1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Di Lello, P.
Nguyen, B.D.
Jones, T.N.
Potempa, K.
Kobor, M.S.
Legault, P.
Omichinski, J.G.
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
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
Biochemistry
BICHAW
0033
0006-2960
44
7678
7686
10.1021/bi050099s
15909982
NMR Structure of the Amino-Terminal Domain from the Tfb1 Subunit of TFIIH and
Characterization of Its Phosphoinositide and VP16 Binding Sites
2005
10.2210/pdb1y5o/pdb
pdb_00001y5o
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
12903.701
RNA polymerase II transcription factor B 73 kDa subunit
sequence database residues 1-115
M1P
1
man
polymer
TFB1
no
no
PSHSGAAIFEKVSGIIAINEDVSPAELTWRSTDGDKVHTVVLSTIDKLQATPASSEKMMLRLIGKVDESKKRKDNEGNEV
VPKPQRHMFSFNNRTVMDNIKMTLQQIISRYKDAD
PSHSGAAIFEKVSGIIAINEDVSPAELTWRSTDGDKVHTVVLSTIDKLQATPASSEKMMLRLIGKVDESKKRKDNEGNEV
VPKPQRHMFSFNNRTVMDNIKMTLQQIISRYKDAD
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
baker's yeast
Saccharomyces
Escherichia
sample
TFB1
4932
Saccharomyces cerevisiae
562
Escherichia coli
TOPP2
Plasmid
pGEX-2T
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2005-05-17
1
1
2008-04-30
1
2
2011-07-13
1
3
2021-10-20
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_ref_seq_dif.details
1H, 15N, and 13C Resonance Assignment of the Amino-terminal Domain of Tfb1 subunit of yeast TFIIH
SEQUENCE
THE FRAGMENT OF TFB1 STUDIED IN THIS CASE CONTAINS TWO
EXTRA RESIDUES (GLY SER) AT THE N-TERMINUS AND FOUR
EXTRA RESIDUES (GLY ASN SER SER) AT THE C-TERMINUS
AS A CONSEQUENCE OF CLONING ARTIFACTS. THESE EXTRA
AMINO ACIDS WERE NOT INCLUDED IN THE STRUCTURE
CALCULATIONS AND THEREFORE THEY ARE NOT PRESENT IN
DEPOSITED STRUCTURES
RCSB
Y
RCSB
2004-12-02
REL
REL
LOWEST ENERGY
THE SUBMITTED MODELS ARE THE 20 STRUCTURES WITH NO UPPER BOUND VIOLATION GREATER THAN 0.2 ARMSTRONG, NO DIHEDRAL ANGLE RESTRAINT VIOLATION GREATER THAN 2 DEGREES AND WITH THE LOWEST ENERGIES.
62
20
2D NOESY
3D 15N-EDITED NOESY -HSQC
2D 1H-15N HSQC
3D 13C- EDITED HMQC-NOESY
20 mM SODIUM PHOSPHATE
6.5
AMBIENT
300
K
THE THREE-DIMENSIONAL STRUCTURES OF THE AMINO-TERMINAL DOMAIN OF TFB1 WERE DETERMINED USING A SET OF 1208 NOE-DERIVED DISTANCE RESTRAINTS, 124 BACKBONE DIHEDRAL ANGLE (PHI AND PSI) RESTRAINTS AND 20 DISTANCE RESTRAINTS FROM HYDROGEN BONDS.
SIMULATED ANNEALING, WITH A COMBINATION OF TORSION ANGLE DYNAMICS AND CARTESIAN DYNAMICS.
