop receptor "platform" motif
25	IL_92321.2	8	Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
26	IL_90459.2	8	cWW AG or UU
27	IL_86357.2	7	LSU Helix 61 IL2
28	IL_83451.2	7	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
29	IL_73000.2	7	cHS-cWS
30	IL_70237.3	6
31	IL_53635.2	6	LSU Helix 32 (H32) IL
32	IL_72158.2	6	LSU Helix 62 (H62) IL
33	IL_13069.2	6	LSU 3WJ H32-H33-H35A
34	IL_24022.2	6
35	IL_25230.2	6	Bacterial 5S rRNA Loop E
36	IL_44067.2	6	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
37	IL_97057.2	6
38	IL_78732.3	5	Double S-turn motif
39	IL_80179.2	5
40	IL_40387.2	5
41	IL_02359.2	5
42	IL_45262.2	5
43	IL_79083.2	5
44	IL_62661.2	4	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
45	IL_98591.2	4
46	IL_39526.2	4
47	IL_38807.2	4
48	IL_64184.2	4
49	IL_16252.2	3	23S H91 IL
50	IL_34628.2	3	Kink-turn
51	IL_58586.2	3
52	IL_34156.2	3	cWW AG or UU
53	IL_23262.3	3
54	IL_80494.2	3	LSU H58 IL2 H.m.
55	IL_09348.2	3
56	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
57	IL_82831.2	2	Kink-turn from 16S H23
58	IL_41397.2	2	LSU Helix 96 (H96) IL2
59	IL_76095.3	2	Motif from Hairpin Ribozyme

Removed motif groups

#	Motif id	Instances	Description
1	IL_11616.1	55	cWH basepair with syn base
2	IL_54307.1	27	C-loop
3	IL_73663.1	15	1 or 2 bulged bases
4	IL_48187.1	11	Single sheared with bulged bases
5	IL_99515.1	11	23S H91 IL
6	IL_68939.1	9	Kink-turn from U4
7	IL_76831.1	8	REV element IL with syn G
8	IL_40239.1	8	Leadzyme Motif
9	IL_82367.4	7
10	IL_29610.1	6
11	IL_24476.1	5
12	IL_78157.1	5
13	IL_92936.1	5
14	IL_93335.2	5
15	IL_59016.1	5
16	IL_11167.3	4
17	IL_49111.1	4	tHS tHH bulge with S-turn
18	IL_11594.1	4
19	IL_92333.1	4
20	IL_18947.1	4
21	IL_69124.1	4
22	IL_13740.1	3
23	IL_99434.1	3	Single-Base Intercalation Site
24	IL_30979.1	3
25	IL_10804.1	3
26	IL_19889.1	2
27	IL_75449.1	2
28	IL_92123.1	2
29	IL_67117.1	2
30	IL_68736.1	2
31	IL_02691.1	2
32	IL_44742.1	2
33	IL_57870.1	2
34	IL_88684.1	2
35	IL_09390.1	2
36	IL_47247.1	2
37	IL_69009.1	2
38	IL_89461.1	2
39	IL_62718.1	2
40	IL_19202.1	2
41	IL_63741.1	2
42	IL_91543.1	2
43	IL_38333.1	1
44	IL_65978.1	1
45	IL_24335.1	1
46	IL_39165.1	1
47	IL_50767.1	1
48	IL_39230.1	1
49	IL_67697.1	1
50	IL_55167.1	1
51	IL_14225.1	1
52	IL_29877.1	1
53	IL_99165.1	1
54	IL_17109.1	1
55	IL_30650.1	1
56	IL_10109.1	1	H71 junction in 23S rRNA of T.th.
57	IL_91513.1	1
58	IL_31793.1	1	Kink-turn from 16S H23
59	IL_48650.1	1

Added motif groups

#	Motif id	Instances	Description
1	IL_06390.1	25	cWH basepair with syn base
2	IL_73276.1	20	C-loop
3	IL_06429.1	16	16S h19 IL and 23S H41 IL \| 1 or 2 bulged bases
4	IL_21304.1	11	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
5	IL_46648.1	11	23S H91 IL \| Single-Base Intercalation Site
6	IL_02809.1	8	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
7	IL_89088.1	6	16S h19 IL and 23S H41 IL
8	IL_10007.1	6	Single sheared with bulged bases
9	IL_08926.1	6	23S H91 IL
10	IL_77263.1	5	Kink-turn from U4
11	IL_07911.1	5
12	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
13	IL_98556.1	4
14	IL_47758.1	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
15	IL_21333.1	4	tSH-tHW-bulge
16	IL_71565.1	3
17	IL_53774.1	3	Single sheared with bulged bases
18	IL_43946.1	3
19	IL_45808.1	3
20	IL_75447.1	3
21	IL_21495.1	2
22	IL_43933.1	2
23	IL_74291.1	2
24	IL_00998.1	2
25	IL_31707.1	2	Vitamin B12 aptamer
26	IL_99575.1	2
27	IL_78674.1	2	tHS tHH bulge with S-turn
28	IL_91026.1	2
29	IL_12269.1	2
30	IL_37406.1	2
31	IL_87548.1	2
32	IL_48285.1	2	Leadzyme Motif
33	IL_14023.1	2
34	IL_16415.1	2	SSU Helix 23 (h23) Kink-turn T. thermophilus
35	IL_01054.1	2
36	IL_12068.1	2
37	IL_65137.1	2	Kink-turn like motif in Group I Intron
38	IL_58454.1	1
39	IL_13942.1	1
40	IL_89794.1	1
41	IL_31241.1	1
42	IL_56779.1	1
43	IL_18755.1	1
44	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
45	IL_27243.1	1
46	IL_82601.1	1	Tandem cWW water-inserted CU pairs
47	IL_12507.1	1
48	IL_41849.1	1
49	IL_90880.1	1
50	IL_91379.1	1
51	IL_13682.1	1
52	IL_17603.1	1
53	IL_23448.1	1
54	IL_07675.1	1	tHS tHH bulge with S-turn
55	IL_47457.1	1
56	IL_60643.1	1
57	IL_95939.1	1
58	IL_56513.1	1
59	IL_57977.1	1
60	IL_11869.1	1
61	IL_53423.1	1
62	IL_21421.1	1