1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Yamasaki, K.
Allen, M.D.
Ohme-Takagi, M.
Tateno, M.
Suzuki, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
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
C10 H14 N5 O6 P
331.222
y
2'-DEOXYADENOSINE-5'-MONOPHOSPHATE
DNA linking
C9 H14 N3 O7 P
307.197
y
2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE
DNA linking
C10 H14 N5 O7 P
347.221
y
2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE
DNA linking
C10 H15 N2 O8 P
322.208
y
THYMIDINE-5'-MONOPHOSPHATE
DNA 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
UK
EMBO J.
EMJODG
0897
0261-4189
17
5484
5496
10.1093/emboj/17.18.5484
9736626
A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA.
1998
10.2210/pdb1gcc/pdb
pdb_00001gcc
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
3319.175
DNA (5'-D(*TP*AP*GP*CP*CP*GP*CP*CP*AP*GP*C)-3')
1
syn
polymer
3390.209
DNA (5'-D(*GP*CP*TP*GP*GP*CP*GP*GP*CP*TP*A)-3')
1
syn
polymer
7247.318
ETHYLENE RESPONSIVE ELEMENT BINDING FACTOR 1
GCC-BOX BINDING DOMAIN
1
man
polymer
no
no
(DT)(DA)(DG)(DC)(DC)(DG)(DC)(DC)(DA)(DG)(DC)
TAGCCGCCAGC
B
polydeoxyribonucleotide
no
no
(DG)(DC)(DT)(DG)(DG)(DC)(DG)(DG)(DC)(DT)(DA)
GCTGGCGGCTA
C
polydeoxyribonucleotide
no
no
KHYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPLRV
KHYRGVRQRPWGKFAAEIRDPAKNGARVWLGTFETAEDAALAYDRAAFRMRGSRALLNFPLRV
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
thale cress
Arabidopsis
Escherichia
Escherichia coli
sample
DNA-BINDING DOMAIN OF ATERF1;
BL21
ATERF1
3702
Arabidopsis thaliana
469008
Escherichia coli BL21(DE3)
BL21 (DE3)
PAF104
0.405
1
20
B
3
C
24
-4.445
B_DT3:DA24_C
1
-7.228
0.063
-0.214
-0.200
-5.458
1
20
B
4
C
23
-4.874
B_DA4:DT23_C
2
-1.154
0.079
-0.343
-0.194
3.485
1
19
B
5
C
22
-2.008
B_DG5:DC22_C
3
-4.366
-0.777
0.105
-0.324
-3.044
1
19
B
6
C
21
-6.612
B_DC6:DG21_C
4
-7.903
0.192
0.533
-0.247
0.809
1
19
B
7
C
20
-3.302
B_DC7:DG20_C
5
-10.288
0.408
0.553
-0.314
5.644
1
19
B
8
C
19
-3.343
B_DG8:DC19_C
6
-2.602
-0.174
0.228
-0.152
-0.231
1
19
B
9
C
18
-3.747
B_DC9:DG18_C
7
-2.275
0.319
-0.087
-0.185
-6.658
1
19
B
10
C
17
-0.529
B_DC10:DG17_C
8
-6.688
0.349
0.314
-0.187
3.906
1
20
B
11
C
16
-6.134
B_DA11:DT16_C
9
-13.318
0.230
0.627
-0.230
7.256
1
19
B
12
C
15
-3.997
B_DG12:DC15_C
10
-6.167
-0.333
1.091
-0.405
2.333
1
19
B
13
C
14
-1.197
B_DC13:DG14_C
11
4.218
0.904
0.307
-0.413
3.372
40.875
B
B
3
4
-0.817
C
C
24
23
3.376
-0.571
-0.107
0.284
BB_DT3DA4:DT23DA24_CC
1
0.136
-0.195
40.871
0.471
0.168
2.981
28.127
B
B
4
5
-8.901
C
C
23
22
3.009
-4.303
0.108
-0.194
