1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Li, Y.
Liew, L.
Li, Q.
Kang, C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
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 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
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
UK
Sci Rep
2045-2322
6
19522
19522
10.1038/srep19522
26776682
Structure of the transmembrane domain of human nicastrin-a component of gamma-secretase
2016
5992.000
Nicastrin
UNP residues 664-709
1
man
polymer
no
no
MAHHHHHHASKELELITLTVGFGILIFSLIVTYCINAKADVLFIAPREPGAVSY
MAHHHHHHASKELELITLTVGFGILIFSLIVTYCINAKADVLFIAPREPGAVSY
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
human
sample
9606
Homo sapiens
562
Escherichia coli
pET29b
vector
repository
Initial release
1
0
2016-04-27
BMRB
Y
PDBJ
2015-09-17
REL
REL
REL
structures with the lowest energy
100
20
1
2D 1H-15N HSQC
3D HNCA
3D HNCACB
3D HN(COCA)CB
3D HNCO
3D 1H-15N NOESY
3D HBHA(CO)NH
0.8
mM
[U-100% 13C; U-100% 15N]
20
mM
100
mM
1
mM
20
6.5
ambient
313
K
simulation annealing was conducted. the structures were then energy minimized.
simulated annealing
1
lowest energy
0.8 mM [U-100% 13C; U-100% 15N] transmembrane domain of human nicastrin-1, 20 mM sodium phosphate-2, 100 mM SDS-3, 1 mM DTT-4, 90% H2O/10% D2O
90% H2O/10% D2O
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
processing
NMRPipe
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
chemical shift assignment
NMRPipe
Delaglio, Grzesiek, Vuister, Zhu, Pfeifer and Bax
structure solution
NMRPipe
Schwieters, Clore
refinement
XPLOR-NIH
700
Bruker
Avance
Bruker Avance
n
1
-7
A
n
2
-6
A
n
3
-5
A
n
4
-4
A
n
5
-3
A
n
6
-2
A
n
7
-1
A
n
8
0
A
ALA
1
n
9
ALA
1
A
SER
2
n
10
SER
2
A
LYS
3
n
11
LYS
3
A
GLU
4
n
12
GLU
4
A
LEU
5
n
13
LEU
5
A
GLU
6
n
14
GLU
6
A
LEU
7
n
15
LEU
7
A
ILE
8
n
16
ILE
8
A
THR
9
n
17
THR
9
A
LEU
10
n
18
LEU
10
A
THR
11
n
19
THR
11
A
VAL
12
