0.5 | 0.6

Changes in PDB files used for clustering

Release 0.5 has 171 PDB files, release 0.6 has 185 PDB files, 158 of them are identical.

10 equivalence classes changed representatives: 1NUJ → 1NUV, 2P7E → 2P7D, 2GIS → 3GX5, 3A3A → 3RG5, 2IPY → 3SNP, 2O3Y → 3TD1, 3O30 → 3U5F, 3O58 → 3U5H, 3MUR → 3UCZ, 3PYO → 3UXR.

17 new structures in release 0.6: 2Y9B, 3NVI, 3Q3Z, 3R1C, 3R1D, 3R2D, 3RW6, 3SD3, 3SIU, 3SIV, 3SJ2, 3SN2, 3SUX, 3T4B, 3TD0, 4A1B, 4A1C.

Obsolete: 2IPY → 3SNP, 3O30 → 4V7R, 3O58 → 4V7R, 3PYO → 4V83.

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 0.5 has 357 motif groups, release 0.6 has 260 motif groups, 71 of them are identical.

12 motif groups were updated, 274 groups are present only in release 0.5, 177 groups are only in release 0.6.

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_82367.4	7
2	IL_01239.1	5
3	IL_39526.1	5
4	IL_11167.3	4
5	IL_82563.1	3	Thi-box riboswitch T-loop
6	IL_16166.1	2
7	IL_97833.1	2
8	IL_19202.1	2
9	IL_98566.1	2
10	IL_09882.1	2
11	IL_88684.1	2
12	IL_02691.1	2
13	IL_74876.1	2
14	IL_50521.1	2
15	IL_57870.1	2
16	IL_94744.1	2	Sarcin-ricin motif with extra cWW GA pair
17	IL_62718.1	2
18	IL_05462.1	1
19	IL_31006.1	1	tSH-tHW-L-bif-cWW
20	IL_40845.1	1
21	IL_52509.1	1
22	IL_63952.1	1
23	IL_75688.1	1	Part of Helix 71 (H71) junction in 23S of D.r.
24	IL_85805.1	1
25	IL_06468.1	1	16S h40 3WJ E.c.
26	IL_31754.1	1	Sarcin-ricin H95 23S rRNA E.c.
27	IL_41009.1	1
28	IL_52958.1	1
29	IL_65788.1	1
30	IL_76263.1	1
31	IL_86981.1	1	Sarcin-ricin motif with CC BIfurcated pair. H.m. LSU H18.
32	IL_09333.1	1	SSU Helix 8 (h8) IL T. thermophilus
33	IL_20775.1	1	tSH-inserted
34	IL_31793.1	1	Kink-turn from 16S H23
35	IL_41791.1	1
36	IL_53988.1	1
37	IL_66744.1	1	SSU Helix 21 (h21) IL2 E.coli
38	IL_77014.1	1
39	IL_88403.1	1
40	IL_21254.1	1	SSU Helix 11 (h11) IL Kink-turn T. thermophilus
41	IL_32080.1	1
42	IL_43316.1	1
43	IL_55167.1	1
44	IL_68827.1	1	Reverse Kink-Turn
45	IL_80505.1	1
46	IL_02690.1	1
47	IL_22579.1	1
48	IL_37715.1	1
49	IL_47687.1	1
50	IL_55649.1	1
51	IL_71942.1	1
52	IL_88865.1	1
53	IL_11302.1	1
54	IL_26241.1	1
55	IL_39230.1	1
56	IL_48650.1	1
57	IL_55934.1	1	kink-turn-like
58	IL_92280.1	1
59	IL_02835.1	1
60	IL_12233.1	1
61	IL_26868.1	1
62	IL_39324.1	1
63	IL_75328.1	1
64	IL_82650.1	1
65	IL_03110.1	1
66	IL_12486.1	1
67	IL_29949.1	1
68	IL_50767.1	1
69	IL_75415.1	1	Pseudo-knot forming internal loop
70	IL_83250.1	1	16S h40 3WJ T.th.
71	IL_97073.1	1

