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_22732.1	4	tSH-inserted-tHS
5	IL_31066.2	4	SSU Helix 44 (h44) extension
6	IL_28572.1	4	16S h18 kink-turn like motif
7	IL_79955.2	3	SSU Helix (23) h23 IL1
8	IL_82563.1	3	Thi-box riboswitch T-loop
9	IL_15840.1	3
10	IL_52173.1	3
11	IL_30840.1	3
12	IL_62499.2	3
13	IL_98421.1	3
14	IL_89028.1	3	Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
15	IL_95150.2	3
16	IL_95652.2	3	SSU Helix 27 (h27) IL Sarcin-Ricin motif
17	IL_34363.1	3	Kink-turn from 23S H42
18	IL_37053.1	3	Kink-turn from 23S H58
19	IL_25271.1	2	SSU Helix 8 (h8) IL E.c. and Yeast
20	IL_37197.1	2
21	IL_50521.1	2
22	IL_87173.1	2
23	IL_97833.1	2
24	IL_80093.1	2
25	IL_92459.1	2
26	IL_16166.1	2
27	IL_23414.1	2
28	IL_74876.1	2
29	IL_09882.1	2
30	IL_16330.1	2
31	IL_55287.1	2
32	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
33	IL_98566.1	2
34	IL_45794.1	2
35	IL_52940.1	2
36	IL_90057.1	2
37	IL_12211.1	2
38	IL_81441.1	2
39	IL_25174.1	2
40	IL_46435.1	2
41	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
42	IL_28942.1	2
43	IL_40892.1	2
44	IL_70280.1	2	Double sheared with wobble cWW.
45	IL_02835.1	1
46	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
47	IL_15205.1	1
48	IL_29949.1	1
49	IL_41009.1	1
50	IL_54450.1	1
51	IL_61730.1	1
52	IL_71685.1	1	Sarcin-like with an intercalated basepair
53	IL_92280.1	1
54	IL_02957.1	1
55	IL_07375.1	1
56	IL_22858.1	1
57	IL_25307.1	1
58	IL_30390.1	1
59	IL_37347.1	1
60	IL_41139.1	1
61	IL_54576.1	1
62	IL_62352.1	1
63	IL_71942.1	1
64	IL_82650.1	1
65	IL_88367.1	1
66	IL_97842.1	1
67	IL_03110.1	1
68	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
69	IL_25739.1	1	M-Box Riboswitch
70	IL_37715.1	1
71	IL_41791.1	1
72	IL_52509.1	1
73	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
74	IL_80505.1	1
75	IL_83250.1	1	16S h40 3WJ T.th.
76	IL_88403.1	1
77	IL_03741.1	1
78	IL_23639.1	1	tWH-tHS-L-cWW
79	IL_26241.1	1
80	IL_37990.1	1
81	IL_43316.1	1
82	IL_52752.1	1
83	IL_63952.1	1
84	IL_75415.1	1	Pseudo-knot forming internal loop
85	IL_80652.1	1
86	IL_83920.1	1
87	IL_05221.1	1
88	IL_11302.1	1
89	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
90	IL_24143.1	1	Yeast 18S
91	IL_26868.1	1
92	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
93	IL_39324.1	1
94	IL_55649.1	1
95	IL_65788.1	1
96	IL_75688.1	1	Part of Helix 71 (H71) junction in 23S of D.r.
97	IL_81398.1	1
98	IL_85510.1	1
99	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
100	IL_05462.1	1
101	IL_20775.1	1	tSH-inserted
102	IL_25082.1	1
103	IL_26971.1	1
104	IL_32080.1	1
105	IL_40527.1	1	Kink-turn
106	IL_46306.1	1
107	IL_52958.1	1
108	IL_55934.1	1	kink-turn-like
109	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
110	IL_76486.1	1	Sarcin-ricin motif with syn G
111	IL_85805.1	1
112	IL_91078.1	1
113	IL_98924.1	1
114	IL_06306.1	1
115	IL_12233.1	1
116	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
117	IL_40845.1	1
118	IL_53323.1	1
119	IL_59529.1	1
120	IL_67735.1	1
121	IL_82113.1	1
122	IL_86059.1	1
123	IL_91089.1	1
124	IL_96260.1	1
125	IL_02690.1	1
126	IL_06468.1	1	16S h40 3WJ E.c.
127	IL_12486.1	1
128	IL_22579.1	1
129	IL_25181.1	1
130	IL_47687.1	1
131	IL_53988.1	1
132	IL_61723.1	1
133	IL_78809.1	1
134	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
135	IL_91904.1	1
136	IL_97073.1	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_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_27618.2	11	23S H73 ILa : Part of larger Motif
