1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
van Pee, K.
Neuhaus, A.
D'Imprima, E.
Mills, D.J.
Kuehlbrandt, W.
Yildiz, O.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.0
90.0
90.0
1.0
1.0
1.0
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
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
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
US
Elife
2050-084X
6
10.7554/eLife.23644
28323617
CryoEM structures of membrane pore and prepore complex reveal cytolytic mechanism of Pneumolysin.
2017
AB INITIO MODEL
A
1-471
5AOD
5LY6
6461
4.5
FSC 0.143 CUT-OFF
POINT
7
1
PHASE FLIPPING AND AMPLITUDE CORRECTION
1
Pneumolysin pore complex
0
RECOMBINANT
ORGANELLE OR CELLULAR COMPONENT
MEGADALTONS
2.2
1313
Streptococcus pneumoniae
511693
Escherichia coli BL21
pET15
PARTICLE
1
1
SINGLE PARTICLE
6
1.02
COUNTING
GATAN K2 SUMMIT (4k x 4k)
300
FIELD EMISSION GUN
FLOOD BEAM
FEI POLARA 300
BRIGHT FIELD
1
5LY6
C42
PARTICLE SELECTION
1
RELION
1.4
IMAGE ACQUISITION
1
RELION
1.4
MASKING
CTF CORRECTION
1
CTFFIND
3
LAYERLINE INDEXING
DIFFRACTION INDEXING
MODEL FITTING
1
Coot
8.4
OTHER
INITIAL EULER ASSIGNMENT
1
RELION
1.4
FINAL EULER ASSIGNMENT
1
RELION
1.4
CLASSIFICATION
1
RELION
1.4
RECONSTRUCTION
1
RELION
1.4
MODEL REFINEMENT
1
Coot
8.4
1
NO
NO
NO
YES
ETHANE
5LY6
52866.066
Pneumolysin
1
man
polymer
Thiol-activated cytolysin
no
no
MANKAVNDFILAMNYDKKKLLTHQGESIENRFIKEGNQLPDEFVVIERKKRSLSTNTSDISVTATNDSRLYPGALLVVDE
TLLENNPTLLAVDRAPMTYSIDLPGLASSDSFLQVEDPSNSSVRGAVNDLLAKWHQDYGQVNNVPARMQYEKITAHSMEQ
LKVKFGSDFEKAANSLDIDFNAVHSGEKQIQIVNFKQIYYTVSVDAVKNPGDVFQDTVTVEDLKQRGISAERPLVYISSV
AYGRQVYLKLETTSKSDEVQAAFEAAILGVKVAPQTQWKQILDNTEVKAVILGGDPSSGARVVTGKVDMVEDLIQEGSRF
TADHPGLPISYTTSFLRDNVVATFQNSTDYVETKVTAYRNGDLLLDHSGAYVAQYYITWDELSYDHQGKEVLTPKAWDRN
GQDLTAHFTTSIPLKGNVRNLSVKIRECTGLAWEWWRTVYEKTDLPLVRKRTISIWGTTLYPQVEDKVEND
MANKAVNDFILAMNYDKKKLLTHQGESIENRFIKEGNQLPDEFVVIERKKRSLSTNTSDISVTATNDSRLYPGALLVVDE
TLLENNPTLLAVDRAPMTYSIDLPGLASSDSFLQVEDPSNSSVRGAVNDLLAKWHQDYGQVNNVPARMQYEKITAHSMEQ
LKVKFGSDFEKAANSLDIDFNAVHSGEKQIQIVNFKQIYYTVSVDAVKNPGDVFQDTVTVEDLKQRGISAERPLVYISSV
AYGRQVYLKLETTSKSDEVQAAFEAAILGVKVAPQTQWKQILDNTEVKAVILGGDPSSGARVVTGKVDMVEDLIQEGSRF
TADHPGLPISYTTSFLRDNVVATFQNSTDYVETKVTAYRNGDLLLDHSGAYVAQYYITWDELSYDHQGKEVLTPKAWDRN
GQDLTAHFTTSIPLKGNVRNLSVKIRECTGLAWEWWRTVYEKTDLPLVRKRTISIWGTTLYPQVEDKVEND
B
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
sample
1
471
ply, SPD_1726
373153
Streptococcus pneumoniae serotype 2 (strain D39 / NCTC 7466)
469008
Escherichia coli BL21(DE3)
Biological sequence
em_image_scans
em_software
em_admin
pdbx_data_processing_status
pdbx_database_proc
pdbx_validate_close_contact
