0.015089
0.008711
0.000000
0.000000
0.017423
0.000000
0.000000
0.000000
0.028413
0.00000
0.00000
0.00000
Yang, X.
Huang, Y.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
66.275
66.275
35.195
C10 H14 N5 O7 P
347.221
y
ADENOSINE-5'-MONOPHOSPHATE
RNA linking
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C9 H14 N3 O8 P
323.197
y
CYTIDINE-5'-MONOPHOSPHATE
RNA linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C9 H13 N2 O9 P
324.181
y
URIDINE-5'-MONOPHOSPHATE
RNA linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
O
N
2
N
P
N
3
N
O
N
4
N
O
N
5
N
O
N
6
N
C
N
7
R
C
N
8
N
O
N
9
S
C
N
10
N
O
N
11
R
C
N
12
N
O
N
13
R
C
Y
14
N
N
Y
15
N
C
Y
16
N
N
Y
17
N
C
Y
18
N
C
N
19
N
N
Y
20
N
N
Y
21
N
C
Y
22
N
N
Y
23
N
C
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
N
N
39
S
C
N
40
N
C
N
41
N
O
N
42
N
C
N
43
N
O
N
44
N
H
N
45
N
H
N
46
N
H
N
47
N
H
N
48
N
H
N
49
N
H
N
50
N
H
N
51
N
N
N
52
S
C
N
53
N
C
N
54
N
O
N
55
N
C
N
56
N
C
N
57
N
C
N
58
N
N
N
59
N
C
N
60
N
N
N
61
N
N
N
62
N
O
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
N
N
79
S
C
N
80
N
C
N
81
N
O
N
82
N
C
N
83
N
C
N
84
N
O
N
85
N
N
N
86
N
O
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
N
N
96
S
C
N
97
N
C
N
98
N
O
N
99
N
C
N
100
N
C
N
101
N
O
N
102
N
O
N
103
N
O
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
O
N
112
N
P
N
113
N
O
N
114
N
O
N
115
N
O
N
116
N
C
N
117
R
C
N
118
N
O
N
119
S
C
N
120
N
O
N
121
R
C
N
122
N
O
N
123
R
C
N
124
N
N
N
125
N
C
N
126
N
O
N
127
N
N
N
128
N
C
N
129
N
N
N
130
N
C
N
131
N
C
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
N
N
147
S
C
N
148
N
C
N
149
N
O
N
150
N
C
N
151
N
C
N
152
N
C
N
153
N
O
N
154
N
N
N
155
N
O
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
N
N
167
S
C
N
168
N
C
N
169
N
O
N
170
N
C
N
171
N
C
N
172
N
C
N
173
N
O
N
174
N
O
N
175
N
O
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
N
N
186
N
C
N
187
N
C
N
188
N
O
N
189
N
O
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
N
N
196
S
C
N
197
N
C
N
198
N
O
N
199
N
C
Y
200
N
C
Y
201
N
N
Y
202
N
C
Y
203
N
C
Y
204
N
N
N
205
N
O
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
O
N
217
N
H
N
218
N
H
N
219
N
N
N
220
S
C
N
221
N
C
N
222
N
O
N
223
S
C
N
224
N
C
N
225
N
C
N
226
N
C
N
227
N
O
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
H
N
241
N
N
N
242
S
C
N
243
N
C
N
244
N
O
N
245
N
C
N
246
N
C
N
247
N
C
N
248
N
C
N
249
N
O
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
H
N
261
N
H
N
262
N
H
N
263
N
N
N
264
S
C
N
265
N
C
N
266
N
O
N
267
N
C
N
268
N
C
N
269
N
C
N
270
N
C
N
271
N
N
N
272
N
O
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
N
N
289
S
C
N
290
N
C
N
291
N
O
N
292
N
C
Y
293
N
C
Y
294
N
C
Y
295
N
C
Y
296
N
C
Y
297
N
C
Y
298
N
C
N
299
N
O
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
H
N
308
N
H
N
309
N
H
N
310
N
H
N
311
N
N
N
312
S
C
N
313
N
C
N
314
N
O
N
315
N
C
N
316
N
C
N
317
N
C
N
318
N
O
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
N
N
329
S
C
N
330
N
C
N
331
N
O
N
332
N
C
N
333
N
O
N
334
N
O
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
N
N
343
S
C
N
344
N
C
N
345
N
O
N
346
R
C
N
347
N
O
N
348
N
C
N
349
N
O
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
N
N
360
S
C
N
361
N
C
N
362
N
O
N
363
N
C
Y
364
N
C
Y
365
N
C
Y
366
N
C
Y
367
N
N
Y
368
N
C
Y
369
N
C
Y
370
N
C
Y
371
N
C
Y
372
N
C
N
373
N
O
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
H
N
378
N
H
N
379
N
H
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
N
N
387
S
C
N
388
N
C
N
389
N
O
N
390
N
C
Y
391
N
C
Y
392
N
C
Y
393
N
C
Y
394
N
C
Y
395
N
C
Y
396
N
C
N
397
N
O
N
398
N
O
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
H
N
403
N
H
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
H
N
408
