0.008244
0.004760
0.000000
0.000000
0.009519
0.000000
0.000000
0.000000
0.018727
0.00000
0.00000
0.00000
Aydin, H.
Sultana, A.
Lee, J.E.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
9
90.00
90.00
120.00
121.300
121.300
53.400
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
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide 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
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C8 H15 N O6
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE
D-saccharide, beta 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
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
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
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
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
N
N
75
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
N
97
N
O
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
N
N
109
S
C
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
O
N
116
N
O
N
117
N
O
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
N
N
128
N
C
N
129
N
C
N
130
N
O
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
N
N
138
S
C
N
139
N
C
N
140
N
O
N
141
N
C
Y
142
N
C
Y
143
N
N
Y
144
N
C
Y
145
N
C
Y
146
N
N
N
147
N
O
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
O
N
159
N
H
N
160
N
H
N
161
N
N
N
162
S
C
N
163
N
C
N
164
N
O
N
165
S
C
N
166
N
C
N
167
N
C
N
168
N
C
N
169
N
O
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
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
N
N
184
S
C
N
185
N
C
N
186
N
O
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
O
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
N
N
206
S
C
N
207
N
C
N
208
N
O
N
209
N
C
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
N
N
214
N
O
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
N
N
231
S
C
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
S
N
237
N
C
N
238
N
O
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
R
C
N
251
R
C
N
252
R
C
N
253
S
C
N
254
R
C
N
255
N
C
N
256
N
C
N
257
N
C
N
258
N
N
N
259
N
O
N
260
N
O
N
261
N
O
N
262
N
O
N
263
N
O
N
264
N
O
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
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
N
N
281
S
C
N
282
N
C
N
283
N
O
N
284
N
C
Y
285
N
C
Y
286
N
C
Y
287
N
C
Y
288
N
C
Y
289
N
C
Y
290
N
C
N
291
N
O
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
N
N
304
S
C
N
305
N
C
N
306
N
O
N
307
N
C
N
308
N
C
N
309
N
C
N
310
N
O
N
311
N
H
N
312
N
H
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
N
N
321
S
C
N
322
N
C
N
323
N
O
N
324
N
C
N
325
N
O
N
326
N
O
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
H
N
333
N
H
N
334
N
N
N
335
S
C
N
336
N
C
N
337
N
O
N
338
R
C
N
339
N
O
N
340
N
C
N
341
N
O
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
N
N
352
S
C
N
353
N
C
N
354
N
O
N
355
N
C
Y
356
N
C
Y
357
N
C
Y
358
N
C
Y
359
N
N
Y
360
N
C
Y
361
N
C
Y
362
N
C
Y
363
N
C
Y
364
N
C
N
365
N
O
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
H
N
378
N
N
N
379
S
C
N
380
N
C
N
381
N
O
N
382
N
C
Y
383
N
C
Y
384
N
C
Y
385
N
C
Y
386
N
C
Y
387
N
C
Y
388
N
C
N
389
N
O
N
390
N
O
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
N
N
403
S
C
N
404
N
C
N
405
N
O
N
406
N
C
N
407
N
C
N
408
N
C
N
409
N
O
N
410
N
H
N
411
N
H
N
412
N
H
N
413
N
H
N
414
N
H
N
415
N
H
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
H
N
420
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
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
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
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
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
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
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
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
sing
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
doub
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
doub
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
doub
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
doub
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
sing
N
138
N
sing
N
139
N
sing
Y
140
N
sing
Y
141
N
doub
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
Y
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
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
doub
N
159
N
sing
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
sing
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
sing
N
179
N
doub
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
sing
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
sing
N
198
N
sing
N
199
N
sing
N
200
N
doub
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
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
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
doub
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
sing
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
doub
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
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
doub
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
Y
278
N
doub
Y
279
N
sing
Y
280
N
sing
N
281
N
sing
Y
282
N
doub
N
283
N
sing
Y
284
N
doub
N
285
N
sing
Y
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
doub
N
297
N
sing
N
298
N
sing
N
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
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
doub
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
sing
N
340
N
sing
N
341
N
sing
N
342
N
doub
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
Y
347
N
doub
Y
348
N
sing
Y
349
N
sing
N
350
N
sing
Y
351
N
doub
Y
352
N
sing
Y
353
N
sing
N
354
N
sing
Y
355
N
sing
Y
356
N
doub
N
357
N
sing
Y
358
N
doub
N
359
N
sing
Y
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
doub
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
sing
Y
375
N
doub
Y
376
N
sing
Y
377
N
sing
N
378
N
sing
Y
379
N
doub
N
380
N
sing
Y
381
N
doub
N
382
N
sing
Y
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
doub
N
395
N
sing
N
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
sing
N
404
N
sing
N
405
N
sing
UK
Nature
NATUAS
0006
1476-4687
534
562
565
10.1038/nature18595
27309818
Molecular architecture of the human sperm IZUMO1 and egg JUNO fertilization complex.