struct_conn
struct_conn_type
atom_sites
cell
repository
Initial release
Data collection
Advisory
Data collection
Derived calculations
Data collection
Other
1
0
2017-04-05
1
1
2017-08-02
1
2
2019-02-20
1
3
2019-10-02
_em_software.name
_em_admin.last_update
_atom_sites.fract_transf_matrix[1][1]
_atom_sites.fract_transf_matrix[2][2]
_atom_sites.fract_transf_matrix[3][3]
_cell.length_a
_cell.length_b
_cell.length_c
Germany
Max Planck Society
Biophysics/Structural Biology
CryoEM structure of the membrane pore complex of Pneumolysin at 4.5A
N
PDBE
Y
PDBE
2016-09-24
REL
MET
1
n
1
MET
1
B
ALA
2
n
2
ALA
2
B
ASN
3
n
3
ASN
3
B
LYS
4
n
4
LYS
4
B
ALA
5
n
5
ALA
5
B
VAL
6
n
6
VAL
6
B
ASN
7
n
7
ASN
7
B
ASP
8
n
8
ASP
8
B
PHE
9
n
9
PHE
9
B
ILE
10
n
10
ILE
10
B
LEU
11
n
11
LEU
11
B
ALA
12
n
12
ALA
12
B
MET
13
n
13
MET
13
B
ASN
14
n
14
ASN
14
B
TYR
15
n
15
TYR
15
B
ASP
16
n
16
ASP
16
B
LYS
17
n
17
LYS
17
B
LYS
18
n
18
LYS
18
B
LYS
19
n
19
LYS
19
B
LEU
20
n
20
LEU
20
B
LEU
21
n
21
LEU
21
B
THR
22
n
22
THR
22
B
HIS
23
n
23
HIS
23
B
GLN
24
n
24
GLN
24
B
GLY
25
n
25
GLY
25
B
GLU
26
n
26
GLU
26
B
SER
27
n
27
SER
27
B
ILE
28
n
28
ILE
28
B
GLU
29
n
29
GLU
29
B
ASN
30
n
30
ASN
30
B
ARG
31
n
31
ARG
31
B
PHE
32
n
32
PHE
32
B
ILE
33
n
33
ILE
33
B
LYS
34
n
34
LYS
34
B
GLU
35
n
35
GLU
35
B
GLY
36
n
36
GLY
36
B
ASN
37
n
37
ASN
37
B
GLN
38
n
38
GLN
38
B
LEU
39
n
39
LEU
39
B
PRO
40
n
40
PRO
40
B
ASP
41
n
41
ASP
41
B
GLU
42
n
42
GLU
42
B
PHE
43
n
43
PHE
43
B
VAL
44
n
44
VAL
44
B
VAL
45
n
45
VAL
45
B
ILE
46
n
46
ILE
46
B
GLU
47
n
47
GLU
47
B
ARG
48
n
48
ARG
48
B
LYS
49
n
49
LYS
49
B
LYS
50
n
50
LYS
50
B
ARG
51
n
51
ARG
51
B
SER
52
n
52
SER
52
B
LEU
53
n
53
LEU
53
B
SER
54
n
54
SER
54
B
THR
55
n
55
THR
55
B
ASN
56
n
56
ASN
56
B
THR
57
n
57
THR
57
B
SER
58
n
58
SER
58
B
ASP
59
n
59
ASP
59
B
ILE
60
n
60
ILE
60
B
SER
61
n
61
SER
61
B
VAL
62
n
62
VAL
62
B
THR
63
n
63
THR
63
B
ALA
64
n
64
ALA
64
B
THR
65
n
65
THR
65
B
ASN
66
n
66
ASN
66
B
ASP
67
n
67
ASP
67
B
SER
68
n
68
SER
68
B
ARG
69
n
69
ARG
69
B
LEU
70
n
70
LEU
70
B
TYR
71
n
71
TYR
71
B
PRO
72
n
72
PRO
72
B
GLY
73
n
73
GLY
73
B
ALA
74
n
74
ALA
74
B
LEU
75
n
75
LEU
75
B
LEU
76
n
76
LEU
76
B
VAL
77
n
77
VAL
77
B
VAL
78
n
78
VAL
78
B
ASP
79
n
79
ASP
79
B
GLU
80
n
80
GLU
80
B
THR
81
n
81
THR
81
B
LEU
82
n
82
LEU
82
B
LEU
83
n
83
LEU
83
B
GLU
84
n
84
GLU
84
B
ASN
85
n
85
ASN
85
B
ASN
86
n
86
ASN
86
B
PRO
87
n
87
PRO
87
B
THR
88
n
88
THR
88
B
LEU
89
n
89
LEU
89
B
LEU
90
n
90
LEU
90
B
ALA
91
n
91
ALA
91
B
VAL
92
n
92
VAL
92
B
ASP
93
n
93
ASP
93
B
ARG
94
n
94
ARG
94
B
ALA
95
n
95
ALA
95
B
PRO
96
n
96
PRO
96
B
MET
97
n
97
MET
97
B
THR
98
n
98
THR
98
B
TYR
99
n
99
TYR
99