BB_DA4DG5:DC22DT23_CC
2
-2.605
5.389
27.682
0.532
-0.787
3.297
42.551
B
B
5
6
-1.353
C
C
22
21
3.278
-0.980
-0.334
-0.093
BB_DG5DC6:DG21DC22_CC
3
-4.657
6.430
42.296
-0.028
-0.014
3.092
35.326
B
B
6
7
-3.513
C
C
21
20
3.063
-2.127
-0.289
-0.351
BB_DC6DC7:DG20DG21_CC
4
-3.752
6.198
35.070
-0.282
-0.047
2.985
20.119
B
B
7
8
3.082
C
C
20
19
3.013
1.075
0.058
-0.295
BB_DC7DG8:DC19DG20_CC
5
1.895
-5.435
20.002
-1.300
0.637
3.326
38.883
B
B
8
9
3.094
C
C
19
18
3.338
2.056
0.344
-0.505
BB_DG8DC9:DG18DC19_CC
6
3.869
-5.824
38.644
-1.014
-0.037
3.404
34.356
B
B
9
10
-3.102
C
C
18
17
3.395
-1.831
-0.200
-0.156
BB_DC9DC10:DG17DG18_CC
7
-1.720
2.914
34.267
0.034
0.059
2.911
34.809
B
B
10
11
-10.083
C
C
17
16
2.946
-5.999
-0.388
0.081
BB_DC10DA11:DT16DG17_CC
8
-2.509
4.216
34.215
0.961
0.304
2.986
34.185
B
B
11
12
-12.508
C
C
16
15
3.029
-7.280
0.395
-0.462
BB_DA11DG12:DC15DT16_CC
9
-4.358
7.487
33.146
0.289
-1.315
3.570
43.031
B
B
12
13
-4.476
C
C
15
14
3.556
-3.276
0.137
-0.345
BB_DG12DC13:DG14DC15_CC
10
3.951
-5.398
42.738
-0.116
0.240
database_2
pdbx_database_status
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_conn
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Other
1
0
1999-03-23
1
1
2008-03-24
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.process_site
_pdbx_nmr_software.name
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
Y
BNL
1998-03-13
REL
REL
SIGNALS DUE TO PROTEINS WERE OBTAINED BY NOESY, TOCSY, DQF-COSY FOR UNLABELED SAMPLE AND 1H-15N HSQC, 3D 1H-15N NOESY-HMQC AND 3D 1H-15N TOCSY-HMQC FOR THE SAMPLE WITH 15N-LABELED PROTEIN. SIGNALS DUE TO DNA WERE OBTAINED BY NOESY, TOCSY, AND DQF-COSY FOR UNLABELED SAMPLE AND 13C,15N-FILTERED NOESY FOR SAMPLE WITH 13C, 15N-LABELED PROTEIN. INTERMOLECULAR NOES WERE IDENTIFIED USING NOESY SPECTRA INCLUDING THOSE WITH AND WITHOUT 13C- OR 15N-DECOUPLING FOR SAMPLE WITH 13C,15N-LABELED PROTEIN.
1
1
NOESY
TOCSY
DQF-COSY
1H-15N HSQC
3D 1H-15N NOESY-HMQC
3D 1H-15N TOCSY-HMQC
13C
15N-FILTERED NOESY
90 mM
6.0
1
ATMOSPHERE
298
K
SEE REMARK 210 OTHER PROGRAMS USED: AMBER 4.1 AUTHORS: PEARLMAN,CASE,CALDWELL,ROSS,CHEATHAM III, FERGUSON,SEIBEL,SINGH,WEINER,KOLLMAN
SIMULATED ANNEALING PROTOCOL IN X-PLOR 3.1 WAS CARRIED OUT TO OBTAIN 25 STRUCTURES. MINIMIZED MEAN STRUCTURE OF THEM WAS FURTHER REVISED BY A 300 PS RESTRAINED MOLECULAR DYNAMICAL CALCULATION IN THE PRESENCE OF APPROXIMATELY 5000 TIP3P WATER MOLSCULES, USING CORNELL FORCE FIELD IN AMBER 4.1. THE MEAN CO-ORDINATE OF 200 STRUCTURES OBTAINED AFTER THE EQUILIBRIUM (100 PS) WAS ENERGY-MINIMIZED.