N
H
N
409
N
H
N
410
N
O
N
411
N
P
N
412
N
O
N
413
N
O
N
414
N
O
N
415
N
C
N
416
R
C
N
417
N
O
N
418
S
C
N
419
N
O
N
420
R
C
N
421
N
O
N
422
R
C
N
423
N
N
N
424
N
C
N
425
N
O
N
426
N
N
N
427
N
C
N
428
N
O
N
429
N
C
N
430
N
C
N
431
N
H
N
432
N
H
N
433
N
H
N
434
N
H
N
435
N
H
N
436
N
H
N
437
N
H
N
438
N
H
N
439
N
H
N
440
N
H
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
N
N
445
S
C
N
446
N
C
N
447
N
O
N
448
N
C
N
449
N
C
N
450
N
C
N
451
N
O
N
452
N
H
N
453
N
H
N
454
N
H
N
455
N
H
N
456
N
H
N
457
N
H
N
458
N
H
N
459
N
H
N
460
N
H
N
461
N
H
N
462
N
H
N
1
N
sing
N
2
N
sing
N
3
N
doub
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
Y
25
N
sing
Y
26
N
sing
Y
27
N
doub
N
28
N
sing
Y
29
N
sing
Y
30
N
sing
Y
31
N
doub
N
32
N
sing
Y
33
N
doub
N
34
N
sing
N
35
N
sing
Y
36
N
sing
Y
37
N
doub
N
38
N
sing
Y
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
doub
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
doub
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
doub
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
doub
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
doub
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
doub
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
doub
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
doub
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
doub
N
136
N
sing
N
137
N
doub
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
doub
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
doub
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
doub
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
doub
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
doub
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
doub
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
doub
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
Y
202
N
sing
Y
203
N
doub
Y
204
N
doub
N
205
N
sing
Y
206
N
sing
N
207
N
sing
Y
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
doub
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
doub
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
doub
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
doub
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
Y
291
N
doub
Y
292
N
sing
Y
293
N
sing
N
294
N
sing
Y
295
N
doub
N
296
N
sing
Y
297
N
doub
N
298
N
sing
Y
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
doub
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
doub
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
doub
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
sing
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
doub
N
356
N
sing
N
357
N
sing
N
358
N
sing
N
359
N
sing
Y
360
N
doub
Y
361
N
sing
Y
362
N
sing
N
363
N
sing
Y
364
N
doub
Y
365
N
sing
Y
366
N
sing
N
367
N
sing
Y
368
N
sing
Y
369
N
doub
N
370
N
sing
Y
371
N
doub
N
372
N
sing
Y
373
N
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
doub
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
Y
388
N
doub
Y
389
N
sing
Y
390
N
sing
N
391
N
sing
Y
392
N
doub
N
393
N
sing
Y
394
N
doub
N
395
N
sing
Y
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
N
403
N
doub
N
404
N
sing
N
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
N
415
N
sing
N
416
N
sing
N
417
N
sing
N
418
N
sing
N
419
N
sing
N
420
N
sing
N
421
N
sing
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
doub
N
428
N
sing
N
429
N
sing
N
430
N
sing
N
431
N
doub
N
432
N
sing
N
433
N
doub
N
434
N
sing
N
435
N
sing
N
436
N
sing
N
437
N
sing
N
438
N
sing
N
439
N
sing
N
440
N
sing
N
441
N
sing
N
442
N
doub
N
443
N
sing
N
444
N
sing
N
445
N
sing
N
446
N
sing
N
447
N
sing
N
448
N
sing
N
449
N
sing
N
450
N
sing
N
451
N
sing
N
452
N
sing
N
453
N
sing
US
J.Biol.Chem.