B
SER
100
n
100
SER
100
B
ILE
101
n
101
ILE
101
B
ASP
102
n
102
ASP
102
B
LEU
103
n
103
LEU
103
B
PRO
104
n
104
PRO
104
B
GLY
105
n
105
GLY
105
B
LEU
106
n
106
LEU
106
B
ALA
107
n
107
ALA
107
B
SER
108
n
108
SER
108
B
SER
109
n
109
SER
109
B
ASP
110
n
110
ASP
110
B
SER
111
n
111
SER
111
B
PHE
112
n
112
PHE
112
B
LEU
113
n
113
LEU
113
B
GLN
114
n
114
GLN
114
B
VAL
115
n
115
VAL
115
B
GLU
116
n
116
GLU
116
B
ASP
117
n
117
ASP
117
B
PRO
118
n
118
PRO
118
B
SER
119
n
119
SER
119
B
ASN
120
n
120
ASN
120
B
SER
121
n
121
SER
121
B
SER
122
n
122
SER
122
B
VAL
123
n
123
VAL
123
B
ARG
124
n
124
ARG
124
B
GLY
125
n
125
GLY
125
B
ALA
126
n
126
ALA
126
B
VAL
127
n
127
VAL
127
B
ASN
128
n
128
ASN
128
B
ASP
129
n
129
ASP
129
B
LEU
130
n
130
LEU
130
B
LEU
131
n
131
LEU
131
B
ALA
132
n
132
ALA
132
B
LYS
133
n
133
LYS
133
B
TRP
134
n
134
TRP
134
B
HIS
135
n
135
HIS
135
B
GLN
136
n
136
GLN
136
B
ASP
137
n
137
ASP
137
B
TYR
138
n
138
TYR
138
B
GLY
139
n
139
GLY
139
B
GLN
140
n
140
GLN
140
B
VAL
141
n
141
VAL
141
B
ASN
142
n
142
ASN
142
B
ASN
143
n
143
ASN
143
B
VAL
144
n
144
VAL
144
B
PRO
145
n
145
PRO
145
B
ALA
146
n
146
ALA
146
B
ARG
147
n
147
ARG
147
B
MET
148
n
148
MET
148
B
GLN
149
n
149
GLN
149
B
TYR
150
n
150
TYR
150
B
GLU
151
n
151
GLU
151
B
LYS
152
n
152
LYS
152
B
ILE
153
n
153
ILE
153
B
THR
154
n
154
THR
154
B
ALA
155
n
155
ALA
155
B
HIS
156
n
156
HIS
156
B
SER
157
n
157
SER
157
B
MET
158
n
158
MET
158
B
GLU
159
n
159
GLU
159
B
GLN
160
n
160
GLN
160
B
LEU
161
n
161
LEU
161
B
LYS
162
n
162
LYS
162
B
VAL
163
n
163
VAL
163
B
LYS
164
n
164
LYS
164
B
PHE
165
n
165
PHE
165
B
GLY
166
n
166
GLY
166
B
SER
167
n
167
SER
167
B
ASP
168
n
168
ASP
168
B
PHE
169
n
169
PHE
169
B
GLU
170
n
170
GLU
170
B
LYS
171
n
171
LYS
171
B
ALA
172
n
172
ALA
172
B
ALA
173
n
173
ALA
173
B
ASN
174
n
174
ASN
174
B
SER
175
n
175
SER
175
B
LEU
176
n
176
LEU
176
B
ASP
177
n
177
ASP
177
B
ILE
178
n
178
ILE
178
B
ASP
179
n
179
ASP
179
B
PHE
180
n
180
PHE
180
B
ASN
181
n
181
ASN
181
B
ALA
182
n
182
ALA
182
B
VAL
183
n
183
VAL
183
B
HIS
184
n
184
HIS
184
B
SER
185
n
185
SER
185
B
GLY
186
n
186
GLY
186
B
GLU
187
n
187
GLU
187
B
LYS
188
n
188
LYS
188
B
GLN
189
n
189
GLN
189
B
ILE
190
n
190
ILE
190
B
GLN
191
n
191
GLN
191
B
ILE
192
n
192
ILE
192
B
VAL
193
n
193
VAL
193
B
ASN
194
n
194
ASN
194
B
PHE
195
n
195
PHE
195
B
LYS
196
n
196
LYS
196
B
GLN
197
n
197
GLN
197
B
ILE
198
n
198
ILE
198
B
TYR
199
n
199
TYR
199
B
TYR
200
n
200
TYR
200
B
THR
201
n
201
THR
201
B
VAL
202
n
202
VAL
202
B
SER
203
n
203
SER
203
B
VAL
204
n
204
VAL
204
B
ASP
205
n
205
ASP
205
B
ALA
206
n
206
ALA
206
B
VAL
207
n
207
VAL
207
B
LYS
208
n
208
LYS
208
B
ASN