POTASIUM PHOSPHATE
BRUNGER
refinement
X-PLOR
3.1
structure solution
X-PLOR
3.1
structure solution
Amber
4.1
750
Bruker
DMX750
500
Bruker
DMX500
T
3
n
1
DT
3
B
A
4
n
2
DA
4
B
G
5
n
3
DG
5
B
C
6
n
4
DC
6
B
C
7
n
5
DC
7
B
G
8
n
6
DG
8
B
C
9
n
7
DC
9
B
C
10
n
8
DC
10
B
A
11
n
9
DA
11
B
G
12
n
10
DG
12
B
C
13
n
11
DC
13
B
G
14
n
1
DG
14
C
C
15
n
2
DC
15
C
T
16
n
3
DT
16
C
G
17
n
4
DG
17
C
G
18
n
5
DG
18
C
C
19
n
6
DC
19
C
G
20
n
7
DG
20
C
G
21
n
8
DG
21
C
C
22
n
9
DC
22
C
T
23
n
10
DT
23
C
A
24
n
11
DA
24
C
LYS
144
n
1
LYS
144
A
HIS
145
n
2
HIS
145
A
TYR
146
n
3
TYR
146
A
ARG
147
n
4
ARG
147
A
GLY
148
n
5
GLY
148
A
VAL
149
n
6
VAL
149
A
ARG
150
n
7
ARG
150
A
GLN
151
n
8
GLN
151
A
ARG
152
n
9
ARG
152
A
PRO
153
n
10
PRO
153
A
TRP
154
n
11
TRP
154
A
GLY
155
n
12
GLY
155
A
LYS
156
n
13
LYS
156
A
PHE
157
n
14
PHE
157
A
ALA
158
n
15
ALA
158
A
ALA
159
n
16
ALA
159
A
GLU
160
n
17
GLU
160
A
ILE
161
n
18
ILE
161
A
ARG
162
n
19
ARG
162
A
ASP
163
n
20
ASP
163
A
PRO
164
n
21
PRO
164
A
ALA
165
n
22
ALA
165
A
LYS
166
n
23
LYS
166
A
ASN
167
n
24
ASN
167
A
GLY
168
n
25
GLY
168
A
ALA
169
n
26
ALA
169
A
ARG
170
n
27
ARG
170
A
VAL
171
n
28
VAL
171
A
TRP
172
n
29
TRP
172
A
LEU
173
n
30
LEU
173
A
GLY
174
n
31
GLY
174
A
THR
175
n
32
THR
175
A
PHE
176
n
33
PHE
176
A
GLU
177
n
34
GLU
177
A
THR
178
n
35
THR
178
A
ALA
179
n
36
ALA
179
A
GLU
180
n
37
GLU
180
A
ASP
181
n
38
ASP
181
A
ALA
182
n
39
ALA
182
A
ALA
183
n
40
ALA
183
A
LEU
184
n
41
LEU
184
A
ALA
185
n
42
ALA
185
A
TYR
186
n
43
TYR
186
A
ASP
187
n
44
ASP
187
A
ARG
188
n
45
ARG
188
A
ALA
189
n
46
ALA
189
A
ALA
190
n
47
ALA
190
A
PHE
191
n
48
PHE
191
A
ARG
192
n
49
ARG
192
A
MET
193
n
50
MET
193
A
ARG
194
n
51
ARG
194
A
GLY
195
n
52
GLY
195
A
SER
196
n
53
SER
196
A
ARG
197
n
54
ARG
197
A
ALA
198
n
55
ALA
198
A
LEU
199
n
56
LEU
199
A
LEU
200
n
57
LEU
200
A
ASN
201
n
58
ASN
201
A
PHE
202
n
59
PHE
202
A
PRO
203
n
60
PRO
203
A
LEU
204
n
61
LEU
204
A
ARG
205
n
62
ARG
205
A
VAL
206
n
63
VAL
206
A
author_defined_assembly
3
trimeric
