1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Barrientos, L.G.
Louis, J.M.
Botos, I.
Mori, T.
Han, Z.
O'Keefe, B.R.
Boyd, M.R.
Wlodawer, A.
Gronenborn, A.M.
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 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
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
UK
Structure
STRUE6
2005
0969-2126
10
673
686
10.1016/S0969-2126(02)00758-X
12015150
The domain-swapped dimer of cyanovirin-N is in a metastable folded state: reconciliation of X-ray and NMR structures.
2002
10.2210/pdb1l5e/pdb
pdb_00001l5e
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
11022.090
Cyanovirin-N
2
man
polymer
CV-N
no
no
LGKFSQTCYNSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKWQPSNFIETCRNTQLAGSSELAAECKTRAQQF
VSTKINLDDHIANIDGTLKYE
LGKFSQTCYNSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKWQPSNFIETCRNTQLAGSSELAAECKTRAQQF
VSTKINLDDHIANIDGTLKYE
A,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
Nostoc
Escherichia
Escherichia coli
sample
45916
Nostoc ellipsosporum
511693
Escherichia coli BL21
BL21
plasmid
pET
database_2
pdbx_struct_assembly
pdbx_struct_oper_list
repository
Initial release
Version format compliance
Version format compliance
Database references
Derived calculations
1
0
2002-06-05
1
1
2008-04-28
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
SOLUTION NMR STRUCTURE OF CYANOVIRIN-N, RESTRAINED REGULARIZED MEAN COORDINATES
X-RAY STRUCTURE OF CYANOVIRIN-N; DOMAIN-SWAPPED DIMER
DOMAIN-SWAPPED CYANOVIRIN-N DIMER
RCSB
Y
RCSB
2002-03-06
REL
Residual dipolar couplings were measured in the presence of a colloidal phage solution of 11.5 mg/ml Pf1.
1
2D IPAP [15N-1H]-HSQC
6.0
1
atm
293
K
The coordinates of the individual domains of the domain swapped dimer CV-N were taken directly from the X-Ray coordinates, 3EZM and 1L5B. The only protons added are the HNE1 of W(49/150) and all the backbone amide protons (HN), since domain-domain orientation was based only on HN/HNE1 residual dipolar couplings.
The starting coordinates were those of two pseudo-monomer units (AB' and A'B)
extracted from the refined trigonal 1.5 X-ray structure, in which proline 51
at the junction between A and B was removed, allowing for free rotation around
this junction. We then treated AB' and A'B as two independent sub-domains.
Assuming that the orientation of the two sub-domains is fixed in solution (at
least to a first approximation), the principal axis systems, or alignment frames,
of sub-domains AB' and A'B should be equivalent to the alignment system of the
entire molecule and, vice versa, to each other. Using the residual dipolar couplings
we calculated the order tensor principal axis systems for each domain. Rotation of
pseudo sub-domain A'B around the hinge at amino acid position 51 until a superposition
of the individual coordinate frames was obtained yielded the final model of the
solution dimer.
Determination of the domain orientation for the solution structure of the dimer was carried out using a procedure analogous to the one described for determining the relative domain orientation in a two-domain protein fragment of a lectin.