1
1.2 MM TFB1 [UNLABELED], 20 MM PHOSPHATE BUFFER, 1MM EDTA, 100% D2O; 1.2 MM TFB1 [U-15N], 20 MM PHOSPHATE BUFFER, 1MM EDTA, 90% H2O, 10% D2O; 1.2 MM TFB1 [U-15N,13C], 20 MM PHOSPHATE BUFFER, 1MM EDTA, 100% D2O
BRUNGER, ADAMS, CLORE, DELANO, GROS, GROSSE- KUNSTLEVE, JIANG, KUSZEWSKI, NILGES, PANNU, READ, RICE, SIMONSON, WARREN
refinement
CNS
1.0
structure solution
VNMR 6.1.C
6.1.C
structure solution
NMRPipe
2.2
structure solution
NMRView
5.0.4
structure solution
CNS
1.0
500
Varian
UNITY
600
Varian
UNITY
800
Varian
UNITY
PRO
1
n
1
PRO
1
A
SER
2
n
2
SER
2
A
HIS
3
n
3
HIS
3
A
SER
4
n
4
SER
4
A
GLY
5
n
5
GLY
5
A
ALA
6
n
6
ALA
6
A
ALA
7
n
7
ALA
7
A
ILE
8
n
8
ILE
8
A
PHE
9
n
9
PHE
9
A
GLU
10
n
10
GLU
10
A
LYS
11
n
11
LYS
11
A
VAL
12
n
12
VAL
12
A
SER
13
n
13
SER
13
A
GLY
14
n
14
GLY
14
A
ILE
15
n
15
ILE
15
A
ILE
16
n
16
ILE
16
A
ALA
17
n
17
ALA
17
A
ILE
18
n
18
ILE
18
A
ASN
19
n
19
ASN
19
A
GLU
20
n
20
GLU
20
A
ASP
21
n
21
ASP
21
A
VAL
22
n
22
VAL
22
A
SER
23
n
23
SER
23
A
PRO
24
n
24
PRO
24
A
ALA
25
n
25
ALA
25
A
GLU
26
n
26
GLU
26
A
LEU
27
n
27
LEU
27
A
THR
28
n
28
THR
28
A
TRP
29
n
29
TRP
29
A
ARG
30
n
30
ARG
30
A
SER
31
n
31
SER
31
A
THR
32
n
32
THR
32
A
ASP
33
n
33
ASP
33
A
GLY
34
n
34
GLY
34
A
ASP
35
n
35
ASP
35
A
LYS
36
n
36
LYS
36
A
VAL
37
n
37
VAL
37
A
HIS
38
n
38
HIS
38
A
THR
39
n
39
THR
39
A
VAL
40
n
40
VAL
40
A
VAL
41
n
41
VAL
41
A
LEU
42
n
42
LEU
42
A
SER
43
n
43
SER
43
A
THR
44
n
44
THR
44
A
ILE
45
n
45
ILE
45
A
ASP
46
n
46
ASP
46
A
LYS
47
n
47
LYS
47
A
LEU
48
n
48
LEU
48
A
GLN
49
n
49
GLN
49
A
ALA
50
n
50
ALA
50
A
THR
51
n
51
THR
51
A
PRO
52
n
52
PRO
52
A
ALA
53
n
53
ALA
53
A
SER
54
n
54
SER
54
A
SER
55
n
55
SER
55
A
GLU
56
n
56
GLU
56
A
LYS
57
n
57
LYS
57
A
MET
58
n
58
MET
58
A
MET
59
n
59
MET
59
A
LEU
60
n
60
LEU
60
A
ARG
61
n
61
ARG
61
A
LEU
62
n
62
LEU
62
A
ILE
63
n
63
ILE
63
A
GLY
64
n
64
GLY
64
A
LYS
65
n
65
LYS
65
A
VAL
66
n
66
VAL
66
A
ASP
67
n
67
ASP
67
A
GLU
68
n
68
GLU
68
A
SER
69
n
69
SER
69
A
LYS
70
n
70
LYS
70
A
LYS
71
n
71
LYS
71
A
ARG
72
n
72
ARG
72
A
LYS
73
n
73
LYS
73
A
ASP
74
n
74
ASP
74
A
ASN
75
n
75
ASN
75
A
GLU
76
n
76
GLU
76
A
GLY
77
n
77
GLY
77
A
ASN
78
n
78
ASN
78
A
GLU
79
n
79
GLU
79
A
VAL
80
n
80
VAL
80
A
VAL
81
n
81
VAL
81
A
PRO
82
n
82
PRO
82
A
LYS
83
n
83
LYS
83
A
PRO
84
n
84
PRO
84
A
GLN
85
n
85
GLN
85
A
ARG
86
n
86
ARG
86
A
HIS
87
n
87
HIS
87
A
MET
88
n
88
MET
88
A
PHE
89
n
89
PHE
89
A
SER
90
n
90
SER
90
A
PHE
91
n
91
PHE
91
A
ASN
92
n
92
ASN
92
A
ASN
93
n
93
ASN
93
A
ARG
94
n
94
ARG
94
A
THR
95
n
95
THR
95
A
VAL
96
n
96
VAL
96
A
MET
97
n
97
MET
97
A
ASP
98
n
98
ASP
98
A
ASN
99
n
99
ASN
99
A
ILE
100
n
100
ILE
100
A
LYS
101
n
101
LYS
101
A
MET
102