Updated motif groups

#	Motif id	Instances	Description
1	IL_24982.2	16	16S h20 IL. Prokaryal Loop E Sub-motif
2	IL_78732.2	6	Double S-turn motif
3	IL_70237.2	6
4	IL_93335.2	5
5	IL_31066.2	4	SSU Helix 44 (h44) extension
6	IL_76095.2	3
7	IL_23262.2	3
8	IL_79955.2	3	SSU Helix (23) h23 IL1
9	IL_95150.2	3
10	IL_57785.4	3
11	IL_95652.2	3	SSU Helix 27 (h27) IL Sarcin-Ricin motif
12	IL_62499.2	3

Removed motif groups

#	Motif id	Instances
1	IL_61133.1	221
2	IL_24421.1	160
3	IL_78918.1	51
4	IL_42829.1	40
5	IL_91286.1	39
6	IL_91075.1	27
7	IL_11266.1	25
8	IL_68930.1	20
9	IL_03728.1	17
10	IL_49994.1	15
11	IL_31491.1	13
12	IL_33235.1	12
13	IL_78374.1	12
14	IL_93479.1	12
15	IL_97493.1	11
16	IL_95015.1	9
17	IL_70242.1	9
18	IL_79143.1	9
19	IL_47067.1	9
20	IL_34442.1	9
21	IL_06751.1	9
22	IL_33032.1	9
23	IL_87738.1	9
24	IL_68211.1	8
25	IL_16498.1	8
26	IL_95965.1	8
27	IL_60288.1	8
28	IL_62873.1	8
29	IL_38336.1	8
30	IL_28693.1	7
31	IL_80407.1	7
32	IL_37996.1	7
33	IL_98047.1	7
34	IL_82768.2	6
35	IL_55276.1	6
36	IL_87608.1	6
37	IL_94031.1	6
38	IL_07547.1	6
39	IL_29784.1	6
40	IL_33144.1	6
41	IL_66688.1	5
42	IL_61831.1	5
43	IL_97736.1	5
44	IL_76133.1	5
45	IL_58440.1	5
46	IL_96804.1	5
47	IL_14611.1	5
48	IL_86121.1	4
49	IL_99388.1	4
50	IL_19771.1	4
51	IL_30092.1	4
52	IL_86221.1	4
53	IL_52210.1	4
54	IL_89295.1	4
55	IL_23428.1	4
56	IL_20328.1	4
57	IL_81468.1	4
58	IL_38028.1	4
59	IL_76795.1	4
60	IL_94438.1	4
61	IL_97554.1	3
62	IL_21341.1	3
63	IL_55113.2	3
64	IL_13224.1	3
65	IL_61616.1	3
66	IL_09233.2	3
67	IL_13468.1	3
68	IL_28399.1	3
69	IL_34435.1	3
70	IL_68345.1	3
71	IL_01628.1	3
72	IL_47671.1	3
73	IL_62437.1	3
74	IL_89586.1	3
75	IL_10326.2	3
76	IL_16722.1	3
77	IL_44213.1	3
78	IL_58388.1	3
79	IL_78493.3	3
80	IL_89613.1	3
81	IL_29583.1	3
82	IL_60708.1	3
83	IL_74605.1	3
84	IL_81608.1	3
85	IL_67582.1	3
86	IL_18488.1	2
87	IL_39081.1	2
88	IL_42644.1	2
89	IL_45797.1	2
90	IL_54567.1	2
91	IL_67609.1	2
92	IL_75000.1	2
93	IL_77104.1	2
94	IL_03978.1	2
95	IL_46873.1	2
96	IL_51412.1	2
97	IL_56765.1	2
98	IL_63749.1	2
99	IL_67617.1	2
100	IL_16360.1	2
101	IL_34305.1	2
102	IL_43113.1	2
103	IL_49468.1	2
104	IL_71985.1	2
105	IL_75870.1	2
106	IL_82794.1	2
107	IL_97713.1	2
108	IL_99404.1	2
109	IL_36852.1	2
110	IL_43333.1	2
111	IL_56029.1	2
112	IL_66718.1	2
113	IL_80202.1	2
114	IL_99637.1	2
115	IL_16614.1	2
116	IL_19935.1	2
117	IL_44024.1	2
118	IL_52634.1	2
119	IL_68486.1	2
120	IL_73213.1	2
121	IL_01955.1	2
122	IL_52844.1	2
123	IL_76618.1	2
124	IL_14562.1	2
125	IL_20679.1	2
126	IL_25228.1	2
127	IL_69110.1	2