0.150 mM protein in 25 mM sodium phosphate buffer, pH 8.0 and 0.02 % NaN3
90% H2O/10% D2O
F.Delaglio, S.Grzesiek, G.W.Vuister, G.Zhu, J.Pfeifer, A.Bax
processing
NMRPipe
2.1
M.Zweckstetter, A.Bax
structure solution
PALES
M.Zweckstetter, A.Bax
refinement
PALES
600
Bruker
DRX
LEU
1
n
1
LEU
1
A
GLY
2
n
2
GLY
2
A
LYS
3
n
3
LYS
3
A
PHE
4
n
4
PHE
4
A
SER
5
n
5
SER
5
A
GLN
6
n
6
GLN
6
A
THR
7
n
7
THR
7
A
CYS
8
n
8
CYS
8
A
TYR
9
n
9
TYR
9
A
ASN
10
n
10
ASN
10
A
SER
11
n
11
SER
11
A
ALA
12
n
12
ALA
12
A
ILE
13
n
13
ILE
13
A
GLN
14
n
14
GLN
14
A
GLY
15
n
15
GLY
15
A
SER
16
n
16
SER
16
A
VAL
17
n
17
VAL
17
A
LEU
18
n
18
LEU
18
A
THR
19
n
19
THR
19
A
SER
20
n
20
SER
20
A
THR
21
n
21
THR
21
A
CYS
22
n
22
CYS
22
A
GLU
23
n
23
GLU
23
A
ARG
24
n
24
ARG
24
A
THR
25
n
25
THR
25
A
ASN
26
n
26
ASN
26
A
GLY
27
n
27
GLY
27
A
GLY
28
n
28
GLY
28
A
TYR
29
n
29
TYR
29
A
ASN
30
n
30
ASN
30
A
THR
31
n
31
THR
31
A
SER
32
n
32
SER
32
A
SER
33
n
33
SER
33
A
ILE
34
n
34
ILE
34
A
ASP
35
n
35
ASP
35
A
LEU
36
n
36
LEU
36
A
ASN
37
n
37
ASN
37
A
SER
38
n
38
SER
38
A
VAL
39
n
39
VAL
39
A
ILE
40
n
40
ILE
40
A
GLU
41
n
41
GLU
41
A
ASN
42
n
42
ASN
42
A
VAL
43
n
43
VAL
43
A
ASP
44
n
44
ASP
44
A
GLY
45
n
45
GLY
45
A
SER
46
n
46
SER
46
A
LEU
47
n
47
LEU
47
A
LYS
48
n
48
LYS
48
A
TRP
49
n
49
TRP
49
A
GLN
50
n
50
GLN
50
A
PRO
51
n
51
PRO
51
A
SER
52
n
52
SER
52
A
ASN
53
n
53
ASN
53
A
PHE
54
n
54
PHE
54
A
ILE
55
n
55
ILE
55
A
GLU
56
n
56
GLU
56
A
THR
57
n
57
THR
57
A
CYS
58
n
58
CYS
58
A
ARG
59
n
59
ARG
59
A
ASN
60
n
60
ASN
60
A
THR
61
n
61
THR
61
A
GLN
62
n
62
GLN
62
A
LEU
63
n
63
LEU
63
A
ALA
64
n
64
ALA
64
A
GLY
65
n
65
GLY
65
A
SER
66
n
66
SER
66
A
SER
67
n
67
SER
67
A
GLU
68
n
68
GLU
68
A
LEU
69
n
69
LEU
69
A
ALA
70
n
70
ALA
70
A
ALA
71
n
71
ALA
71
A
GLU
72
n
72
GLU
72
A
CYS
73
n
73
CYS
73
A
LYS
74
n
74
LYS
74
A
THR
75
n
75
THR
75
A
ARG
76
n
76
ARG
76
A
ALA
77
n
77
ALA
77
A
GLN
78
n
78
GLN
78
A
GLN
79
n
79
GLN
79
A
PHE
80
n
80
PHE
80
A
VAL
81
n
81
VAL
81
A
SER
82
n
82
SER
82
A
THR
83
n
83
THR
83
A
LYS
84
n
84
LYS
84
A
ILE
85
n
85
ILE
85
A
ASN
86
n
86
ASN
86
A
LEU
87
n
87
LEU
87
A
ASP
88
n
88
ASP
88
A
ASP
89
n
89
ASP
89
A
HIS
90
n
90
HIS
90
A
ILE
91
n
91
ILE
91
A
ALA
92
n
92
ALA
92
A
ASN
93
n
93
ASN
93
A
ILE
94
n
94
ILE
94
A
ASP
95
n
95
ASP
95
A
GLY
96
n
96
GLY
96
A
THR
97
n
97
THR
97
A
LEU
98
n
98
LEU
98
A
LYS
99
n
99
LYS
99
A
TYR
100
n
100
TYR
100
A
GLU
101
n
101
GLU
101
A
LEU
102
n
1
LEU
102
B
GLY
103
n
2
GLY
103
B
LYS
104