n
102
MET
102
A
THR
103
n
103
THR
103
A
LEU
104
n
104
LEU
104
A
GLN
105
n
105
GLN
105
A
GLN
106
n
106
GLN
106
A
ILE
107
n
107
ILE
107
A
ILE
108
n
108
ILE
108
A
SER
109
n
109
SER
109
A
ARG
110
n
110
ARG
110
A
TYR
111
n
111
TYR
111
A
LYS
112
n
112
LYS
112
A
ASP
113
n
113
ASP
113
A
ALA
114
n
114
ALA
114
A
ASP
115
n
115
ASP
115
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
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
GLY
5
A
N
GLY
5
A
O
ILE
16
A
O
ILE
16
A
N
ASN
19
A
N
ASN
19
A
O
GLU
26
A
O
GLU
26
A
N
TRP
29
A
N
TRP
29
A
O
HIS
38
A
O
HIS
38
A
N
GLN
49
A
N
GLN
49
A
O
ARG
61
A
O
ARG
61
A
N
MET
58
A
N
MET
58
A
O
PHE
91
A
O
PHE
91
14
A
A
H
O
TRP
HIS
29
38
1.59
1
A
GLU
10
78.08
49.97
1
A
SER
23
-165.82
113.41
1
A
ALA
25
-54.32
172.04
1
A
LYS
65
50.09
-176.44
1
A
VAL
66
-107.87
-67.87
1
A
GLU
68
-147.82
38.90
1
A
VAL
81
-55.69
108.83
2
A
SER
2
-159.98
-45.15
2
A
GLU
10
78.01
49.77
2
A
ALA
25
-54.33
172.05
2
A
ILE
45
-66.43
97.99
2
A
GLU
68
-155.57
43.87
2
A
LYS
83
179.86
-61.23
3
A
SER
4
-179.90
121.50
3
A
GLU
10
77.89
49.91
3
A
SER
23
-166.50
113.38
3
A
PRO
84
-68.44
93.24
4
A
SER
4
58.14
170.31
4
A
GLU
10
78.18
49.91
4
A
SER
23
-165.48
112.86
4
A
ALA
25
-54.26
170.15
4
A
ILE
45
-64.81
94.56
4
A
LYS
65
55.30
166.44
4
A
LYS
71
57.98
104.86
4
A
ARG
72
62.81
129.04
4
A
LYS
83
179.38
-54.57
5
A
SER
2
59.01
167.04
5
A
HIS
3
62.90
128.81
5
A
SER
4
62.98
127.37
5
A
GLU
10
78.04
49.85
5
A
SER
23
-166.77
113.11
5
A
ILE
45
-62.39
94.03
5
A
VAL
66
-127.15
-67.47
5
A
GLU
76
-96.16
39.08
5
A
VAL
80
-178.26
44.77
6
A
SER
2
-160.93
-45.05
6
A
SER
4
57.65
172.12
6
A
GLU
10
77.87
49.66
6
A
ALA
25
-54.46
172.18
6
A
ILE
45
-59.84
93.61
6
A
LYS
71
59.56
102.99
6
A
GLU
76
-98.93
32.50
6
A
ASN
78
45.99
-171.46
7
A
SER
4
-179.14
118.29
7
A
GLU
10
77.96
49.70
7
A
SER
23
-166.20
113.14
7
A
ALA
25
-54.39
170.48
7
A
ILE
45
-58.76
92.09
7
A
GLU
68
-141.45
38.92
7
A
GLU
76
-95.69
38.22
7
A
PRO
82
-59.62
-70.93
7
A
LYS
83
-178.54
95.88
8
A
SER
2
-166.89
-43.32
8
A
SER
4
61.08
118.75
8
A
GLU
10
78.09
49.83
8
A
LYS
65
49.84
-175.07
8
A
GLU
68
-148.71
38.81
8
A
ASN
78
-56.53
89.12
8
A
GLU
79
-156.02
47.35
8
A
PRO
82
-57.04
-162.98
8
A
LYS
83
61.41
165.31
9
A
GLU
10
77.99
49.74
9
A
ALA
25
-54.38
172.21
9
A
ILE
45
-62.63
91.56
9
A
ASP
67
61.60
69.27
9
A
GLU
79
60.08
-172.22
9
A
LYS
83
-119.85
73.36
10
A
GLU
10
78.02
49.79
10
A
ALA
25
-54.36
172.13
10
A
ILE
45
-63.48
93.70
10
A
LYS
65
51.59
-179.42
10
A
VAL
66
-124.89
-67.10
10
A
GLU
76
-96.55
38.09
10
A
VAL
80
-151.46
-56.95
11
A
HIS
3
178.06
-36.09
11
A
GLU
10
78.14
49.83
11
A
SER
23
-165.52
113.13
11
A
ALA
25
-54.37
172.00
11
A
ARG
72
63.63
136.60
11
A
LYS
73
-60.26