209
n
209
ASN
209
B
PRO
210
n
210
PRO
210
B
GLY
211
n
211
GLY
211
B
ASP
212
n
212
ASP
212
B
VAL
213
n
213
VAL
213
B
PHE
214
n
214
PHE
214
B
GLN
215
n
215
GLN
215
B
ASP
216
n
216
ASP
216
B
THR
217
n
217
THR
217
B
VAL
218
n
218
VAL
218
B
THR
219
n
219
THR
219
B
VAL
220
n
220
VAL
220
B
GLU
221
n
221
GLU
221
B
ASP
222
n
222
ASP
222
B
LEU
223
n
223
LEU
223
B
LYS
224
n
224
LYS
224
B
GLN
225
n
225
GLN
225
B
ARG
226
n
226
ARG
226
B
GLY
227
n
227
GLY
227
B
ILE
228
n
228
ILE
228
B
SER
229
n
229
SER
229
B
ALA
230
n
230
ALA
230
B
GLU
231
n
231
GLU
231
B
ARG
232
n
232
ARG
232
B
PRO
233
n
233
PRO
233
B
LEU
234
n
234
LEU
234
B
VAL
235
n
235
VAL
235
B
TYR
236
n
236
TYR
236
B
ILE
237
n
237
ILE
237
B
SER
238
n
238
SER
238
B
SER
239
n
239
SER
239
B
VAL
240
n
240
VAL
240
B
ALA
241
n
241
ALA
241
B
TYR
242
n
242
TYR
242
B
GLY
243
n
243
GLY
243
B
ARG
244
n
244
ARG
244
B
GLN
245
n
245
GLN
245
B
VAL
246
n
246
VAL
246
B
TYR
247
n
247
TYR
247
B
LEU
248
n
248
LEU
248
B
LYS
249
n
249
LYS
249
B
LEU
250
n
250
LEU
250
B
GLU
251
n
251
GLU
251
B
THR
252
n
252
THR
252
B
THR
253
n
253
THR
253
B
SER
254
n
254
SER
254
B
LYS
255
n
255
LYS
255
B
SER
256
n
256
SER
256
B
ASP
257
n
257
ASP
257
B
GLU
258
n
258
GLU
258
B
VAL
259
n
259
VAL
259
B
GLN
260
n
260
GLN
260
B
ALA
261
n
261
ALA
261
B
ALA
262
n
262
ALA
262
B
PHE
263
n
263
PHE
263
B
GLU
264
n
264
GLU
264
B
ALA
265
n
265
ALA
265
B
ALA
266
n
266
ALA
266
B
ILE
267
n
267
ILE
267
B
LEU
268
n
268
LEU
268
B
GLY
269
n
269
GLY
269
B
VAL
270
n
270
VAL
270
B
LYS
271
n
271
LYS
271
B
VAL
272
n
272
VAL
272
B
ALA
273
n
273
ALA
273
B
PRO
274
n
274
PRO
274
B
GLN
275
n
275
GLN
275
B
THR
276
n
276
THR
276
B
GLN
277
n
277
GLN
277
B
TRP
278
n
278
TRP
278
B
LYS
279
n
279
LYS
279
B
GLN
280
n
280
GLN
280
B
ILE
281
n
281
ILE
281
B
LEU
282
n
282
LEU
282
B
ASP
283
n
283
ASP
283
B
ASN
284
n
284
ASN
284
B
THR
285
n
285
THR
285
B
GLU
286
n
286
GLU
286
B
VAL
287
n
287
VAL
287
B
LYS
288
n
288
LYS
288
B
ALA
289
n
289
ALA
289
B
VAL
290
n
290
VAL
290
B
ILE
291
n
291
ILE
291
B
LEU
292
n
292
LEU
292
B
GLY
293
n
293
GLY
293
B
GLY
294
n
294
GLY
294
B
ASP
295
n
295
ASP
295
B
PRO
296
n
296
PRO
296
B
SER
297
n
297
SER
297
B
SER
298
n
298
SER
298
B
GLY
299
n
299
GLY
299
B
ALA
300
n
300
ALA
300
B
ARG
301
n
301
ARG
301
B
VAL
302
n
302
VAL
302
B
VAL
303
n
303
VAL
303
B
THR
304
n
304
THR
304
B
GLY
305
n
305
GLY
305
B
LYS
306
n
306
LYS
306
B
VAL
307
n
307
VAL
307
B
ASP
308
n
308
ASP
308
B
MET
309
n
309
MET
309
B
VAL
310
n
310
VAL
310
B
GLU
311
n
311
GLU
311
B
ASP
312
n
312
ASP
312
B
LEU
313
n
313
LEU
313
B
ILE
314
n
314
ILE
314
B
GLN
315
n
315
GLN
315
B
GLU
316
n
316
GLU
316
B
GLY
317
n
317
GLY
317
B
SER
318
n
