0.6 | 0.7

Changes in PDB files used for clustering

Release 0.6 has 185 PDB files, release 0.7 has 191 PDB files, 180 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_01239.1	5
3	IL_82188.1	5	LSU H68 IL from H.m.
4	IL_28572.1	4	16S h18 kink-turn like motif
5	IL_22732.1	4	tSH-inserted-tHS
6	IL_31066.2	4	SSU Helix 44 (h44) extension
7	IL_98421.1	3
8	IL_89028.1	3	Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
9	IL_34363.1	3	Kink-turn from 23S H42
10	IL_95150.2	3
11	IL_37053.1	3	Kink-turn from 23S H58
12	IL_95652.2	3	SSU Helix 27 (h27) IL Sarcin-Ricin motif
13	IL_15840.1	3
14	IL_52173.1	3
15	IL_30840.1	3
16	IL_62499.2	3
17	IL_79955.2	3	SSU Helix (23) h23 IL1
18	IL_82563.1	3	Thi-box riboswitch T-loop
19	IL_45794.1	2
20	IL_52940.1	2
21	IL_12211.1	2
22	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
23	IL_98566.1	2
24	IL_25174.1	2
25	IL_46435.1	2
26	IL_90057.1	2
27	IL_28942.1	2
28	IL_40892.1	2
29	IL_81441.1	2
30	IL_25271.1	2	SSU Helix 8 (h8) IL E.c. and Yeast
31	IL_37197.1	2
32	IL_50521.1	2
33	IL_70280.1	2	Double sheared with wobble cWW.
34	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
35	IL_16166.1	2
36	IL_23414.1	2
37	IL_87173.1	2
38	IL_97833.1	2
39	IL_09882.1	2
40	IL_16330.1	2
41	IL_55287.1	2
42	IL_74876.1	2
43	IL_80093.1	2
44	IL_92459.1	2
45	IL_05221.1	1
46	IL_11302.1	1
47	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
48	IL_24143.1	1	Yeast 18S
49	IL_26868.1	1
50	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
51	IL_39324.1	1
52	IL_55649.1	1
53	IL_65788.1	1
54	IL_75415.1	1	Pseudo-knot forming internal loop
55	IL_80505.1	1
56	IL_83250.1	1	16S h40 3WJ T.th.
57	IL_88403.1	1
58	IL_05462.1	1
59	IL_20775.1	1	tSH-inserted
60	IL_25082.1	1
61	IL_26971.1	1
62	IL_32080.1	1
63	IL_40527.1	1	Kink-turn
64	IL_46306.1	1
65	IL_52958.1	1
66	IL_55934.1	1	kink-turn-like
67	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
68	IL_75688.1	1	Part of Helix 71 (H71) junction in 23S of D.r.
69	IL_80652.1	1
70	IL_83920.1	1
71	IL_06306.1	1
72	IL_12233.1	1
73	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
74	IL_40845.1	1
75	IL_53323.1	1
76	IL_59529.1	1
77	IL_67735.1	1
78	IL_76263.1	1
79	IL_81398.1	1
80	IL_85510.1	1
81	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
82	IL_02690.1	1
83	IL_06468.1	1	16S h40 3WJ E.c.
84	IL_12486.1	1
85	IL_22579.1	1
86	IL_25181.1	1
87	IL_47687.1	1
88	IL_53988.1	1
89	IL_61723.1	1
90	IL_68827.1	1	Reverse Kink-Turn
91	IL_76486.1	1	Sarcin-ricin motif with syn G
92	IL_85805.1	1
93	IL_91078.1	1
94	IL_98924.1	1
95	IL_02835.1	1
96	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
97	IL_15205.1	1
98	IL_29949.1	1
99	IL_41009.1	1
100	IL_54450.1	1
101	IL_61730.1	1
102	IL_82113.1	1
103	IL_86059.1	1
104	IL_91089.1	1
105	IL_96260.1	1
106	IL_02957.1	1
107	IL_07375.1	1
108	IL_22858.1	1
109	IL_25307.1	1
110	IL_30390.1	1
111	IL_37347.1	1
112	IL_41139.1	1
113	IL_54576.1	1
114	IL_62352.1	1
115	IL_71685.1	1	Sarcin-like with an intercalated basepair
116	IL_78809.1	1
117	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
118	IL_91904.1	1
119	IL_97073.1	1
120	IL_03110.1	1
121	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
122	IL_25739.1	1	M-Box Riboswitch
123	IL_37715.1	1
124	IL_41791.1	1
125	IL_52509.1	1
126	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
127	IL_71942.1	1
128	IL_92280.1	1
129	IL_03741.1	1
130	IL_23639.1	1	tWH-tHS-L-cWW
131	IL_26241.1	1
132	IL_37990.1	1
133	IL_43316.1	1
134	IL_52752.1	1
135	IL_63952.1	1
136	IL_82650.1	1
137	IL_88367.1	1
138	IL_97842.1	1