n
20
VAL
12
A
GLY
13
n
21
GLY
13
A
PHE
14
n
22
PHE
14
A
GLY
15
n
23
GLY
15
A
ILE
16
n
24
ILE
16
A
LEU
17
n
25
LEU
17
A
ILE
18
n
26
ILE
18
A
PHE
19
n
27
PHE
19
A
SER
20
n
28
SER
20
A
LEU
21
n
29
LEU
21
A
ILE
22
n
30
ILE
22
A
VAL
23
n
31
VAL
23
A
THR
24
n
32
THR
24
A
TYR
25
n
33
TYR
25
A
CYS
26
n
34
CYS
26
A
ILE
27
n
35
ILE
27
A
ASN
28
n
36
ASN
28
A
ALA
29
n
37
ALA
29
A
LYS
30
n
38
LYS
30
A
ALA
31
n
39
ALA
31
A
ASP
32
n
40
ASP
32
A
VAL
33
n
41
VAL
33
A
LEU
34
n
42
LEU
34
A
PHE
35
n
43
PHE
35
A
ILE
36
n
44
ILE
36
A
ALA
37
n
45
ALA
37
A
PRO
38
n
46
PRO
38
A
ARG
39
n
47
ARG
39
A
GLU
40
n
48
GLU
40
A
PRO
41
n
49
PRO
41
A
GLY
42
n
50
GLY
42
A
ALA
43
n
51
ALA
43
A
VAL
44
n
52
VAL
44
A
SER
45
n
53
SER
45
A
TYR
46
n
54
TYR
46
A
author_defined_assembly
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
1
A
MET
-7
A
MET
1
1
Y
1
A
ALA
-6
A
ALA
2
1
Y
1
A
HIS
-5
A
HIS
3
1
Y
1
A
HIS
-4
A
HIS
4
1
Y
1
A
HIS
-3
A
HIS
5
1
Y
1
A
HIS
-2
A
HIS
6
1
Y
1
A
HIS
-1
A
HIS
7
1
Y
1
A
HIS
0
A
HIS
8
1
Y
2
A
MET
-7
A
MET
1
1
Y
2
A
ALA
-6
A
ALA
2
1
Y
2
A
HIS
-5
A
HIS
3
1
Y
2
A
HIS
-4
A
HIS
4
1
Y
2
A
HIS
-3
A
HIS
5
1
Y
2
A
HIS
-2
A
HIS
6
1
Y
2
A
HIS
-1
A
HIS
7
1
Y
2
A
HIS
0
A
HIS
8
1
Y
3
A
MET
-7
A
MET
1
1
Y
3
A
ALA
-6
A
ALA
2
1
Y
3
A
HIS
-5
A
HIS
3
1
Y
3
A
HIS
-4
A
HIS
4
1
Y
3
A
HIS
-3
A
HIS
5
1
Y
3
A
HIS
-2
A
HIS
6
1
Y
3
A
HIS
-1
A
HIS
7
1
Y
3
A
HIS
0
A
HIS
8
1
Y
4
A
MET
-7
A
MET
1
1
Y
4
A
ALA
-6
A
ALA
2
1
Y
4
A
HIS
-5
A
HIS
3
1
Y
4
A
HIS
-4
A
HIS
4
1
Y
4
A
HIS
-3
A
HIS
5
1
Y
4
A
HIS
-2
A
HIS
6
1
Y
4
A
HIS
-1
A
HIS
7
1
Y
4
A
HIS
0
A
HIS
8
1
Y
5
A
MET
-7
A
MET
1
1
Y
5
A
ALA
-6
A
ALA
2
1
Y
5
A
HIS
-5
A
HIS
3
1
Y
5
A
HIS
-4
A
HIS
4
1
Y
5
A
HIS
-3
A
HIS
5
1
Y
5
A
HIS
-2
A
HIS
6
1
Y
5
A
HIS
-1
A
HIS
7
1
Y
5
A
HIS
0
A
HIS
8
1
Y
6
A
MET
-7
A
MET
1
1
Y
6
A
ALA
-6
A
ALA
2
1
Y
6
A
HIS
-5
A
HIS
3
1
Y
6
A
HIS
-4
A
HIS
4
1
Y
6
A
HIS
-3
A
HIS
5
1
Y
6
A
HIS
-2
A
HIS
6
1
Y
6
A
HIS
-1
A
HIS
7
1
Y
6
A
HIS
0
A