n
3
LYS
104
B
PHE
105
n
4
PHE
105
B
SER
106
n
5
SER
106
B
GLN
107
n
6
GLN
107
B
THR
108
n
7
THR
108
B
CYS
109
n
8
CYS
109
B
TYR
110
n
9
TYR
110
B
ASN
111
n
10
ASN
111
B
SER
112
n
11
SER
112
B
ALA
113
n
12
ALA
113
B
ILE
114
n
13
ILE
114
B
GLN
115
n
14
GLN
115
B
GLY
116
n
15
GLY
116
B
SER
117
n
16
SER
117
B
VAL
118
n
17
VAL
118
B
LEU
119
n
18
LEU
119
B
THR
120
n
19
THR
120
B
SER
121
n
20
SER
121
B
THR
122
n
21
THR
122
B
CYS
123
n
22
CYS
123
B
GLU
124
n
23
GLU
124
B
ARG
125
n
24
ARG
125
B
THR
126
n
25
THR
126
B
ASN
127
n
26
ASN
127
B
GLY
128
n
27
GLY
128
B
GLY
129
n
28
GLY
129
B
TYR
130
n
29
TYR
130
B
ASN
131
n
30
ASN
131
B
THR
132
n
31
THR
132
B
SER
133
n
32
SER
133
B
SER
134
n
33
SER
134
B
ILE
135
n
34
ILE
135
B
ASP
136
n
35
ASP
136
B
LEU
137
n
36
LEU
137
B
ASN
138
n
37
ASN
138
B
SER
139
n
38
SER
139
B
VAL
140
n
39
VAL
140
B
ILE
141
n
40
ILE
141
B
GLU
142
n
41
GLU
142
B
ASN
143
n
42
ASN
143
B
VAL
144
n
43
VAL
144
B
ASP
145
n
44
ASP
145
B
GLY
146
n
45
GLY
146
B
SER
147
n
46
SER
147
B
LEU
148
n
47
LEU
148
B
LYS
149
n
48
LYS
149
B
TRP
150
n
49
TRP
150
B
GLN
151
n
50
GLN
151
B
PRO
152
n
51
PRO
152
B
SER
153
n
52
SER
153
B
ASN
154
n
53
ASN
154
B
PHE
155
n
54
PHE
155
B
ILE
156
n
55
ILE
156
B
GLU
157
n
56
GLU
157
B
THR
158
n
57
THR
158
B
CYS
159
n
58
CYS
159
B
ARG
160
n
59
ARG
160
B
ASN
161
n
60
ASN
161
B
THR
162
n
61
THR
162
B
GLN
163
n
62
GLN
163
B
LEU
164
n
63
LEU
164
B
ALA
165
n
64
ALA
165
B
GLY
166
n
65
GLY
166
B
SER
167
n
66
SER
167
B
SER
168
n
67
SER
168
B
GLU
169
n
68
GLU
169
B
LEU
170
n
69
LEU
170
B
ALA
171
n
70
ALA
171
B
ALA
172
n
71
ALA
172
B
GLU
173
n
72
GLU
173
B
CYS
174
n
73
CYS
174
B
LYS
175
n
74
LYS
175
B
THR
176
n
75
THR
176
B
ARG
177
n
76
ARG
177
B
ALA
178
n
77
ALA
178
B
GLN
179
n
78
GLN
179
B
GLN
180
n
79
GLN
180
B
PHE
181
n
80
PHE
181
B
VAL
182
n
81
VAL
182
B
SER
183
n
82
SER
183
B
THR
184
n
83
THR
184
B
LYS
185
n
84
LYS
185
B
ILE
186
n
85
ILE
186
B
ASN
187
n
86
ASN
187
B
LEU
188
n
87
LEU
188
B
ASP
189
n
88
ASP
189
B
ASP
190
n
89
ASP
190
B
HIS
191
n
90
HIS
191
B
ILE
192
n
91
ILE
192
B
ALA
193
n
92
ALA
193
B
ASN
194
n
93
ASN
194
B
ILE
195
n
94
ILE
195
B
ASP
196
n
95
ASP
196
B
GLY
197
n
96
GLY
197
B
THR
198
n
97
THR
198
B
LEU
199
n
98
LEU
199
B
LYS
200
n
99
LYS
200
B
TYR
201
n
100
TYR
201
B
GLU
202
n
101
GLU
202
B
author_defined_assembly
2
dimeric
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
ALA
12
A
N
ALA
12
A
O
THR
19
A
O
THR
19
A
N
CYS
22
A
N
CYS
22
A
O
ASN
30