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_65553.2	21	Kink-turn
11	IL_32390.2	21	16S h19 IL and 23S H41 IL
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_94430.2	14	16S h32-h33-h34 3WJ
18	IL_49493.2	14	Sarcin-ricin Parent Motif - bacterial LSU H95 IL
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_97057.2	6
31	IL_70237.3	6
32	IL_53635.2	6	LSU Helix 32 (H32) IL
33	IL_72158.2	6	LSU Helix 62 (H62) IL
34	IL_13069.2	6	LSU 3WJ H32-H33-H35A
35	IL_24022.2	6
36	IL_25230.2	6	Bacterial 5S rRNA Loop E
37	IL_44067.2	6	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
38	IL_45262.2	5
39	IL_79083.2	5
40	IL_78732.3	5	Double S-turn motif
41	IL_80179.2	5
42	IL_40387.2	5
43	IL_02359.2	5
44	IL_64184.2	4
45	IL_62661.2	4	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
46	IL_98591.2	4
47	IL_39526.2	4
48	IL_38807.2	4
49	IL_80494.2	3	LSU H58 IL2 H.m.
50	IL_09348.2	3
51	IL_16252.2	3	23S H91 IL
52	IL_34628.2	3	Kink-turn
53	IL_58586.2	3
54	IL_34156.2	3	cWW AG or UU
55	IL_23262.3	3
56	IL_82831.2	2	Kink-turn from 16S H23
57	IL_41397.2	2	LSU Helix 96 (H96) IL2
58	IL_76095.3	2	Motif from Hairpin Ribozyme
59	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS

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_40239.1	8	Leadzyme Motif
8	IL_76831.1	8	REV element IL with syn G
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_18947.1	4
17	IL_69124.1	4
18	IL_11167.3	4
19	IL_49111.1	4	tHS tHH bulge with S-turn
20	IL_11594.1	4
21	IL_92333.1	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_68736.1	2
27	IL_02691.1	2
28	IL_44742.1	2
29	IL_57870.1	2
30	IL_88684.1	2
31	IL_09390.1	2
32	IL_47247.1	2
33	IL_69009.1	2
34	IL_89461.1	2
35	IL_62718.1	2
36	IL_19202.1	2
37	IL_63741.1	2
38	IL_91543.1	2
39	IL_19889.1	2
40	IL_75449.1	2
41	IL_92123.1	2
42	IL_67117.1	2
43	IL_39230.1	1
44	IL_67697.1	1
45	IL_55167.1	1
46	IL_14225.1	1
47	IL_29877.1	1
48	IL_99165.1	1
49	IL_17109.1	1
50	IL_30650.1	1
51	IL_10109.1	1	H71 junction in 23S rRNA of T.th.
52	IL_91513.1	1
53	IL_31793.1	1	Kink-turn from 16S H23
54	IL_48650.1	1
55	IL_38333.1	1
56	IL_65978.1	1
57	IL_24335.1	1
58	IL_39165.1	1
59	IL_50767.1	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_46648.1	11	23S H91 IL \| Single-Base Intercalation Site
5	IL_21304.1	11	Single sheared (tHS) with bulged bases. LSU Helix 75 (H75)
6	IL_02809.1	8	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
7	IL_08926.1	6	23S H91 IL
8	IL_10007.1	6	Single sheared with bulged bases
9	IL_89088.1	6	16S h19 IL and 23S H41 IL
10	IL_07911.1	5
11	IL_77263.1	5	Kink-turn from U4
12	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
13	IL_47758.1	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
14	IL_98556.1	4
15	IL_21333.1	4	tSH-tHW-bulge
16	IL_75447.1	3
17	IL_53774.1	3	Single sheared with bulged bases
18	IL_71565.1	3
19	IL_43946.1	3
20	IL_45808.1	3
21	IL_21495.1	2
22	IL_91026.1	2
23	IL_14023.1	2
24	IL_00998.1	2
25	IL_16415.1	2	SSU Helix 23 (h23) Kink-turn T. thermophilus
26	IL_31707.1	2	Vitamin B12 aptamer
27	IL_78674.1	2	tHS tHH bulge with S-turn
28	IL_01054.1	2
29	IL_37406.1	2
30	IL_48285.1	2	Leadzyme Motif
31	IL_65137.1	2	Kink-turn like motif in Group I Intron
32	IL_12068.1	2
33	IL_87548.1	2
34	IL_99575.1	2
35	IL_12269.1	2
36	IL_43933.1	2
37	IL_74291.1	2
38	IL_13942.1	1
39	IL_57977.1	1
40	IL_31241.1	1
41	IL_47457.1	1
42	IL_58454.1	1
43	IL_95939.1	1
44	IL_60643.1	1
45	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
46	IL_11869.1	1
47	IL_17603.1	1
48	IL_82601.1	1	Tandem cWW water-inserted CU pairs
49	IL_18755.1	1
50	IL_41849.1	1
51	IL_53423.1	1
52	IL_12507.1	1
53	IL_56513.1	1
54	IL_89794.1	1
55	IL_07675.1	1	tHS tHH bulge with S-turn
56	IL_13682.1	1
57	IL_21421.1	1
58	IL_56779.1	1
59	IL_90880.1	1