2016
10.2210/pdb5f4v/pdb
pdb_00005f4v
100
1
CCD
2015-04-30
RAYONIX MX-300
SINGLE WAVELENGTH
M
x-ray
1
0.97949
1.0
08ID-1
CLSI
0.97949
SYNCHROTRON
CLSI BEAMLINE 08ID-1
28780.166
Izumo sperm-egg fusion protein 1
UNP residues 22-268
1
man
polymer
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
1
man
non-polymer
18.015
water
13
nat
water
Oocyte binding/fusion factor,OBF,Sperm-specific protein izumo
no
no
CVICDPSVVLALKSLEKDYLPGHLDAKHHKAMMERVENAVKDFQELSLNEDAYMGVVDEATLQKGSWSLLKDLKRITDSD
VKGDLFVKELFWMLHLQKETFATYVARFQKEAYCPNKCGVMLQTLIWCKNCKKEVHACRKSYDCGERNVEVPQMEDMILD
CELNWHQASEGLTDYSFYRVWGNNTETLVSKGKEATLTKPMVGPEDAGSYRCELGSVNSSPATIINFHVTVLPKMIKEEK
PSPNIVTGRLVPR
CVICDPSVVLALKSLEKDYLPGHLDAKHHKAMMERVENAVKDFQELSLNEDAYMGVVDEATLQKGSWSLLKDLKRITDSD
VKGDLFVKELFWMLHLQKETFATYVARFQKEAYCPNKCGVMLQTLIWCKNCKKEVHACRKSYDCGERNVEVPQMEDMILD
CELNWHQASEGLTDYSFYRVWGNNTETLVSKGKEATLTKPMVGPEDAGSYRCELGSVNSSPATIINFHVTVLPKMIKEEK
PSPNIVTGRLVPR
A
polypeptide(L)
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
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
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
fruit fly
sample
1
253
IZUMO1
9606
Homo sapiens
7227
Drosophila melanogaster
Biological sequence
1
2.83
56.46
VAPOR DIFFUSION, SITTING DROP
7.5
0.085 M HEPES sodium salt (pH 7.5), 8.5% (v/v) isopropanol, 17% (w/v) PEG 4000 and 15% (v/v) glycerol
295
chem_comp
entity
pdbx_chem_comp_identifier
pdbx_entity_nonpoly
struct_conn
struct_site
struct_site_gen
chem_comp
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
repository
Initial release
Carbohydrate remediation
repository
Remediation
Database references
Database references
Structure summary
Data collection
Derived calculations
Structure summary
Data collection
Database references
Refinement description
Structure summary
1
0
2016-06-15
1
1
2016-06-29
1
2
2016-07-06
1
3
2016-12-28
1
4
2020-07-29
1
5
2023-09-27
_chem_comp.name
_chem_comp.type
_entity.pdbx_description
_pdbx_entity_nonpoly.name
_struct_conn.pdbx_role
_chem_comp.pdbx_synonyms
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
DGlcpNAcb