JBCHA3
0071
1083-351X
294
10998
11010
10.1074/jbc.RA119.007545
31160337
Crystal structure of a Y-box binding protein 1 (YB-1)-RNA complex reveals key features and residues interacting with RNA.
2019
0000-0002-6647-8491
0000-0002-1999-4776
0000-0002-2806-2874
10.2210/pdb5ytv/pdb
pdb_00005ytv
100
1
CCD
2011-03-06
ADSC QUANTUM 315
SINGLE WAVELENGTH
M
x-ray
1
0.979
1.0
BL17U1
SSRF
0.979
SYNCHROTRON
SSRF BEAMLINE BL17U1
8997.026
Nuclease-sensitive element-binding protein 1
1
man
polymer
1813.109
RNA (5'-R(P*UP*CP*AP*UP*CP*U)-3')
1
syn
polymer
18.015
water
53
nat
water
CCAAT-binding transcription factor I subunit A,CBF-A,DNA-binding protein B,DBPB,Enhancer factor I subunit A,EFI-A,Y-box transcription factor,Y-box-binding protein 1,YB-1
no
no
GSGDKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTG
PGG
GSGDKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTG
PGG
A
polypeptide(L)
no
no
UCAUCU
UCAUCU
B
polyribonucleotide
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
Human
sample
1
83
YBX1, NSEP1, YB1
9606
Homo sapiens
562
Escherichia coli
Biological sequence
1
2.06
40.41
VAPOR DIFFUSION, HANGING DROP
4.5
30 % (v/v) 2-methyl-2,4-pentanediol, 0.1 M sodium acetate, pH 4.5, 25 % (w/v) PEG 1500
290
citation
citation_author
citation
citation_author
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
repository
Initial release
Data collection
Database references
Data collection
Database references
Data collection
Database references
Refinement description
1
0
2018-12-05
1
1
2019-06-19
1
2
2019-07-24
1
3
2023-11-22
_citation.country
_citation.journal_abbrev
_citation.journal_id_ASTM
_citation.journal_id_CSD
_citation.journal_id_ISSN
_citation.pdbx_database_id_DOI
_citation.pdbx_database_id_PubMed
_citation.title
_citation.year
_citation.journal_volume
_citation.page_first
_citation.page_last
_citation_author.identifier_ORCID
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
China
National Natural Science Foundation of China
91640102
China
Strategic Priority Research Program of the Chinese Academy of Sciences
XDB08010202
N
PDBJ
Y
PDBJ
2017-11-20
REL
REL
HOH
water
32630
synthetic construct
sample
1
6
3PF5
PDB
experimental model
HOH
46
3
HOH
HOH
201
A
HOH
45
3
HOH
HOH
202
A
HOH
53
3
HOH
HOH
203
A
HOH
27
3
HOH
HOH
204
A
HOH
48
3
HOH
HOH
205
A
HOH
21
3
HOH
HOH
206
A
HOH
3
3
HOH
HOH
207
A
HOH
14
3
HOH
HOH
208
A
HOH
13
3
HOH
HOH
209
A
HOH
8
3
HOH
HOH
210
A
HOH
10
3
HOH
HOH
211
A
HOH
4
3
HOH
HOH
212
A
HOH
51
3
HOH
HOH
213
A
HOH
12
3
HOH
HOH
214