318
SER
318
B
ARG
319
n
319
ARG
319
B
PHE
320
n
320
PHE
320
B
THR
321
n
321
THR
321
B
ALA
322
n
322
ALA
322
B
ASP
323
n
323
ASP
323
B
HIS
324
n
324
HIS
324
B
PRO
325
n
325
PRO
325
B
GLY
326
n
326
GLY
326
B
LEU
327
n
327
LEU
327
B
PRO
328
n
328
PRO
328
B
ILE
329
n
329
ILE
329
B
SER
330
n
330
SER
330
B
TYR
331
n
331
TYR
331
B
THR
332
n
332
THR
332
B
THR
333
n
333
THR
333
B
SER
334
n
334
SER
334
B
PHE
335
n
335
PHE
335
B
LEU
336
n
336
LEU
336
B
ARG
337
n
337
ARG
337
B
ASP
338
n
338
ASP
338
B
ASN
339
n
339
ASN
339
B
VAL
340
n
340
VAL
340
B
VAL
341
n
341
VAL
341
B
ALA
342
n
342
ALA
342
B
THR
343
n
343
THR
343
B
PHE
344
n
344
PHE
344
B
GLN
345
n
345
GLN
345
B
ASN
346
n
346
ASN
346
B
SER
347
n
347
SER
347
B
THR
348
n
348
THR
348
B
ASP
349
n
349
ASP
349
B
TYR
350
n
350
TYR
350
B
VAL
351
n
351
VAL
351
B
GLU
352
n
352
GLU
352
B
THR
353
n
353
THR
353
B
LYS
354
n
354
LYS
354
B
VAL
355
n
355
VAL
355
B
THR
356
n
356
THR
356
B
ALA
357
n
357
ALA
357
B
TYR
358
n
358
TYR
358
B
ARG
359
n
359
ARG
359
B
ASN
360
n
360
ASN
360
B
GLY
361
n
361
GLY
361
B
ASP
362
n
362
ASP
362
B
LEU
363
n
363
LEU
363
B
LEU
364
n
364
LEU
364
B
LEU
365
n
365
LEU
365
B
ASP
366
n
366
ASP
366
B
HIS
367
n
367
HIS
367
B
SER
368
n
368
SER
368
B
GLY
369
n
369
GLY
369
B
ALA
370
n
370
ALA
370
B
TYR
371
n
371
TYR
371
B
VAL
372
n
372
VAL
372
B
ALA
373
n
373
ALA
373
B
GLN
374
n
374
GLN
374
B
TYR
375
n
375
TYR
375
B
TYR
376
n
376
TYR
376
B
ILE
377
n
377
ILE
377
B
THR
378
n
378
THR
378
B
TRP
379
n
379
TRP
379
B
ASP
380
n
380
ASP
380
B
GLU
381
n
381
GLU
381
B
LEU
382
n
382
LEU
382
B
SER
383
n
383
SER
383
B
TYR
384
n
384
TYR
384
B
ASP
385
n
385
ASP
385
B
HIS
386
n
386
HIS
386
B
GLN
387
n
387
GLN
387
B
GLY
388
n
388
GLY
388
B
LYS
389
n
389
LYS
389
B
GLU
390
n
390
GLU
390
B
VAL
391
n
391
VAL
391
B
LEU
392
n
392
LEU
392
B
THR
393
n
393
THR
393
B
PRO
394
n
394
PRO
394
B
LYS
395
n
395
LYS
395
B
ALA
396
n
396
ALA
396
B
TRP
397
n
397
TRP
397
B
ASP
398
n
398
ASP
398
B
ARG
399
n
399
ARG
399
B
ASN
400
n
400
ASN
400
B
GLY
401
n
401
GLY
401
B
GLN
402
n
402
GLN
402
B
ASP
403
n
403
ASP
403
B
LEU
404
n
404
LEU
404
B
THR
405
n
405
THR
405
B
ALA
406
n
406
ALA
406
B
HIS
407
n
407
HIS
407
B
PHE
408
n
408
PHE
408
B
THR
409
n
409
THR
409
B
THR
410
n
410
THR
410
B
SER
411
n
411
SER
411
B
ILE
412
n
412
ILE
412
B
PRO
413
n
413
PRO
413
B
LEU
414
n
414
LEU
414
B
LYS
415
n
415
LYS
415
B
GLY
416
n
416
GLY
416
B
ASN
417
n
417
ASN
417
B
VAL
418
n
418
VAL
418
B
ARG
419
n
419
ARG
419
B
ASN
420
n
420
ASN
420
B
LEU
421
n
421
LEU
421
B
SER
422
n
422
SER
422
B
VAL
423
n
423
VAL
423
B
LYS
424
n
424
LYS
424
B
ILE
425
n
425
ILE
425
B
ARG
426
n
426
ARG
426
B
GLU
427
n
427
GLU