20	IL_40090.2	11	16S h34 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_47444.2	9	SRP Loop E-like motif
23	IL_92114.2	9	GAAA loop receptor "platform" motif
24	IL_58291.2	9	Recurrent Sub-motif found in junctions
25	IL_90459.2	8	cWW AG or UU
26	IL_92321.2	8	Triple sheared (tSH-tHS-tHS) with cWW Wobble base flanking motif
27	IL_83451.2	7	cHS-cWS triple and Wobble. SSU Helix 44 (h44) IL1.
28	IL_73000.2	7	cHS-cWS
29	IL_86357.2	7	LSU Helix 61 IL2
30	IL_13069.2	6	LSU 3WJ H32-H33-H35A
31	IL_53635.2	6	LSU Helix 32 (H32) IL
32	IL_70237.3	6
33	IL_24022.2	6
34	IL_44067.2	6	Quadruple sheared (tSH-tHS-tHS-tHS). LSU Helix 2 (H2).
35	IL_72158.2	6	LSU Helix 62 (H62) IL
36	IL_97057.2	6
37	IL_25230.2	6	Bacterial 5S rRNA Loop E
38	IL_79083.2	5
39	IL_40387.2	5
40	IL_80179.2	5
41	IL_02359.2	5
42	IL_45262.2	5
43	IL_78732.3	5	Double S-turn motif
44	IL_62661.2	4	Double-sheared with two unpaired, stacked As. LSU Helix 68 IL4.
45	IL_98591.2	4
46	IL_64184.2	4
47	IL_38807.2	4
48	IL_39526.2	4
49	IL_16252.2	3	23S H91 IL
50	IL_80494.2	3	LSU H58 IL2 H.m.
51	IL_23262.3	3
52	IL_34156.2	3	cWW AG or UU
53	IL_34628.2	3	Kink-turn
54	IL_09348.2	3
55	IL_58586.2	3
56	IL_41397.2	2	LSU Helix 96 (H96) IL2
57	IL_82831.2	2	Kink-turn from 16S H23
58	IL_57785.5	2	SSU Decoding Site -- Human. Bulge-cSW-tHS
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_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_30979.1	3
23	IL_10804.1	3
24	IL_13740.1	3
25	IL_99434.1	3	Single-Base Intercalation Site
26	IL_62718.1	2
27	IL_19202.1	2
28	IL_63741.1	2
29	IL_91543.1	2
30	IL_19889.1	2
31	IL_75449.1	2
32	IL_92123.1	2
33	IL_67117.1	2
34	IL_68736.1	2
35	IL_02691.1	2
36	IL_44742.1	2
37	IL_57870.1	2
38	IL_88684.1	2
39	IL_09390.1	2
40	IL_47247.1	2
41	IL_69009.1	2
42	IL_89461.1	2
43	IL_10109.1	1	H71 junction in 23S rRNA of T.th.
44	IL_91513.1	1
45	IL_31793.1	1	Kink-turn from 16S H23
46	IL_48650.1	1
47	IL_38333.1	1
48	IL_65978.1	1
49	IL_24335.1	1
50	IL_39165.1	1
51	IL_50767.1	1
52	IL_39230.1	1
53	IL_67697.1	1
54	IL_55167.1	1
55	IL_14225.1	1
56	IL_29877.1	1
57	IL_99165.1	1
58	IL_17109.1	1
59	IL_30650.1	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_08926.1	6	23S H91 IL
9	IL_10007.1	6	Single sheared with bulged bases
10	IL_71288.1	5	Leadzyme Motif. LSU H101 IL2. SSU Decoding site.
11	IL_07911.1	5
12	IL_77263.1	5	Kink-turn from U4
13	IL_21333.1	4	tSH-tHW-bulge
14	IL_47758.1	4	REV element IL with syn G \| Tandem cWW pairs (Not AU or GC)
15	IL_98556.1	4
16	IL_53774.1	3	Single sheared with bulged bases
17	IL_71565.1	3
18	IL_43946.1	3
19	IL_45808.1	3
20	IL_75447.1	3
21	IL_12068.1	2
22	IL_87548.1	2
23	IL_99575.1	2
24	IL_12269.1	2
25	IL_43933.1	2
26	IL_74291.1	2
27	IL_21495.1	2
28	IL_91026.1	2
29	IL_14023.1	2
30	IL_00998.1	2
31	IL_16415.1	2	SSU Helix 23 (h23) Kink-turn T. thermophilus
32	IL_31707.1	2	Vitamin B12 aptamer
33	IL_78674.1	2	tHS tHH bulge with S-turn
34	IL_01054.1	2
35	IL_37406.1	2
36	IL_48285.1	2	Leadzyme Motif
37	IL_65137.1	2	Kink-turn like motif in Group I Intron
38	IL_18755.1	1
39	IL_41849.1	1
40	IL_53423.1	1
41	IL_12507.1	1
42	IL_56513.1	1
43	IL_89794.1	1
44	IL_07675.1	1	tHS tHH bulge with S-turn
45	IL_13682.1	1
46	IL_21421.1	1
47	IL_56779.1	1
48	IL_90880.1	1
49	IL_13942.1	1
50	IL_57977.1	1
51	IL_31241.1	1
52	IL_47457.1	1
53	IL_58454.1	1
54	IL_95939.1	1
55	IL_60643.1	1
56	IL_97191.1	1	Sarcin-ricin motif with cWW UU instead of tSH basepair.
57	IL_11869.1	1
58	IL_17603.1	1
59	IL_82601.1	1	Tandem cWW water-inserted CU pairs