N-acetyl-b-D-glucopyranosamine
b-D-GlcpNAc
GlcNAc
N
RCSB
Y
RCSB
2015-12-03
REL
REL
NAG
2-acetamido-2-deoxy-beta-D-glucopyranose
HOH
water
5F4E
PDB
experimental model
NAG
275
2
NAG
NAG
301
A
HOH
5
3
HOH
HOH
401
A
HOH
8
3
HOH
HOH
402
A
HOH
9
3
HOH
HOH
403
A
HOH
11
3
HOH
HOH
404
A
HOH
7
3
HOH
HOH
405
A
HOH
10
3
HOH
HOH
406
A
HOH
13
3
HOH
HOH
407
A
HOH
12
3
HOH
HOH
408
A
HOH
2
3
HOH
HOH
409
A
HOH
1
3
HOH
HOH
410
A
HOH
4
3
HOH
HOH
411
A
HOH
3
3
HOH
HOH
412
A
HOH
6
3
HOH
HOH
413
A
CYS
22
n
1
CYS
22
A
VAL
23
n
2
VAL
23
A
ILE
24
n
3
ILE
24
A
CYS
25
n
4
CYS
25
A
ASP
26
n
5
ASP
26
A
PRO
27
n
6
PRO
27
A
SER
28
n
7
SER
28
A
VAL
29
n
8
VAL
29
A
VAL
30
n
9
VAL
30
A
LEU
31
n
10
LEU
31
A
ALA
32
n
11
ALA
32
A
LEU
33
n
12
LEU
33
A
LYS
34
n
13
LYS
34
A
SER
35
n
14
SER
35
A
LEU
36
n
15
LEU
36
A
GLU
37
n
16
GLU
37
A
LYS
38
n
17
LYS
38
A
ASP
39
n
18
ASP
39
A
TYR
40
n
19
TYR
40
A
LEU
41
n
20
LEU
41
A
PRO
42
n
21
PRO
42
A
GLY
43
n
22
GLY
43
A
HIS
44
n
23
HIS
44
A
LEU
45
n
24
LEU
45
A
ASP
46
n
25
ASP
46
A
ALA
47
n
26
ALA
47
A
LYS
48
n
27
LYS
48
A
HIS
49
n
28
HIS
49
A
HIS
50
n
29
HIS
50
A
LYS
51
n
30
LYS
51
A
ALA
52
n
31
ALA
52
A
MET
53
n
32
MET
53
A
MET
54
n
33
MET
54
A
GLU
55
n
34
GLU
55
A
ARG
56
n
35
ARG
56
A
VAL
57
n
36
VAL
57
A
GLU
58
n
37
GLU
58
A
ASN
59
n
38
ASN
59
A
ALA
60
n
39
ALA
60
A
VAL
61
n
40
VAL
61
A
LYS
62
n
41
LYS
62
A
ASP
63
n
42
ASP
63
A
PHE
64
n
43
PHE
64
A
GLN
65
n
44
GLN
65
A
GLU
66
n
45
GLU
66
A
LEU
67
n
46
LEU
67
A
SER
68
n
47
SER
68
A
LEU
69
n
48
LEU
69
A
ASN
70
n
49
ASN
70
A
GLU
71
n
50
GLU
71
A
ASP
72
n
51
ASP
72
A
ALA
73
n
52
ALA
73
A
TYR
74
n
53
TYR
74
A
MET
75
n
54
MET
75
A
GLY
76
n
55
GLY
76
A
VAL
77
n
56
VAL
77
A
VAL
78
n
57
VAL
78
A
ASP
79
n
58
ASP
79
A
GLU
80
n
59
GLU
80
A
ALA
81
n
60
ALA
81
A
THR
82
n
61
THR
82
A
LEU
83
n
62
LEU
83
A
GLN
84
n
63
GLN
84
A
LYS
85
n
64
LYS
85
A
GLY
86
n
65
GLY
86
A
SER
87
n
66
SER
87
A
TRP
88
n
67
TRP
88
A
SER
89
n
68
SER
89
A
LEU
90
n
69
LEU
90
A
LEU
91
n
70
LEU
91
A
LYS
92
n
71
LYS
92
A
ASP
93
n
72
ASP
93
A
LEU
94
n
73
LEU
94
A
LYS
95
n
74
LYS
95
A
ARG
96
n
75
ARG
96
A
ILE
97
n
76
ILE
97
A
THR
98
n
77
THR
98
A