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
O
ARG
150
C
O
ARG
7
A
N
ALA
158
C
N
ALA
15
A
O
PHE
157
C
O
PHE
14
A
N
PHE
176
C
N
PHE
33
1
B
DC
7
0.075
SIDE CHAIN
1
C
DT
16
0.068
SIDE CHAIN
1
C
DG
17
0.064
SIDE CHAIN
1
C
DC
19
0.089
SIDE CHAIN
1
C
DC
22
0.071
SIDE CHAIN
1
A
ARG
147
0.137
SIDE CHAIN
1
A
ARG
170
0.076
SIDE CHAIN
1
A
TYR
186
0.096
SIDE CHAIN
1
3.73
0.60
106.00
109.73
B
B
B
O4'
C4'
C3'
DC
DC
DC
6
6
6
N
1
3.70
0.60
106.00
109.70
B
B
B
O4'
C4'
C3'
DC
DC
DC
10
10
10
N
1
1.99
0.30
108.30
110.29
C
C
C
O4'
C1'
N1
DC
DC
DC
15
15
15
N
1
4.00
0.60
106.00
110.00
C
C
C
O4'
C4'
C3'
DT
DT
DT
16
16
16
N
1
2.05
0.30
108.30
110.35
C
C
C
O4'
C1'
N9
DG
DG
DG
18
18
18
N
1
2.10
0.30
108.30
110.40
C
C
C
O4'
C1'
N9
DG
DG
DG
20
20
20
N
1
3.71
0.60
106.00
109.71
C
C
C
O4'
C4'
C3'
DC
DC
DC
22
22
22
N
1
4.08
0.50
120.30
124.38
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
147
147
147
N
1
3.31
0.50
120.30
123.61
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
150
150
150
N
1
-3.36
0.50
120.30
116.94
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
150
150
150
N
1
A
ARG
197
51.83
74.04
model building
X-PLOR
3.1
refinement
X-PLOR
3.1
phasing
X-PLOR
3.1
SOLUTION NMR STRUCTURE OF THE COMPLEX OF GCC-BOX BINDING DOMAIN OF ATERF1 AND GCC-BOX DNA, MINIMIZED AVERAGE STRUCTURE
1
N
N
2
N
N
3
N
N
A
ALA
179
C
ALA
36
HELX_P
A
ARG
194
C
ARG
51
1
1
16
covale
1.342
both
A
LYS
144
C
C
LYS
1
1_555
A
HIS
145
C
N
HIS
2
1_555
covale
1.338
both
A
HIS
145
C
C
HIS
2
1_555
A
TYR
146
C
N
TYR
3
1_555
hydrog
WATSON-CRICK
B
DT
3
A
N3
DT
1
1_555
C
DA
24
B
N1
DA
11
1_555
hydrog
WATSON-CRICK
B
DT
3
A
O4
DT
1
1_555
C
DA
24
B
N6
DA
11
1_555
hydrog
WATSON-CRICK
B
DA
4
A
N1
DA
2
1_555
C
DT
23
B
N3
DT
10
1_555
hydrog
WATSON-CRICK
B
DA
4
A
N6
DA
2
1_555
C
DT
23
B
O4
DT
10
1_555
hydrog
WATSON-CRICK
B
DG
5
A
N1
DG
3
1_555
C
DC
22
B
N3
DC
9
1_555
hydrog
WATSON-CRICK
B
DG
5
A
N2
DG
3
1_555
C
DC
22
B
O2
DC
9
1_555
hydrog
WATSON-CRICK
B
DG
5
A
O6
DG
3
1_555
C
DC
22
B
N4
DC
9
1_555
hydrog