128	IL_76760.1	2
129	IL_50828.1	2
130	IL_01251.1	1
131	IL_08624.1	1
132	IL_12536.1	1
133	IL_14812.1	1
134	IL_21025.1	1
135	IL_26134.1	1
136	IL_29920.1	1
137	IL_35361.1	1
138	IL_48723.1	1
139	IL_50881.1	1
140	IL_56427.1	1
141	IL_58626.1	1
142	IL_63662.1	1
143	IL_65519.1	1
144	IL_69835.1	1
145	IL_79119.1	1
146	IL_82472.1	1
147	IL_85789.1	1
148	IL_87841.1	1
149	IL_98615.1	1
150	IL_01299.1	1
151	IL_08947.1	1
152	IL_12912.1	1
153	IL_15075.1	1
154	IL_18581.1	1
155	IL_26929.1	1
156	IL_30028.1	1
157	IL_33509.1	1
158	IL_36240.1	1
159	IL_39643.1	1
160	IL_49431.1	1
161	IL_58873.1	1
162	IL_61401.1	1
163	IL_65931.1	1
164	IL_75765.1	1
165	IL_77549.1	1
166	IL_89238.1	1
167	IL_95735.1	1
168	IL_97624.1	1
169	IL_01594.1	1
170	IL_04040.1	1
171	IL_09107.1	1
172	IL_22907.1	1
173	IL_27364.1	1
174	IL_36331.1	1
175	IL_40073.1	1
176	IL_51922.1	1
177	IL_57195.1	1
178	IL_59183.1	1
179	IL_63760.1	1
180	IL_77562.1	1
181	IL_79913.1	1
182	IL_89283.1	1
183	IL_91604.1	1
184	IL_95813.1	1
185	IL_01618.1	1
186	IL_05754.1	1
187	IL_19830.1	1
188	IL_23044.1	1
189	IL_30763.1	1
190	IL_40287.1	1
191	IL_47493.1	1
192	IL_49866.1	1
193	IL_57517.1	1
194	IL_59424.1	1
195	IL_63867.1	1
196	IL_72595.1	1
197	IL_76093.1	1
198	IL_78215.1	1
199	IL_82910.1	1
200	IL_86397.1	1
201	IL_92311.1	1
202	IL_05865.1	1
203	IL_10310.1	1
204	IL_13608.1	1
205	IL_37987.1	1
206	IL_40303.1	1
207	IL_49911.1	1
208	IL_56093.1	1
209	IL_58040.1	1
210	IL_59905.1	1
211	IL_64796.1	1
212	IL_66760.1	1
213	IL_83485.1	1
214	IL_87056.1	1
215	IL_92348.1	1
216	IL_96468.1	1
217	IL_97912.1	1
218	IL_99663.1	1
219	IL_00209.1	1
220	IL_13649.1	1
221	IL_28819.1	1
222	IL_31920.1	1
223	IL_34469.1	1
224	IL_40672.1	1
225	IL_47741.1	1
226	IL_56096.1	1
227	IL_64973.1	1
228	IL_67277.1	1
229	IL_74594.1	1
230	IL_84234.1	1
231	IL_96697.1	1
232	IL_98023.1	1
233	IL_99755.1	1
234	IL_00439.1	1
235	IL_02478.1	1
236	IL_07220.1	1
237	IL_10746.1	1
238	IL_17247.1	1
239	IL_34589.1	1
240	IL_40914.1	1
241	IL_44362.1	1
242	IL_48662.1	1
243	IL_50779.1	1
244	IL_53202.1	1
245	IL_56170.1	1
246	IL_63594.1	1
247	IL_65001.1	1
248	IL_67286.1	1
249	IL_78858.1	1
250	IL_84341.1	1
251	IL_87637.1	1
252	IL_89769.1	1
253	IL_99757.1	1
254	IL_00739.1	1
255	IL_02980.1	1
256	IL_17323.1	1
257	IL_20815.1	1
258	IL_25897.1	1
259	IL_35012.1	1
260	IL_42300.1	1
261	IL_45155.1	1
262	IL_48709.1	1
263	IL_54320.1	1
264	IL_56237.1	1
265	IL_58545.1	1
266	IL_60867.1	1
267	IL_63624.1	1
268	IL_65375.1	1
269	IL_69599.1	1
270	IL_74622.1	1
271	IL_81728.1	1
272	IL_84840.1	1
273	IL_90734.1	1
274	IL_98249.1	1