ASP
99
n
78
ASP
99
A
SER
100
n
79
SER
100
A
ASP
101
n
80
ASP
101
A
VAL
102
n
81
VAL
102
A
LYS
103
n
82
LYS
103
A
GLY
104
n
83
GLY
104
A
ASP
105
n
84
ASP
105
A
LEU
106
n
85
LEU
106
A
PHE
107
n
86
PHE
107
A
VAL
108
n
87
VAL
108
A
LYS
109
n
88
LYS
109
A
GLU
110
n
89
GLU
110
A
LEU
111
n
90
LEU
111
A
PHE
112
n
91
PHE
112
A
TRP
113
n
92
TRP
113
A
MET
114
n
93
MET
114
A
LEU
115
n
94
LEU
115
A
HIS
116
n
95
HIS
116
A
LEU
117
n
96
LEU
117
A
GLN
118
n
97
GLN
118
A
LYS
119
n
98
LYS
119
A
GLU
120
n
99
GLU
120
A
THR
121
n
100
THR
121
A
PHE
122
n
101
PHE
122
A
ALA
123
n
102
ALA
123
A
THR
124
n
103
THR
124
A
TYR
125
n
104
TYR
125
A
VAL
126
n
105
VAL
126
A
ALA
127
n
106
ALA
127
A
ARG
128
n
107
ARG
128
A
PHE
129
n
108
PHE
129
A
GLN
130
n
109
GLN
130
A
LYS
131
n
110
LYS
131
A
GLU
132
n
111
GLU
132
A
ALA
133
n
112
ALA
133
A
TYR
134
n
113
TYR
134
A
CYS
135
n
114
CYS
135
A
PRO
136
n
115
PRO
136
A
ASN
137
n
116
ASN
137
A
LYS
138
n
117
LYS
138
A
CYS
139
n
118
CYS
139
A
GLY
140
n
119
GLY
140
A
VAL
141
n
120
VAL
141
A
MET
142
n
121
MET
142
A
LEU
143
n
122
LEU
143
A
GLN
144
n
123
GLN
144
A
THR
145
n
124
THR
145
A
LEU
146
n
125
LEU
146
A
ILE
147
n
126
ILE
147
A
TRP
148
n
127
TRP
148
A
CYS
149
n
128
CYS
149
A
LYS
150
n
129
LYS
150
A
ASN
151
n
130
ASN
151
A
CYS
152
n
131
CYS
152
A
LYS
153
n
132
LYS
153
A
LYS
154
n
133
LYS
154
A
GLU
155
n
134
GLU
155
A
VAL
156
n
135
VAL
156
A
HIS
157
n
136
HIS
157
A
ALA
158
n
137
ALA
158
A
CYS
159
n
138
CYS
159
A
ARG
160
n
139
ARG
160
A
LYS
161
n
140
LYS
161
A
SER
162
n
141
SER
162
A
TYR
163
n
142
TYR
163
A
ASP
164
n
143
ASP
164
A
CYS
165
n
144
CYS
165
A
GLY
166
n
145
GLY
166
A
GLU
167
n
146
GLU
167
A
ARG
168
n
147
ARG
168
A
ASN
169
n
148
ASN
169
A
VAL
170
n
149
VAL
170
A
GLU
171
n
150
GLU
171
A
VAL
172
n
151
VAL
172
A
PRO
173
n
152
PRO
173
A
GLN
174
n
153
GLN
174
A
MET
175
n
154
MET
175
A
GLU
176
n
155
GLU
176
A
ASP
177
n
156
ASP
177
A
MET
178
n
157
MET
178
A
ILE
179
n
158
ILE
179
A
LEU
180
n
159
LEU
180
A
ASP
181
n
160
ASP
181
A
CYS
182
n
161
CYS
182
A
GLU
183
n
162
GLU
183
A
LEU
184
n
163
LEU
184
A
ASN
185
n
164
ASN
185
A
TRP
186
n
165
TRP