WATSON-CRICK
B
DC
6
A
N3
DC
4
1_555
C
DG
21
B
N1
DG
8
1_555
hydrog
WATSON-CRICK
B
DC
6
A
N4
DC
4
1_555
C
DG
21
B
O6
DG
8
1_555
hydrog
WATSON-CRICK
B
DC
6
A
O2
DC
4
1_555
C
DG
21
B
N2
DG
8
1_555
hydrog
WATSON-CRICK
B
DC
7
A
N3
DC
5
1_555
C
DG
20
B
N1
DG
7
1_555
hydrog
WATSON-CRICK
B
DC
7
A
N4
DC
5
1_555
C
DG
20
B
O6
DG
7
1_555
hydrog
WATSON-CRICK
B
DC
7
A
O2
DC
5
1_555
C
DG
20
B
N2
DG
7
1_555
hydrog
WATSON-CRICK
B
DG
8
A
N1
DG
6
1_555
C
DC
19
B
N3
DC
6
1_555
hydrog
WATSON-CRICK
B
DG
8
A
N2
DG
6
1_555
C
DC
19
B
O2
DC
6
1_555
hydrog
WATSON-CRICK
B
DG
8
A
O6
DG
6
1_555
C
DC
19
B
N4
DC
6
1_555
hydrog
WATSON-CRICK
B
DC
9
A
N3
DC
7
1_555
C
DG
18
B
N1
DG
5
1_555
hydrog
WATSON-CRICK
B
DC
9
A
N4
DC
7
1_555
C
DG
18
B
O6
DG
5
1_555
hydrog
WATSON-CRICK
B
DC
9
A
O2
DC
7
1_555
C
DG
18
B
N2
DG
5
1_555
hydrog
WATSON-CRICK
B
DC
10
A
N3
DC
8
1_555
C
DG
17
B
N1
DG
4
1_555
hydrog
WATSON-CRICK
B
DC
10
A
N4
DC
8
1_555
C
DG
17
B
O6
DG
4
1_555
hydrog
WATSON-CRICK
B
DC
10
A
O2
DC
8
1_555
C
DG
17
B
N2
DG
4
1_555
hydrog
WATSON-CRICK
B
DA
11
A
N1
DA
9
1_555
C
DT
16
B
N3
DT
3
1_555
hydrog
WATSON-CRICK
B
DA
11
A
N6
DA
9
1_555
C
DT
16
B
O4
DT
3
1_555
hydrog
WATSON-CRICK
B
DG
12
A
N1
DG
10
1_555
C
DC
15
B
N3
DC
2
1_555
hydrog
WATSON-CRICK
B
DG
12
A
N2
DG
10
1_555
C
DC
15
B
O2
DC
2
1_555
hydrog
WATSON-CRICK
B
DG
12
A
O6
DG
10
1_555
C
DC
15
B
N4
DC
2
1_555
hydrog
WATSON-CRICK
B
DC
13
A
N3
DC
11
1_555
C
DG
14
B
N1
DG
1
1_555
hydrog
WATSON-CRICK
B
DC
13
A
N4
DC
11
1_555
C
DG
14
B
O6
DG
1
1_555
hydrog
WATSON-CRICK
B
DC
13
A
O2
DC
11
1_555
C
DG
14
B
N2
DG
1
1_555
TRANSCRIPTION/DNA
TRANSCRIPTION FACTOR, PROTEIN-DNA COMPLEX, ETHYLENE INDUCIBLE, COMPLEX (TRANSCRIPTION FACTOR-DNA), TRANSCRIPTION-DNA COMPLEX
ERF1A_ARATH
UNP
3
O80337
1GCC
PDB
1
1GCC
1GCC
PDB
2
1GCC
144
206
1GCC
144
206
O80337
A
1
1
63
3
13
1GCC
3
13
1GCC
B
2
1
11
14
24
1GCC
14
24
1GCC
C
3
1
11
3
anti-parallel
anti-parallel
A
VAL
149
C
VAL
6
A
ARG
152
C
ARG
9
A
LYS
156
C
LYS
13
A
ASP
163
C
ASP
20
A
ALA
169
C
ALA
26
A
PHE
176
C
PHE
33
1
P 1