427
B
CYS
428
n
428
CYS
428
B
THR
429
n
429
THR
429
B
GLY
430
n
430
GLY
430
B
LEU
431
n
431
LEU
431
B
ALA
432
n
432
ALA
432
B
TRP
433
n
433
TRP
433
B
GLU
434
n
434
GLU
434
B
TRP
435
n
435
TRP
435
B
TRP
436
n
436
TRP
436
B
ARG
437
n
437
ARG
437
B
THR
438
n
438
THR
438
B
VAL
439
n
439
VAL
439
B
TYR
440
n
440
TYR
440
B
GLU
441
n
441
GLU
441
B
LYS
442
n
442
LYS
442
B
THR
443
n
443
THR
443
B
ASP
444
n
444
ASP
444
B
LEU
445
n
445
LEU
445
B
PRO
446
n
446
PRO
446
B
LEU
447
n
447
LEU
447
B
VAL
448
n
448
VAL
448
B
ARG
449
n
449
ARG
449
B
LYS
450
n
450
LYS
450
B
ARG
451
n
451
ARG
451
B
THR
452
n
452
THR
452
B
ILE
453
n
453
ILE
453
B
SER
454
n
454
SER
454
B
ILE
455
n
455
ILE
455
B
TRP
456
n
456
TRP
456
B
GLY
457
n
457
GLY
457
B
THR
458
n
458
THR
458
B
THR
459
n
459
THR
459
B
LEU
460
n
460
LEU
460
B
TYR
461
n
461
TYR
461
B
PRO
462
n
462
PRO
462
B
GLN
463
n
463
GLN
463
B
VAL
464
n
464
VAL
464
B
GLU
465
n
465
GLU
465
B
ASP
466
n
466
ASP
466
B
LYS
467
n
467
LYS
467
B
VAL
468
n
468
VAL
468
B
GLU
469
n
469
GLU
469
B
ASN
470
n
470
ASN
470
B
ASP
471
n
471
ASP
471
B
software_defined_assembly
PISA
1
monomeric
0
0
29420
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
B
O
GLU
29
A
O
GLU
29
B
N
ILE
46
A
N
ILE
46
B
O
PHE
43
A
O
PHE
43
B
N
ALA
357
A
N
ALA
357
B
O
SER
100
A
O
SER
100
B
N
SER
203
A
N
SER
203
B
O
ARG
147
A
O
ARG
147
B
N
ILE
198
A
N
ILE
198
B
O
ASN
181
A
O
ASN
181
B
N
GLN
260
A
N
GLN
260
B
O
LYS
249
A
O
LYS
249
B
N
LYS
288
A
N
LYS
288
B
O
ILE
153
A
O
ILE
153
B
N
ILE
192
A
N
ILE
192
B
O
TYR
236
A
O
TYR
236
B
N
SER
334
A
N
SER
334
B
O
TYR
331
A
O
TYR
331
B
N
GLN
345
A
N
GLN
345
B
O
ALA
261
A
O
ALA
261
B
N
THR
276
A
N
THR
276
B
O
PHE
408
A
O
PHE
408
B
N
HIS
367
A
N
HIS
367
B
O
ASP
362
A
O
ASP
362
B
N
ARG
451
A
N
ARG
451
B
O
LYS
450
A
O
LYS
450
B
N
GLU
469
A
N
GLU
469
B
O
VAL
372
A
O
VAL
372
B
N
CYS
428
A
N
CYS
428
B
O
SER
383
A
O
SER
383
B
N
VAL
391
A
N
VAL
391
B
O
TYR
440
A
O
TYR
440
B
N
ILE
425
A
N
ILE
425
B
O
ARG
419
A
O
ARG
419
B
N
ASP
380
A
N
ASP
380
1
B
B
CG1
CD
VAL
PRO
78
233
1.53
1
B
B
OD2
ND1
ASP
HIS
295
324
1.81
1
B
B
CG2
CD1
VAL
LEU
302
313
1.85
1
B
B
N
O
LEU
VAL
76
235
1.88
1
B
B
CG1
CG
VAL
PRO
78
233
1.89
1
B
B
O
N
TYR
SER
236
334
2.02
1
B
B
OH
CD1
TYR
ILE
371
455
2.07
1
B
B
N
O
TYR
SER
236
334
2.08
1
B
B
O
CB
ALA
TYR
74
236
2.09
1
B
B
CG2
CE1
VAL
PHE
235
335
2.10
1
B
B
CB
CA
ARG
GLY
244
293
2.11
1
B
B
O
OG1
VAL
THR
62
65
2.11
1
B
B
O
OG1
ILE
THR
60
63
2.11
1
B
B
CB
NH2
PRO
ARG
233
337
2.12
1
B
B
OH
NE
TYR
ARG
199
244
2.12
1
B
B
CE1
CB
HIS
ALA
135
322
2.16
1
B
B
CB
CZ
PRO
ARG
233
337
2.18
1
B
B
OG1
CB
THR
PRO
81
87
2.18
1
B
B
O
N
LEU
HIS
161
184
2.18
1
B
B
O
OG
SER
SER
58
61