Added motif groups

#	Motif id	Instances	Description
1	IL_97217.1	260
2	IL_47174.1	198
3	IL_39199.1	59	Hoogsteen-edge Platform, Single-base
4	IL_11616.1	55	cWH basepair with syn base
5	IL_41766.1	49	Tandem cWW pairs (Not AU or GC)
6	IL_56465.1	48	Single, unpaired intercalated base, consensus A
7	IL_44540.1	46	Sugar-edge, 1-base platform, consensus tHS
8	IL_87904.1	31	Triple sheared
9	IL_54307.1	27	C-loop
10	IL_13959.1	26	Double sheared
11	IL_93424.1	23	tWH-inserted-tHS
12	IL_32390.1	22	16S h19 IL and 23S H41 IL
13	IL_55938.1	20	23S H89 IL1 and others
14	IL_65553.1	19	Kink-turn
15	IL_92027.1	18	16S h21 S8 binding site
16	IL_85647.1	18	Sarcin-ricin
17	IL_31555.1	17	16S decoding site
18	IL_73663.1	15	1 or 2 bulged bases
19	IL_49493.1	14	Sarcin-ricin H95 23S rRNA H.m.
20	IL_94430.1	14	16S h32-h33-h34 3WJ
21	IL_40090.1	12	16S h34 ILa : Part of larger motif
22	IL_48187.1	11	Single sheared with bulged bases
23	IL_99515.1	11	23S H91 IL
24	IL_27618.1	11	23S H73 ILa : Part of larger Motif
25	IL_92114.1	10	GAAA loop receptor "platform" motif
26	IL_24546.1	10	23S H41 IL and 16S h18 IL : Has large bulge on one side
27	IL_47444.1	10	SRP Loop E-like motif
28	IL_58291.1	10	Recurrent Sub-motif found in junctions
29	IL_68939.1	9	Kink-turn from U4
30	IL_73000.1	8
31	IL_86357.1	8
32	IL_76831.1	8	REV element IL with syn G
33	IL_92321.1	8	Triple sheared with wobble
34	IL_90459.1	8	cWW AG or UU
35	IL_40239.1	8	Leadzyme Motif
36	IL_80179.1	7
37	IL_25230.1	7
38	IL_24022.1	6
39	IL_40387.1	6
40	IL_97057.1	6
41	IL_53635.1	6
42	IL_29610.1	6
43	IL_44067.1	6
44	IL_13069.1	6
45	IL_45262.1	5
46	IL_78157.1	5
47	IL_59016.1	5
48	IL_92484.1	5
49	IL_24476.1	5
50	IL_72158.1	5
51	IL_83451.1	5
52	IL_92936.1	5
53	IL_02359.1	5
54	IL_82188.1	5	LSU H68 IL from H.m.
55	IL_79083.1	5
56	IL_92333.1	4
57	IL_49111.1	4	tHS tHH bulge with S-turn
58	IL_69124.1	4
59	IL_38807.1	4
60	IL_11594.1	4
61	IL_18947.1	4
62	IL_28572.1	4	16S h18 kink-turn like motif
63	IL_98591.1	4
64	IL_62661.1	4	Double-sheared with stacked As
65	IL_34628.1	4	Kink-turn
66	IL_22732.1	4	tSH-inserted-tHS
67	IL_80494.1	4
68	IL_98421.1	3
69	IL_10804.1	3
70	IL_99434.1	3	Single-Base Intercalation Site
71	IL_34363.1	3	Kink-turn from 23S H42
72	IL_13740.1	3
73	IL_30840.1	3
74	IL_30979.1	3
75	IL_64184.1	3
76	IL_52173.1	3
77	IL_41397.1	3