186
A
HIS
187
n
166
HIS
187
A
GLN
188
n
167
GLN
188
A
ALA
189
n
168
ALA
189
A
SER
190
n
169
SER
190
A
GLU
191
n
170
GLU
191
A
GLY
192
n
171
GLY
192
A
LEU
193
n
172
LEU
193
A
THR
194
n
173
THR
194
A
ASP
195
n
174
ASP
195
A
TYR
196
n
175
TYR
196
A
SER
197
n
176
SER
197
A
PHE
198
n
177
PHE
198
A
TYR
199
n
178
TYR
199
A
ARG
200
n
179
ARG
200
A
VAL
201
n
180
VAL
201
A
TRP
202
n
181
TRP
202
A
GLY
203
n
182
GLY
203
A
ASN
204
n
183
ASN
204
A
ASN
205
n
184
ASN
205
A
THR
206
n
185
THR
206
A
GLU
207
n
186
GLU
207
A
THR
208
n
187
THR
208
A
LEU
209
n
188
LEU
209
A
VAL
210
n
189
VAL
210
A
SER
211
n
190
SER
211
A
LYS
212
n
191
LYS
212
A
GLY
213
n
192
GLY
213
A
LYS
214
n
193
LYS
214
A
GLU
215
n
194
GLU
215
A
ALA
216
n
195
ALA
216
A
THR
217
n
196
THR
217
A
LEU
218
n
197
LEU
218
A
THR
219
n
198
THR
219
A
LYS
220
n
199
LYS
220
A
PRO
221
n
200
PRO
221
A
MET
222
n
201
MET
222
A
VAL
223
n
202
VAL
223
A
GLY
224
n
203
GLY
224
A
PRO
225
n
204
PRO
225
A
GLU
226
n
205
GLU
226
A
ASP
227
n
206
ASP
227
A
ALA
228
n
207
ALA
228
A
GLY
229
n
208
GLY
229
A
SER
230
n
209
SER
230
A
TYR
231
n
210
TYR
231
A
ARG
232
n
211
ARG
232
A
CYS
233
n
212
CYS
233
A
GLU
234
n
213
GLU
234
A
LEU
235
n
214
LEU
235
A
GLY
236
n
215
GLY
236
A
SER
237
n
216
SER
237
A
VAL
238
n
217
VAL
238
A
ASN
239
n
218
ASN
239
A
SER
240
n
219
SER
240
A
SER
241
n
220
SER
241
A
PRO
242
n
221
PRO
242
A
ALA
243
n
222
ALA
243
A
THR
244
n
223
THR
244
A
ILE
245
n
224
ILE
245
A
ILE
246
n
225
ILE
246
A
ASN
247
n
226
ASN
247
A
PHE
248
n
227
PHE
248
A
HIS
249
n
228
HIS
249
A
VAL
250
n
229
VAL
250
A
THR
251
n
230
THR
251
A
VAL
252
n
231
VAL
252
A
LEU
253
n
232
LEU
253
A
PRO
254
n
233
PRO
254
A
LYS
255
n
234
LYS
255
A
MET
256
n
235
MET
256
A
n
236
257
A
n
237
258
A
n
238
259
A
n
239
260
A
n
240
261
A
n
241
262
A
n
242
263
A
n
243
264
A
n
244
265
A
n
245
266
A
n
246
267
A
n
247
268
A
n
248
269
A
n
249
270
A
n
250
271
A
n
251
272
A
n
252
273
A
n
253
274
A
1.8702
-0.3485
1.3998
1.2099
-1.1245
1.6804
-0.0756
0.1544
-0.4615
-0.0955
0.1742
0.3675
-0.0150
-0.3273
-0.1318
0.3486
0.0051
-0.0199
0.3414
0.0065
0.3354
refined
43.5649
45.8374