HIS
8
1
Y
7
A
MET
-7
A
MET
1
1
Y
7
A
ALA
-6
A
ALA
2
1
Y
7
A
HIS
-5
A
HIS
3
1
Y
7
A
HIS
-4
A
HIS
4
1
Y
7
A
HIS
-3
A
HIS
5
1
Y
7
A
HIS
-2
A
HIS
6
1
Y
7
A
HIS
-1
A
HIS
7
1
Y
7
A
HIS
0
A
HIS
8
1
Y
8
A
MET
-7
A
MET
1
1
Y
8
A
ALA
-6
A
ALA
2
1
Y
8
A
HIS
-5
A
HIS
3
1
Y
8
A
HIS
-4
A
HIS
4
1
Y
8
A
HIS
-3
A
HIS
5
1
Y
8
A
HIS
-2
A
HIS
6
1
Y
8
A
HIS
-1
A
HIS
7
1
Y
8
A
HIS
0
A
HIS
8
1
Y
9
A
MET
-7
A
MET
1
1
Y
9
A
ALA
-6
A
ALA
2
1
Y
9
A
HIS
-5
A
HIS
3
1
Y
9
A
HIS
-4
A
HIS
4
1
Y
9
A
HIS
-3
A
HIS
5
1
Y
9
A
HIS
-2
A
HIS
6
1
Y
9
A
HIS
-1
A
HIS
7
1
Y
9
A
HIS
0
A
HIS
8
1
Y
10
A
MET
-7
A
MET
1
1
Y
10
A
ALA
-6
A
ALA
2
1
Y
10
A
HIS
-5
A
HIS
3
1
Y
10
A
HIS
-4
A
HIS
4
1
Y
10
A
HIS
-3
A
HIS
5
1
Y
10
A
HIS
-2
A
HIS
6
1
Y
10
A
HIS
-1
A
HIS
7
1
Y
10
A
HIS
0
A
HIS
8
1
Y
11
A
MET
-7
A
MET
1
1
Y
11
A
ALA
-6
A
ALA
2
1
Y
11
A
HIS
-5
A
HIS
3
1
Y
11
A
HIS
-4
A
HIS
4
1
Y
11
A
HIS
-3
A
HIS
5
1
Y
11
A
HIS
-2
A
HIS
6
1
Y
11
A
HIS
-1
A
HIS
7
1
Y
11
A
HIS
0
A
HIS
8
1
Y
12
A
MET
-7
A
MET
1
1
Y
12
A
ALA
-6
A
ALA
2
1
Y
12
A
HIS
-5
A
HIS
3
1
Y
12
A
HIS
-4
A
HIS
4
1
Y
12
A
HIS
-3
A
HIS
5
1
Y
12
A
HIS
-2
A
HIS
6
1
Y
12
A
HIS
-1
A
HIS
7
1
Y
12
A
HIS
0
A
HIS
8
1
Y
13
A
MET
-7
A
MET
1
1
Y
13
A
ALA
-6
A
ALA
2
1
Y
13
A
HIS
-5
A
HIS
3
1
Y
13
A
HIS
-4
A
HIS
4
1
Y
13
A
HIS
-3
A
HIS
5
1
Y
13
A
HIS
-2
A
HIS
6
1
Y
13
A
HIS
-1
A
HIS
7
1
Y
13
A
HIS
0
A
HIS
8
1
Y
14
A
MET
-7
A
MET
1
1
Y
14
A
ALA
-6
A
ALA
2
1
Y
14
A
HIS
-5
A
HIS
3
1
Y
14
A
HIS
-4
A
HIS
4
1
Y
14
A
HIS
-3
A
HIS
5
1
Y
14
A
HIS
-2
A
HIS
6
1
Y
14
A
HIS
-1
A
HIS
7
1
Y
14
A
HIS
0
A
HIS
8
1
Y
15
A
MET
-7
A
MET
1
1
Y
15
A
ALA
-6
A
ALA
2
1
Y
15
A
HIS
-5
A
HIS
3
1
Y
15
A
HIS
-4
A
HIS
4
1
Y
15
A
HIS
-3
A
HIS
5
1
Y
15
A
HIS
-2
A
HIS
6
1
Y
15
A
HIS
-1
A
HIS
7
1
Y
15
A
HIS
0
A
HIS
8
1
Y
16
A
MET
-7
A
MET
1
1
Y
16
A
ALA
-6
A
ALA
2
1
Y
16
A
HIS
-5
A
HIS
3
1
Y
16
A
HIS
-4
A
HIS
4
1
Y
16
A
HIS
-3
A
HIS
5
1
Y
16
A
HIS
-2
A
HIS
6
1
Y
16
A
HIS
-1
A
HIS
7
1
Y
16
A
HIS
0
A
HIS
8
1