78	IL_15840.1	3
79	IL_58586.1	3
80	IL_34156.1	3
81	IL_82831.1	3	Kink-turn from 16S H23
82	IL_37053.1	3	Kink-turn from 23S H58
83	IL_89028.1	3	Part of H71 junction in 23S rRNA E.c. H.m. and Tetrahymena
84	IL_78744.1	2	Quadruple Sheared (tSH-tSH-tHS-tHS)
85	IL_46435.1	2
86	IL_28942.1	2
87	IL_81441.1	2
88	IL_52940.1	2
89	IL_47247.1	2
90	IL_09390.1	2
91	IL_68736.1	2
92	IL_91543.1	2
93	IL_92123.1	2
94	IL_90057.1	2
95	IL_75449.1	2
96	IL_67117.1	2
97	IL_37197.1	2
98	IL_63741.1	2
99	IL_25271.1	2	SSU Helix 8 (h8) IL E.c. and Yeast
100	IL_69009.1	2
101	IL_92459.1	2
102	IL_44742.1	2
103	IL_45794.1	2
104	IL_80093.1	2
105	IL_12211.1	2
106	IL_16330.1	2
107	IL_70280.1	2	Double sheared with wobble cWW.
108	IL_89461.1	2
109	IL_55287.1	2
110	IL_40892.1	2
111	IL_87173.1	2
112	IL_09348.1	2
113	IL_19889.1	2
114	IL_16252.1	2
115	IL_25174.1	2
116	IL_23414.1	2
117	IL_39165.1	1
118	IL_86059.1	1
119	IL_25739.1	1	M-Box Riboswitch
120	IL_61723.1	1
121	IL_03741.1	1
122	IL_25082.1	1
123	IL_53323.1	1
124	IL_26971.1	1
125	IL_07375.1	1
126	IL_15205.1	1
127	IL_91089.1	1
128	IL_25307.1	1
129	IL_06808.1	1	Double sheared (tSH-tSH) one bulged base.
130	IL_54450.1	1
131	IL_91078.1	1
132	IL_29877.1	1
133	IL_98924.1	1
134	IL_59529.1	1
135	IL_24335.1	1
136	IL_30390.1	1
137	IL_22858.1	1
138	IL_38333.1	1
139	IL_61730.1	1
140	IL_24143.1	1	Yeast 18S
141	IL_71685.1	1	Sarcin-like with an intercalated basepair
142	IL_25181.1	1
143	IL_02957.1	1
144	IL_85510.1	1
145	IL_83920.1	1
146	IL_78809.1	1
147	IL_67735.1	1
148	IL_54954.1	1	Sarcin-Ricin with extra tSH UA basepair. Yeast LSU H11.
149	IL_23639.1	1	tWH-tHS-L-cWW
150	IL_88367.1	1
151	IL_80652.1	1
152	IL_62352.1	1
153	IL_54576.1	1
154	IL_76486.1	1	Sarcin-ricin motif with syn G
155	IL_37990.1	1
156	IL_67697.1	1
157	IL_40527.1	1	Kink-turn
158	IL_99165.1	1
159	IL_30650.1	1
160	IL_06306.1	1
161	IL_97842.1	1
162	IL_98655.1	1	Part of H71 Junction in 26S rRNA from Yeast
163	IL_65978.1	1
164	IL_41139.1	1
165	IL_17109.1	1
166	IL_81398.1	1
167	IL_37347.1	1
168	IL_46306.1	1
169	IL_10109.1	1	H71 junction in 23S rRNA of T.th.
170	IL_14225.1	1
171	IL_52752.1	1
172	IL_82113.1	1
173	IL_05221.1	1
174	IL_91513.1	1
175	IL_91904.1	1
176	IL_17682.1	1	Sarcin-ricin motif from Eukaryal LSU Helix 11
177	IL_96260.1	1

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