39.6646
X-RAY DIFFRACTION
3.3071
-1.6930
1.0590
2.2791
-0.7239
2.3714
0.0777
-0.2670
0.0204
0.2388
-0.0339
0.2163
0.0777
-0.1476
-0.0762
0.3198
-0.0281
0.0241
0.2641
-0.0343
0.2550
refined
40.9731
53.3630
45.2007
X-RAY DIFFRACTION
1.5719
-0.0638
-0.6293
3.3587
-0.8508
0.9678
0.0950
0.1075
0.2795
0.0576
0.0570
0.2423
-0.1929
-0.0751
-0.1434
0.3199
-0.0322
-0.0284
0.3793
0.0117
0.2638
refined
32.7244
85.3877
25.2586
X-RAY DIFFRACTION
X-RAY DIFFRACTION
1
chain 'A' and (resid 22 through 76 )
X-RAY DIFFRACTION
2
chain 'A' and (resid 77 through 132 )
X-RAY DIFFRACTION
3
chain 'A' and (resid 133 through 256 )
author_and_software_defined_assembly
PISA
1
monomeric
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
VAL
78
A
N
VAL
57
A
O
ILE
147
A
O
ILE
126
A
N
GLN
144
A
N
GLN
123
A
O
HIS
157
A
O
HIS
136
A
N
ARG
168
A
N
ARG
147
A
O
HIS
249
A
O
HIS
228
A
O
VAL
250
A
O
VAL
229
A
N
GLY
229
A
N
GLY
208
A
O
ARG
232
A
O
ARG
211
A
N
TYR
199
A
N
TYR
178
A
N
PHE
198
A
N
PHE
177
A
O
VAL
210
A
O
VAL
189
A
N
LEU
180
A
N
LEU
159
A
O
LEU
218
A
O
LEU
197
1
A
HOH
412
C
HOH
1
A
CG
LYS
51
A
CG
LYS
30
1
Y
1
A
CD
LYS
51
A
CD
LYS
30
1
Y
1
A
CE
LYS
51
A
CE
LYS
30
1
Y
1
A
NZ
LYS
51
A
NZ
LYS
30
1
Y
1
A
CG
ASP
63
A
CG
ASP
42
1
Y
1
A
OD1
ASP
63
A
OD1
ASP
42
1
Y
1
A
OD2
ASP
63
A
OD2
ASP
42
1
Y
1
A
CG
ASN
70
A
CG
ASN
49
1
Y
1
A
OD1
ASN
70
A
OD1
ASN
49
1
Y
1
A
ND2
ASN
70
A
ND2
ASN
49
1
Y
1
A
CG
GLU
71
A
CG
GLU
50
1
Y
1
A
CD
GLU
71
A
CD
GLU
50
1
Y
1
A
OE1
GLU
71
A
OE1
GLU
50
1
Y
1
A
OE2
GLU
71
A
OE2
GLU
50
1
Y
1
A
CG
LYS
131
A
CG
LYS
110
1
Y
1
A
CD
LYS
131
A
CD
LYS
110
1
Y
1
A
CE
LYS
131
A
CE
LYS
110
1
Y
1
A
NZ
LYS
131
A
NZ
LYS
110
1
Y
1
A
CG
GLU
132
A
CG
GLU
111
1
Y
1
A
CD
GLU
132
A
CD
GLU
111
1
Y
1
A
OE1
GLU
132
A
OE1
GLU
111
1
Y
1
A
OE2
GLU
132
A
OE2
GLU
111
1
Y
1
A
CG
LYS
153
A
CG
LYS
132
1
Y
1
A
CD
LYS
153
A
CD
LYS
132
1
Y
1
A
CE
LYS
153
A
CE
LYS
132
1
Y
1
A
NZ
LYS
153
A
NZ
LYS
132
1
Y
1
A
CG
GLN
174
A
CG
GLN
153
1
Y
1
A
CD
GLN
174
A
CD
GLN
153
1
Y
1
A
OE1
GLN
174
A
OE1
GLN
153
1
Y
1
A
NE2
GLN
174
A
NE2
GLN
153
1
Y
1
A
CG
GLU
176
A
CG
GLU
155
1
Y
1
A
CD
GLU
176
A
CD
GLU
155