Y
17
A
MET
-7
A
MET
1
1
Y
17
A
ALA
-6
A
ALA
2
1
Y
17
A
HIS
-5
A
HIS
3
1
Y
17
A
HIS
-4
A
HIS
4
1
Y
17
A
HIS
-3
A
HIS
5
1
Y
17
A
HIS
-2
A
HIS
6
1
Y
17
A
HIS
-1
A
HIS
7
1
Y
17
A
HIS
0
A
HIS
8
1
Y
18
A
MET
-7
A
MET
1
1
Y
18
A
ALA
-6
A
ALA
2
1
Y
18
A
HIS
-5
A
HIS
3
1
Y
18
A
HIS
-4
A
HIS
4
1
Y
18
A
HIS
-3
A
HIS
5
1
Y
18
A
HIS
-2
A
HIS
6
1
Y
18
A
HIS
-1
A
HIS
7
1
Y
18
A
HIS
0
A
HIS
8
1
Y
19
A
MET
-7
A
MET
1
1
Y
19
A
ALA
-6
A
ALA
2
1
Y
19
A
HIS
-5
A
HIS
3
1
Y
19
A
HIS
-4
A
HIS
4
1
Y
19
A
HIS
-3
A
HIS
5
1
Y
19
A
HIS
-2
A
HIS
6
1
Y
19
A
HIS
-1
A
HIS
7
1
Y
19
A
HIS
0
A
HIS
8
1
Y
20
A
MET
-7
A
MET
1
1
Y
20
A
ALA
-6
A
ALA
2
1
Y
20
A
HIS
-5
A
HIS
3
1
Y
20
A
HIS
-4
A
HIS
4
1
Y
20
A
HIS
-3
A
HIS
5
1
Y
20
A
HIS
-2
A
HIS
6
1
Y
20
A
HIS
-1
A
HIS
7
1
Y
20
A
HIS
0
A
HIS
8
1
Y
3
A
A
HG
H
SER
TYR
45
46
1.35
4
A
A
H
H
ALA
SER
1
2
1.32
1
A
ILE
36
1.51
70.89
1
A
ALA
43
48.84
23.45
2
A
SER
2
75.47
-0.24
2
A
ILE
36
36.22
29.53
2
A
ALA
37
-46.05
160.63
2
A
PRO
41
-38.88
139.90
2
A
VAL
44
58.80
154.11
2
A
SER
45
60.10
160.29
3
A
ILE
36
-0.21
70.51
3
A
ALA
37
-40.15
160.23
3
A
PRO
41
-71.85
29.20
3
A
VAL
44
-52.44
100.07
4
A
ILE
36
35.03
64.17
4
A
ALA
37
-42.77
162.14
4
A
PRO
41
-64.73
90.45
5
A
ILE
36
35.71
28.30
5
A
ALA
37
-46.65
160.61
5
A
PRO
41
-66.76
14.37
5
A
VAL
44
40.48
-129.93
6
A
ILE
36
2.70
66.19
6
A
PRO
38
-53.42
171.14
6
A
GLU
40
-44.69
156.83
6
A
PRO
41
-63.10
-83.87
6
A
SER
45
-94.48
57.80
7
A
SER
2
-58.01
-3.95
7
A
PHE
35
-133.96
-157.44
7
A
ALA
37
-43.25
162.73
7
A
PRO
41
-41.24
-16.72
8
A
ILE
36
32.22
64.40
8
A
ALA
37
-42.40
162.42
8
A
ALA
43
-59.26
-7.51
9
A
PHE
35
-133.97
-155.78
9
A
ALA
37
-41.54
159.98
9
A
PRO
41
-68.60
93.82
10
A
ILE
36
-0.97
72.34
10
A
ALA
37
-46.46
161.30
10
A
PRO
41
-68.24
99.91
10
A
ALA
43
-41.20
104.15
10
A
VAL
44
51.52
-87.17
10
A
SER
45
65.95
177.94
11
A
ILE
36
32.91
61.13
11
A
ALA
37
-40.54
161.89
11
A
ALA
43
47.89
-89.50
11
A
SER
45
-154.96