A
O
ASN
30
A
N
GLU
41
A
N
GLU
41
A
O
LYS
48
A
O
LYS
48
A
N
ALA
64
A
N
ALA
64
A
O
GLU
68
A
O
GLU
68
A
N
LEU
69
A
N
LEU
69
A
O
ILE
85
A
O
ILE
85
A
N
ALA
92
A
N
ALA
92
A
O
LYS
99
A
O
LYS
99
B
N
ALA
113
B
N
ALA
12
B
O
THR
120
B
O
THR
19
B
N
CYS
123
B
N
CYS
22
B
O
ASN
131
B
O
ASN
30
B
N
GLU
142
B
N
GLU
41
B
O
LYS
149
B
O
LYS
48
B
N
ALA
165
B
N
ALA
64
B
O
GLU
169
B
O
GLU
68
B
N
LEU
170
B
N
LEU
69
B
O
ILE
186
B
O
ILE
85
B
N
ALA
193
B
N
ALA
92
B
O
LYS
200
B
O
LYS
99
1
A
VAL
39
14.44
1
B
VAL
140
14.57
1
-11.70
1.90
111.40
99.70
A
A
A
CB
CA
C
VAL
VAL
VAL
39
39
39
N
1
-15.78
1.80
110.60
94.82
A
A
A
N
CA
CB
GLN
GLN
GLN
50
50
50
N
1
-11.94
1.90
111.40
99.46
B
B
B
CB
CA
C
VAL
VAL
VAL
140
140
140
N
1
-15.80
1.80
110.60
94.80
B
B
B
N
CA
CB
GLN
GLN
GLN
151
151
151
N
1
A
GLN
50
-124.94
-155.93
1
A
ASN
53
169.59
-174.73
1
A
SER
67
-151.08
5.10
1
B
GLN
151
-124.60
-155.28
1
B
ASN
154
169.40
-174.65
1
B
SER
168
-151.18
5.10
The domain-swapped dimer of CV-N in solution
1
N
N
1
N
N
A
LYS
3
A
LYS
3
HELX_P
A
GLN
6
A
GLN
6
5
1
4
B
LYS
104
B
LYS
3
HELX_P
B
GLN
107
B
GLN
6
5
2
4
disulf
2.031
A
CYS
8
A
SG
CYS
8
1_555
A
CYS
22
A
SG
CYS
22
1_555
disulf
2.038
A
CYS
58
A
SG
CYS
58
1_555
A
CYS
73
A
SG
CYS
73
1_555
disulf
2.030
B
CYS
109
B
SG
CYS
8
1_555
B
CYS
123
B
SG
CYS
22
1_555
disulf
2.038
B
CYS
159
B
SG
CYS
58
1_555
B
CYS
174
B
SG
CYS
73
1_555
ANTIVIRAL PROTEIN
3D domain-swapping, cyanovirin-N, protein folding, ANTIVIRAL PROTEIN
CVN_NOSEL
UNP
1
1
P81180
LGKFSQTCYNSAIQGSVLTSTCERTNGGYNTSSIDLNSVIENVDGSLKWQPSNFIETCRNTQLAGSSELAAECKTRAQQF
VSTKINLDDHIANIDGTLKYE
1
101
1L5E
1
101
P81180
A
1
1
101
1
101
1L5E
102
202
P81180
B
1
1
101
3
2
3
2
3
2
3
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
CYS
8
A
CYS
8
A
GLN
14
A
GLN
14
A
VAL
17
A
VAL
17
A
GLU
23
A
GLU
23
A
TYR
29
A
TYR
29
A
ASP
35
A
ASP
35
A
ILE
40
A
ILE
40
A
VAL
43
A
VAL
43
A
SER
46
A
SER
46
A
TRP
49
A
TRP
49
A
CYS
58
A
CYS
58
A
ALA
64
A
ALA
64
A
GLU
68
A
GLU
68
A
LYS
74
A
LYS
74
A
PHE
80
A
PHE
80
A
ASN
86
A
ASN
86
A
ILE
91
A
ILE
91
A
ILE
94
A
ILE
94
A
THR
97
A
THR
97
A
TYR
100
A
TYR
100
B
CYS
109
B
CYS
8
B
GLN
115
B
GLN
14
B
VAL
118
B
VAL
17
B
GLU
124
B
GLU
23
B
TYR
130
B
TYR
29
B
ASP
136
B
ASP
35
B
ILE
141
B
ILE
40
B
VAL
144
B
VAL
43
B
SER
147
B
SER
46
B
TRP
150
B
TRP
49
B
CYS
159
B
CYS
58
B
ALA
165
B
ALA
64
B
GLU
169
B
GLU
68
B
LYS
175
B
LYS
74
B
PHE
181
B
PHE
80
B
ASN
187
B
ASN
86
B
ILE
192
B
ILE
91
B
ILE
195
B
ILE
94
B
THR
198
B
THR
97
B
TYR
201
B
TYR
100