2.18
1
B
B
OG1
CA
THR
PRO
81
87
2.19
1
-30.61
2.10
128.40
97.79
B
B
B
C
N
CD
LEU
PRO
PRO
39
40
40
Y
1
-11.32
1.60
122.70
111.38
B
B
B
O
C
N
THR
THR
SER
57
57
58
Y
1
-25.31
2.10
128.40
103.09
B
B
B
C
N
CD
TYR
PRO
PRO
71
72
72
Y
1
-13.83
2.10
128.40
114.57
B
B
B
C
N
CD
ASN
PRO
PRO
86
87
87
Y
1
-28.73
2.10
128.40
99.67
B
B
B
C
N
CD
ASP
PRO
PRO
117
118
118
Y
1
-14.01
2.10
128.40
114.39
B
B
B
C
N
CD
ASN
PRO
PRO
209
210
210
Y
1
-26.20
2.10
128.40
102.20
B
B
B
C
N
CD
ALA
PRO
PRO
273
274
274
Y
1
-19.61
2.10
128.40
108.79
B
B
B
C
N
CD
ASP
PRO
PRO
295
296
296
Y
1
-13.54
2.10
128.40
114.86
B
B
B
C
N
CD
LEU
PRO
PRO
445
446
446
Y
1
B
B
C
N
THR
SER
57
58
0.261
0.023
1.336
1.597
Y
1
B
HIS
23
-115.79
77.00
1
B
GLU
26
-107.08
-145.68
1
B
SER
27
-89.35
-94.71
1
B
ILE
33
-161.23
116.70
1
B
GLN
38
-160.02
-23.94
1
B
LEU
39
-91.00
-101.31
1
B
ASP
41
-160.29
113.66
1
B
SER
52
-160.06
-68.53
1
B
SER
54
-71.93
-82.04
1
B
SER
68
-109.29
63.49
1
B
ARG
69
-99.61
38.74
1
B
LEU
75
-152.06
83.21
1
B
ASP
79
-138.72
-73.06
1
B
GLU
80
-138.65
-43.10
1
B
ASN
86
-177.51
83.71
1
B
PRO
87
-111.80
-165.46
1
B
LEU
89
-109.99
41.28
1
B
LEU
103
-142.01
-150.73
1
B
LEU
113
-127.96
-136.64
1
B
GLU
116
-93.00
-144.27
1
B
ASN
120
-153.93
40.52
1
B
GLN
136
-72.85
-70.76
1
B
GLN
140
-150.54
-99.76
1
B
VAL
141
49.80
-90.59
1
B
ALA
172
-75.20
37.11
1
B
ALA
173
-159.25
-63.93
1
B
TYR
199
-114.09
-70.13
1
B
ALA
206
-22.62
151.69
1
B
ASN
209
-138.36
-152.27
1
B
GLN
215
-92.51
-154.94
1
B
ARG
226
-66.60
-74.83
1
B
SER
229
-104.88
-150.77
1
B
SER
238
-87.76
-100.07
1
B
GLN
245
-160.21
110.61
1
B
ALA
266
-161.56
62.14
1
B
LEU
268
-67.93
92.78
1
B
PRO
296
-137.24
-83.95
1
B
LYS
306
-131.83
-99.75
1
B
VAL
307
-131.67
-41.25
1
B
ASP
308
-97.84
57.43
1
B
MET
309
-99.87
-64.10
1
B
ILE
314
-107.90
45.39
1
B
GLN
315
-158.74
-25.94
1
B
THR
321
-143.28
-69.64
1
B
ALA
322
-146.44
-22.59
1
B
ILE
329
-118.41
-79.60
1
B
ARG
337
-153.61
-47.35
1
B
ASP
338
-143.09
16.59
1
B
VAL
340
-141.43
-63.82
1
B
VAL
341
-54.72
105.20
1
B
ASN
346
-109.41
-145.59
1
B
TYR
376
-117.94
72.84
1
B
LEU
382
-67.22
-166.95
1
B
SER
383
168.59
144.52
1
B
GLN
387
-60.65
-71.46
1
B
ARG
399
-108.07
68.83
1
B
GLN
402
176.36
153.67
1
B
THR
410
-162.45
-163.44
1
B
SER
411
174.51
127.91
1
B
LEU
414
-69.62
-154.02
1
B
LYS
415
-177.78
87.61
1
B
ARG
419
176.70
125.28
1
B
ASN
420
75.83
144.45
1
B
LEU
421
-160.13
105.47
1
B
LEU
431
49.93
-134.51
1
B
ALA
432
-146.99
-28.66
1
B
GLU
434
-100.51
-168.95
1
B
TRP
435
-149.01
-44.89
1
B
VAL
439
-81.64
-79.88
1
B
LEU
447
-61.33
94.13
1
B
THR
458
-106.50
-150.23
1
B
LEU
460
-132.68
-53.03
1
B
GLN
463
-101.25
54.80
N
Pneumolysin