A
HOH
49
3
HOH
HOH
215
A
HOH
7
3
HOH
HOH
216
A
HOH
31
3
HOH
HOH
217
A
HOH
30
3
HOH
HOH
218
A
HOH
1
3
HOH
HOH
219
A
HOH
2
3
HOH
HOH
220
A
HOH
42
3
HOH
HOH
221
A
HOH
33
3
HOH
HOH
222
A
HOH
20
3
HOH
HOH
223
A
HOH
16
3
HOH
HOH
224
A
HOH
32
3
HOH
HOH
225
A
HOH
9
3
HOH
HOH
226
A
HOH
24
3
HOH
HOH
227
A
HOH
19
3
HOH
HOH
228
A
HOH
22
3
HOH
HOH
229
A
HOH
15
3
HOH
HOH
230
A
HOH
26
3
HOH
HOH
231
A
HOH
6
3
HOH
HOH
232
A
HOH
25
3
HOH
HOH
233
A
HOH
18
3
HOH
HOH
234
A
HOH
11
3
HOH
HOH
235
A
HOH
52
3
HOH
HOH
236
A
HOH
40
3
HOH
HOH
237
A
HOH
37
3
HOH
HOH
238
A
HOH
29
3
HOH
HOH
239
A
HOH
28
3
HOH
HOH
240
A
HOH
50
3
HOH
HOH
241
A
HOH
23
3
HOH
HOH
242
A
HOH
35
3
HOH
HOH
243
A
HOH
47
3
HOH
HOH
244
A
HOH
41
3
HOH
HOH
245
A
HOH
36
3
HOH
HOH
246
A
HOH
43
3
HOH
HOH
247
A
HOH
34
3
HOH
HOH
248
A
HOH
44
3
HOH
HOH
101
B
HOH
39
3
HOH
HOH
102
B
HOH
17
3
HOH
HOH
103
B
HOH
5
3
HOH
HOH
104
B
HOH
38
3
HOH
HOH
105
B
n
1
48
A
n
2
49
A
n
3
50
A
n
4
51
A
LYS
52
n
5
LYS
52
A
LYS
53
n
6
LYS
53
A
VAL
54
n
7
VAL
54
A
ILE
55
n
8
ILE
55
A
ALA
56
n
9
ALA
56
A
THR
57
n
10
THR
57
A
LYS
58
n
11
LYS
58
A
VAL
59
n
12
VAL
59
A
LEU
60
n
13
LEU
60
A
GLY
61
n
14
GLY
61
A
THR
62
n
15
THR
62
A
VAL
63
n
16
VAL
63
A
LYS
64
n
17
LYS
64
A
TRP
65
n
18
TRP
65
A
PHE
66
n
19
PHE
66
A
ASN
67
n
20
ASN
67
A
VAL
68
n
21
VAL
68
A
ARG
69
n
22
ARG
69
A
ASN
70
n
23
ASN
70
A
GLY
71
n
24
GLY
71
A
TYR
72
n
25
TYR
72
A
GLY
73
n
26
GLY
73
A
PHE
74
n
27
PHE
74
A
ILE
75
n
28
ILE
75
A
ASN
76
n
29
ASN
76
A
ARG
77
n
30
ARG
77
A
ASN
78
n
31
ASN
78
A
ASP
79
n
32
ASP
79
A
THR
80
n
33
THR
80
A
LYS
81
n
34
LYS
81
A
GLU
82
n
35
GLU
82
A
ASP
83
n
36
ASP
83
A
VAL
84
n
37
VAL
84
A
PHE
85
n
38
PHE
85
A
VAL
86
n
39
VAL
86
A
HIS
87
n
40
HIS
87
A
GLN
88
n
41
GLN
88
A
THR
89
n
42
THR
89
A
ALA
90
n
43
ALA
90
A
ILE
91
n
44
ILE
91
A
LYS
92
n
45
LYS
92
A
LYS
93
n
46
LYS
93
A
ASN
94
n
47
ASN
94
A
n
48
95
A
n
49
96
A
n
50
97
A
LYS
98
n
51
LYS
98
A
TYR
99
n
52
TYR
99
A
LEU
100
n
53
LEU
100
A
ARG
101
n
54
ARG
101
A
SER
102
n
55
SER
102
A
VAL
103
n
56
VAL
103
A
GLY
104
n
57
GLY
104
A
ASP
105
n
58
ASP
105
A
GLY
106
n
59
GLY
106
A
GLU
107
n
60
GLU
107
A
THR
108
n
61
THR
108
A
VAL
109
n
62
VAL
109
A
GLU
110
n
63
GLU
110
A
PHE
111
n
64
PHE
111
A
ASP
112
n
65
ASP
112
A
VAL
113
n
66
VAL
113
A
VAL
114
n
67
VAL
114
A
GLU
115
n
68
GLU
115
A
GLY
116
n
69
GLY
116
A
GLU
117
n
70
GLU
117
A
LYS
118
n
71
LYS
118
A
GLY
119
n
72
GLY
119
A
ALA
120
n
73
ALA
120
A
GLU
121
n
74
GLU
121
A
ALA
122
n
75
ALA
122
A
ALA
123
n
76
ALA
123
A
ASN
124
n
77
ASN
124
A
VAL
125
n