1
Y
1
A
OE1
GLU
176
A
OE1
GLU
155
1
Y
1
A
OE2
GLU
176
A
OE2
GLU
155
1
Y
1
A
CG
GLU
215
A
CG
GLU
194
1
Y
1
A
CD
GLU
215
A
CD
GLU
194
1
Y
1
A
OE1
GLU
215
A
OE1
GLU
194
1
Y
1
A
OE2
GLU
215
A
OE2
GLU
194
1
Y
1
A
CG
LYS
220
A
CG
LYS
199
1
Y
1
A
CD
LYS
220
A
CD
LYS
199
1
Y
1
A
CE
LYS
220
A
CE
LYS
199
1
Y
1
A
NZ
LYS
220
A
NZ
LYS
199
1
Y
1
A
CG
MET
256
A
CG
MET
235
1
Y
1
A
SD
MET
256
A
SD
MET
235
1
Y
1
A
CE
MET
256
A
CE
MET
235
1
Y
1
A
ILE
257
A
ILE
236
1
Y
1
A
LYS
258
A
LYS
237
1
Y
1
A
GLU
259
A
GLU
238
1
Y
1
A
GLU
260
A
GLU
239
1
Y
1
A
LYS
261
A
LYS
240
1
Y
1
A
PRO
262
A
PRO
241
1
Y
1
A
SER
263
A
SER
242
1
Y
1
A
PRO
264
A
PRO
243
1
Y
1
A
ASN
265
A
ASN
244
1
Y
1
A
ILE
266
A
ILE
245
1
Y
1
A
VAL
267
A
VAL
246
1
Y
1
A
THR
268
A
THR
247
1
Y
1
A
GLY
269
A
GLY
248
1
Y
1
A
ARG
270
A
ARG
249
1
Y
1
A
LEU
271
A
LEU
250
1
Y
1
A
VAL
272
A
VAL
251
1
Y
1
A
PRO
273
A
PRO
252
1
Y
1
A
ARG
274
A
ARG
253
1
Y
1
A
A
NH1
OE1
ARG
GLU
232
234
2.17
1
A
A
GLU
ASP
71
72
47.11
1
A
A
VAL
ASN
238
239
-46.62
1
-19.67
2.00
110.40
90.73
A
A
A
CB
CA
C
ASP
ASP
ASP
46
46
46
N
1
A
A
CB
SG
CYS
CYS
22
22
0.152
0.017
1.818
1.970
N
1
A
A
NZ
OD1
LYS
ASN
85
239
2.03
1_555
8_655
1
A
HIS
44
-143.43
-3.77
1
A
LEU
69
85.15
6.65
1
A
ASN
70
60.28
-128.16
1
A
GLU
132
-136.69
-32.35
1
A
LYS
161
-116.38
-168.63
1
A
THR
194
-116.41
-79.56
1
A
MET
222
35.74
56.15
1
A
SER
240
-163.32
-162.56
0.2318
0.1882
0.1907
2.900
47.603
367
6482
5.66
99.97
0.36
1
FREE R-VALUE
2.00
MOLECULAR REPLACEMENT
24.31
0.90
1.11
5F4E
ML
FLAT BULK SOLVENT MODEL
2.900
47.603
13
1849
14
0
1822
0.012
1873
1.270
2534
15.444
670
0.055
289
0.006
320
0.2966
0.2305
3.3198
124
2024
100.00
0.2328
0.1895
4.1822
114
2060
100.00
0.2064
0.1707
47.6090
129
2031
100.00
49.330
2.900
47.603
5F4V
6484
0.996
0.120
0.055
1
12.900
37350
5.800
100.000
0.526
2.900
3.080
3.700
5979
1026
0.889
0.239
1
5.800
0
100.000
0.041
8.700
47.600
33.200
1351
238
0.998
0.019
1
5.700
0
99.400
refinement
PHENIX
1.9_1692
data scaling
Aimless
0.5.8
data extraction
PDB_EXTRACT
3.15
data reduction
XDS
phasing
PHASER
Crystal structure of the human sperm Izumo1 residues 22-268