CryoEM structure of the membrane pore complex of Pneumolysin at 4.5A
1
N
N
B
ALA
2
A
ALA
2
HELX_P
B
ALA
12
A
ALA
12
1
1
11
B
LYS
17
A
LYS
17
HELX_P
B
LEU
21
A
LEU
21
1
2
5
B
ASP
59
A
ASP
59
HELX_P
B
ASP
67
A
ASP
67
1
3
9
B
SER
122
A
SER
122
HELX_P
B
ASP
137
A
ASP
137
1
4
16
B
ASP
222
A
ASP
222
HELX_P
B
GLY
227
A
GLY
227
1
5
6
B
SER
297
A
SER
297
HELX_P
B
THR
304
A
THR
304
1
6
8
B
VAL
310
A
VAL
310
HELX_P
B
LEU
313
A
LEU
313
1
7
4
TOXIN
Bacterial toxins, pore complex, cryoEM structure, cholesterol-dependent cytolysin, Pneumolysin, membrane pore, TOXIN
B
ALA
406
A
ALA
406
1
B
HIS
407
A
HIS
407
0.00
TACY_STRP2
UNP
1
1
Q04IN8
MANKAVNDFILAMNYDKKKLLTHQGESIENRFIKEGNQLPDEFVVIERKKRSLSTNTSDISVTATNDSRLYPGALLVVDE
TLLENNPTLLAVDRAPMTYSIDLPGLASSDSFLQVEDPSNSSVRGAVNDLLAKWHQDYGQVNNVPARMQYEKITAHSMEQ
LKVKFGSDFEKTGNSLDIDFNSVHSGEKQIQIVNFKQIYYTVSVDAVKNPGDVFQDTVTVEDLKQRGISAERPLVYISSV
AYGRQVYLKLETTSKSDEVEAAFEALIKGVKVAPQTEWKQILDNTEVKAVILGGDPSSGARVVTGKVDMVEDLIQEGSRF
TADHPGLPISYTTSFLRDNVVATFQNSTDYVETKVTAYRNGDLLLDHSGAYVAQYYITWDELSYDHQGKEVLTPKAWDRN
GQDLTAHFTTSIPLKGNVRNLSVKIRECTGLAWEWWRTVYEKTDLPLVRKRTISIWGTTLYPQVEDKVEND
1
471
5LY6
1
471
Q04IN8
B
1
1
471
1
THR
conflict
ALA
172
5LY6
B
Q04IN8
UNP
172
172
1
GLY
conflict
ALA
173
5LY6
B
Q04IN8
UNP
173
173
1
SER
conflict
ALA
182
5LY6
B
Q04IN8
UNP
182
182
1
GLU
conflict
GLN
260
5LY6
B
Q04IN8
UNP
260
260
1
LEU
conflict
ALA
266
5LY6
B
Q04IN8
UNP
266
266
1
LYS
conflict
LEU
268
5LY6
B
Q04IN8
UNP
268
268
1
GLU
conflict
GLN
277
5LY6
B
Q04IN8
UNP
277
277
3
2
4
2
3
2
4
2
2
3
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
B
ILE
28
A
ILE
28
B
ARG
31
A
ARG
31
B
PHE
43
A
PHE
43
B
ARG
48
A
ARG
48
B
GLU
352
A
GLU
352
B
ALA
357
A
ALA
357
B
TYR
99
A
TYR
99
B
ILE
101
A
ILE
101
B
VAL
202
A
VAL
202
B
VAL
204
A
VAL
204
B
ARG
147
A
ARG
147
B
GLN
149
A
GLN
149
B
PHE
180
A
PHE
180
B
ILE
198
A
ILE
198
B
GLY
243
A
GLY
243
B
ALA
261
A
ALA
261
B
ILE
281
A
ILE
281
B
LYS
288
A
LYS
288
B
LYS
152
A
LYS
152
B
PHE
165
A
PHE
165
B
PHE
180
A
PHE
180
B
VAL
193
A
VAL
193
B
VAL
235
A
VAL
235
B
ILE
237
A
ILE
237
B
TYR
331
A
TYR
331
B
PHE
335
A
PHE
335
B
ALA
342
A
ALA
342
B
GLN
345
A
GLN
345
B
ALA
261
A
ALA
261
B
GLU
264
A
GLU
264
B
ALA
273
A
ALA
273
B
THR
276
A
THR
276
B
PHE
408
A
PHE
408
B
PRO
413
A
PRO
413
B
ASP
362
A
ASP
362
B
GLY
369
A
GLY
369
B
LYS
450
A
LYS
450
B
GLY
457
A
GLY
457
B
GLN
463
A
GLN
463
B
GLU
469
A
GLU
469
B
VAL
372
A
VAL
372
B
GLN
374
A
GLN
374
B
ARG
426
A
ARG
426
B
CYS
428
A
CYS
428
B
LEU
382
A
LEU
382
B
TYR
384
A
TYR
384
B
GLU
390
A
GLU
390
B
LEU
392
A
LEU
392
B
TYR
440
A
TYR
440
B
LYS
442
A
LYS
442
B
ARG
419
A
ARG
419
B
ILE
425
A
ILE
425
B
ILE
377
A
ILE
377
B
ASP
380
A
ASP
380
1
P 1