-45.51
12
A
ILE
36
-0.70
72.36
12
A
ALA
37
-39.09
163.00
12
A
PRO
38
-39.73
136.38
12
A
PRO
41
-39.99
94.94
12
A
ALA
43
45.53
20.51
13
A
ILE
36
-1.39
73.29
13
A
ALA
37
-40.94
159.05
13
A
PRO
41
-69.68
23.44
13
A
ALA
43
-66.12
0.86
14
A
PHE
35
-133.43
-157.69
14
A
ALA
37
-38.77
157.57
14
A
GLU
40
-45.27
155.37
14
A
PRO
41
-39.24
-19.72
15
A
SER
2
45.33
21.22
15
A
ILE
36
4.69
67.55
15
A
ALA
37
-37.82
160.44
15
A
PRO
38
-66.16
-176.74
15
A
VAL
44
-68.35
99.85
16
A
PHE
35
-126.53
-159.14
16
A
PRO
38
-69.50
-171.76
16
A
ALA
43
59.19
105.46
16
A
SER
45
-144.70
-27.26
17
A
ILE
36
1.36
65.93
17
A
PRO
38
-39.65
137.46
17
A
PRO
41
-37.68
146.77
17
A
ALA
43
55.55
-109.68
17
A
SER
45
79.19
31.35
18
A
SER
2
-42.28
153.21
18
A
ILE
36
6.58
66.45
18
A
ALA
37
-43.29
161.14
18
A
PRO
38
-39.12
136.56
18
A
PRO
41
-49.85
-165.93
18
A
ALA
43
174.75
17.76
18
A
VAL
44
53.31
88.47
18
A
SER
45
46.13
-172.38
19
A
PHE
35
-105.06
78.58
19
A
ILE
36
36.97
44.21
19
A
ALA
37
-41.04
163.94
19
A
PRO
38
-73.03
-93.95
19
A
PRO
41
-68.29
29.00
20
A
SER
2
-59.17
-9.61
20
A
ILE
36
3.24
67.78
20
A
PRO
38
-62.87
-169.49
20
A
GLU
40
-44.20
155.79
20
A
PRO
41
-41.37
94.72
Nicastrin
lowest energy, model1
Structure of the transmembrane domain of human nicastrin in SDS micelles
1
N
N
A
ALA
1
A
ALA
9
HELX_P
A
PHE
35
A
PHE
43
1
1
35
A
GLU
40
A
GLU
48
HELX_P
A
VAL
44
A
VAL
52
5
2
5
MEMBRANE PROTEIN
Detergent micelles, gamma-secretase, nicastrin, MEMBRANE PROTEIN
NICA_HUMAN
UNP
1
664
Q92542
ASKELELITLTVGFGILIFSLIVTYCINAKADVLFIAPREPGAVSY
664
709
2N7Q
1
46
Q92542
A
1
9
54
1
EXPRESSION TAG
MET
-7
2N7Q
A
Q92542
UNP
1
1
EXPRESSION TAG
ALA
-6
2N7Q
A
Q92542
UNP
2
1
EXPRESSION TAG
HIS
-5
2N7Q
A
Q92542
UNP
3
1
EXPRESSION TAG
HIS
-4
2N7Q
A
Q92542
UNP
4
1
EXPRESSION TAG
HIS
-3
2N7Q
A
Q92542
UNP
5
1
EXPRESSION TAG
HIS
-2
2N7Q
A
Q92542
UNP
6
1
EXPRESSION TAG
HIS
-1
2N7Q
A
Q92542
UNP
7
1
EXPRESSION TAG
HIS
0
2N7Q
A
Q92542
UNP
8