1
N
N
2
N
N
3
N
N
A
CYS
22
A
CYS
1
HELX_P
A
CYS
25
A
CYS
4
5
AA1
4
A
ASP
26
A
ASP
5
HELX_P
A
TYR
40
A
TYR
19
1
AA2
15
A
LEU
41
A
LEU
20
HELX_P
A
HIS
44
A
HIS
23
5
AA3
4
A
ASP
46
A
ASP
25
HELX_P
A
ASP
63
A
ASP
42
1
AA4
18
A
PHE
64
A
PHE
43
HELX_P
A
GLU
66
A
GLU
45
5
AA5
3
A
GLU
80
A
GLU
59
HELX_P
A
ASP
101
A
ASP
80
1
AA6
22
A
LYS
103
A
LYS
82
HELX_P
A
ALA
133
A
ALA
112
1
AA7
31
A
LEU
184
A
LEU
163
HELX_P
A
SER
190
A
SER
169
5
AA8
7
A
GLY
224
A
GLY
203
HELX_P
A
ALA
228
A
ALA
207
5
AA9
5
disulf
2.073
A
CYS
22
A
SG
CYS
1
1_555
A
CYS
149
A
SG
CYS
128
1_555
disulf
2.052
A
CYS
25
A
SG
CYS
4
1_555
A
CYS
152
A
SG
CYS
131
1_555
disulf
2.063
A
CYS
135
A
SG
CYS
114
1_555
A
CYS
159
A
SG
CYS
138
1_555
disulf
2.106
A
CYS
139
A
SG
CYS
118
1_555
A
CYS
165
A
SG
CYS
144
1_555
disulf
1.932
A
CYS
182
A
SG
CYS
161
1_555
A
CYS
233
A
SG
CYS
212
1_555
covale
1.460
one
N-Glycosylation
A
ASN
204
A
ND2
ASN
183
1_555
A
NAG
301
B
C1
NAG
1_555
CELL ADHESION
glycoprotein, membrane-bound, cysteine-rich, adhesion, fusion, CELL ADHESION
IZUM1_HUMAN
UNP
1
22
Q8IYV9
CVICDPSVVLALKSLEKDYLPGHLDAKHHKAMMERVENAVKDFQELSLNEDAYMGVVDEATLQKGSWSLLKDLKRITDSD
VKGDLFVKELFWMLHLQKETFATYVARFQKEAYCPNKCGVMLQTLIWCKNCKKEVHACRKSYDCGERNVEVPQMEDMILD
CELNWHQASEGLTDYSFYRVWGNNTETLVSKGKEATLTKPMVGPEDAGSYRCELGSVNSSPATIINFHVTVLPKMIKEEK
PSPNIVT
22
268
5F4V
22
268
Q8IYV9
A
1
1
247
1
expression tag
GLY
269
5F4V
A
Q8IYV9
UNP
248
1
expression tag
ARG
270
5F4V
A
Q8IYV9
UNP
249
1
expression tag
LEU
271
5F4V
A
Q8IYV9
UNP
250
1
expression tag
VAL
272
5F4V
A
Q8IYV9
UNP
251
1
expression tag
PRO
273
5F4V
A
Q8IYV9
UNP
252
1
expression tag
ARG
274
5F4V
A
Q8IYV9
UNP
253
3
5
2
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
VAL
77
A
VAL
56
A
ASP
79
A
ASP
58
A
VAL
141
A
VAL
120
A
TRP
148
A
TRP
127
A
LYS
154
A
LYS
133
A
ARG
160
A
ARG
139
A
ARG
168
A
ARG
147
A
PRO
173
A
PRO
152
A
SER
240
A
SER
219
A
LEU
253
A
LEU
232
A
GLY
229
A
GLY
208
A
SER
237
A
SER
216
A
LEU
193
A
LEU
172
A
VAL
201
A
VAL
180
A
GLU
207
A
GLU
186
A
GLY
213
A
GLY
192
A
MET
178
A
MET
157
A
ASP
181
A
ASP
160
A
THR
217
A
THR
196
A
LYS
220
A
LYS
199
146
H 3