78
VAL
125
A
THR
126
n
79
THR
126
A
GLY
127
n
80
GLY
127
A
PRO
128
n
81
PRO
128
A
GLY
129
n
82
GLY
129
A
n
83
130
A
n
1
1
B
C
2
n
2
C
2
B
A
3
n
3
A
3
B
U
4
n
4
U
4
B
C
5
n
5
C
5
B
n
6
6
B
author_defined_assembly
2
dimeric
YB1 can form homodimer in vivo
immunoprecipitation
1090
-1
5170
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
THR
62
A
N
THR
15
A
O
ASN
76
A
O
ASN
29
A
N
ILE
75
A
N
ILE
28
A
O
VAL
84
A
O
VAL
37
A
N
PHE
85
A
N
PHE
38
A
O
ALA
122
A
O
ALA
75
A
O
GLU
121
A
O
GLU
74
A
N
VAL
114
A
N
VAL
67
A
O
VAL
113
A
O
VAL
66
A
N
ILE
55
A
N
ILE
8
1
B
HOH
104
D
HOH
1
A
GLY
48
A
GLY
1
1
Y
1
A
SER
49
A
SER
2
1
Y
1
A
GLY
50
A
GLY
3
1
Y
1
A
ASP
51
A
ASP
4
1
Y
1
A
ASN
95
A
ASN
48
1
Y
1
A
PRO
96
A
PRO
49
1
Y
1
A
ARG
97
A
ARG
50
1
Y
1
A
GLY
130
A
GLY
83
1
Y
1
B
U
1
B
U
1
1
Y
1
B
U
6
B
U
6
1
Y
1
A
A
OE1
O
GLU
HOH
115
201
1.99
1
A
A
O
O
ALA
HOH
120
202
2.07
1
A
A
NZ
O
LYS
HOH
53
203
2.12
1
A
A
NZ
O
LYS
HOH
98
204
2.15
1
A
B
O
O
HOH
HOH
242
105
2.18
1
A
B
O
O
HOH
HOH
237
105
1.86
1_555
5_454
1
A
A
O
O
HOH
HOH
204
222
2.11
1_555
6_665
1
A
A
O
O
HOH
HOH
241
244
2.12
1_555
3_565
0.2276
0.1961
0.1992
1.700
30.003
976
9677
10.09
98.28
0.17
1
FREE R-VALUE
1.66
MOLECULAR REPLACEMENT
24.65
0.90
1.11
3PF5
1.700
30.003
53
717
0
82
582
0.007
680
1.071
929
12.701
259
0.060
108
0.004
106
0.2823
0.2315
1.7898
123
1111
88.00
0.2269
0.2008
1.9019
137
1240
100.00
0.2517
0.1885
2.0487
139
1257
100.00
0.2135
0.1811
2.2548
143
1254
100.00
0.2268
0.1894
2.5810
142
1258
100.00
0.2182
0.2096
3.2511
145
1276
100.00
0.2258
0.1923
30.0080
147
1305
100.00
1.7
30.003
5YTV
9693
1
30.0
16.6
100.00
1.70
1.76
1
refinement
PHENIX
1.9_1692
data reduction
HKL-2000
data scaling
HKL-2000
phasing
PHENIX
N
Crystal structure of YB1 cold-shock domain in complex with UCAUCU
1
N
N
2
N
N
3
N
N
3
N
N
A
THR
89
A
THR
42
HELX_P
A
ILE
91
A
ILE
44
5
AA1
3
RNA BINDING PROTEIN/RNA
YB1, cold-shock domain, CAUC, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA complex
YBOX1_HUMAN
UNP
1
50
P67809
GDKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPG
G
5YTV
PDB
2
1
5YTV
50
130
5YTV
50
130
P67809
A
1
3
83
1
6
5YTV
1
6
5YTV
B
2
1
6
1
expression tag
GLY
48
5YTV
A
P67809
UNP
1
1
expression tag
SER
49
5YTV
A
P67809
UNP
2
6
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
VAL
54
A
VAL
7
A
ASN
67
A
ASN
20
A
TYR
72
A
TYR
25
A
ARG
77
A
ARG
30
A
ASP
83
A
ASP
36
A
HIS
87
A
HIS
40
A
GLY
119
A
GLY
72
A
THR
126
A
THR
79
A
THR
108
A
THR
61
A
GLY
116
A
GLY
69
A
VAL
54
A
VAL
7
A
ASN
67
A
ASN
20
171
P 62