-165.33
12
A
GLU
10
78.24
49.51
12
A
SER
23
-166.01
113.06
12
A
LYS
65
54.62
169.38
12
A
VAL
66
-97.69
49.15
12
A
VAL
80
60.17
159.20
12
A
PRO
82
-69.85
63.30
13
A
GLU
10
77.97
49.94
13
A
ILE
45
-68.49
93.75
13
A
GLU
76
-97.26
39.03
13
A
VAL
81
-178.26
65.44
14
A
SER
2
68.24
-68.85
14
A
GLU
10
77.57
49.80
14
A
SER
23
-165.98
113.31
14
A
ALA
25
-54.35
171.13
14
A
LYS
47
-172.18
149.26
14
A
LYS
65
-64.77
-179.06
14
A
SER
69
-145.73
26.19
14
A
LYS
70
-143.30
-51.82
14
A
GLU
76
-91.42
43.68
15
A
GLU
10
78.23
49.54
15
A
SER
23
-166.18
113.22
15
A
ALA
25
-54.35
171.13
15
A
LYS
70
-96.20
-69.18
15
A
ASP
74
-177.78
-40.60
15
A
ASN
75
61.85
-77.58
15
A
VAL
80
65.02
100.31
16
A
SER
2
-158.72
-45.68
16
A
GLU
10
78.55
49.26
16
A
SER
23
-165.53
112.96
16
A
LYS
71
61.45
87.26
16
A
ARG
72
-60.72
-157.58
16
A
VAL
80
-169.80
59.30
16
A
LYS
83
58.58
163.37
17
A
SER
2
-117.12
-75.35
17
A
GLU
10
77.61
50.20
17
A
SER
23
-167.42
113.92
17
A
ALA
25
-54.18
172.05
17
A
VAL
66
-133.40
-45.17
17
A
ASN
75
76.48
-0.10
17
A
PRO
82
-72.01
-169.73
18
A
GLU
10
77.50
49.91
18
A
ALA
25
-54.43
172.23
18
A
ILE
45
-62.34
94.19
18
A
ASP
67
-176.50
40.99
18
A
ASP
74
-179.34
-36.43
18
A
GLU
76
-97.18
38.56
19
A
SER
4
-177.93
121.29
19
A
GLU
10
78.26
49.40
19
A
SER
23
-166.46
113.38
19
A
ALA
25
-54.32
172.14
19
A
LYS
65
49.70
-175.27
19
A
ASP
67
-96.44
39.23
19
A
GLU
76
-93.08
39.52
19
A
LYS
83
-171.59
54.39
20
A
SER
2
68.64
-67.70
20
A
SER
4
-176.01
118.93
20
A
GLU
10
78.21
49.59
20
A
SER
23
-166.87
113.68
20
A
ALA
25
-54.27
172.08
20
A
ILE
45
-62.03
93.22
20
A
VAL
66
-97.14
45.96
20
A
ASP
74
-63.45
-80.90
20
A
ASN
75
174.83
-33.97
20
A
LYS
83
-166.48
59.99
NMR structure of the amino-terminal domain from the Tfb1 subunit of yeast TFIIH
1
N
N
A
ASN
93
A
ASN
93
HELX_P
A
ASP
115
A
ASP
115
1
1
23
TRANSCRIPTION
TFIIH, Tfb1, PH domain, phosphoinositides, VP16, TRANSCRIPTION
A
SER
23
A
SER
23
1
A
PRO
24
A
PRO
24
0.08
A
SER
23
A
SER
23
2
A
PRO
24
A
PRO
24
0.23
A
SER
23
A
SER
23
3
A
PRO
24
A
PRO
24
0.07
A
SER
23
A
SER
23
4
A
PRO
24
A
PRO
24
0.02
A
SER
23
A
SER
23
5
A
PRO
24
A
PRO
24
-0.01
A
SER
23
A
SER
23
6
A
PRO
24
A
PRO
24
0.18
A
SER
23
A
SER
23
7
A
PRO
24
A
PRO
24
0.05
A
SER
23
A
SER
23
8
A
PRO
24
A
PRO
24
0.11
A
SER
23
A
SER
23
9
A
PRO
24
A
PRO
24
0.08
A
SER
23
A
SER
23
10
A
PRO
24
A
PRO
24
0.13
A
SER
23
A
SER
23
11
A
PRO
24
A
PRO
24
-0.01
A
SER
23
A
SER
23
12
A
PRO
24
A
PRO
24
-0.04
A
SER
23
A
SER
23
13
A
PRO
24
A
PRO
24
0.09
A
SER
23
A
SER
23
14
A
PRO
24
A
PRO
24
-0.04
A
SER
23
A
SER
23
15
A
PRO
24
A
PRO
24
-0.01
A
SER
23
A
SER
23
16
A
PRO
24
A
PRO
24
0.11
A
SER
23
A
SER
23
17
A
PRO
24
A
PRO
24
0.09
A
SER
23
A
SER
23
18
A
PRO
24
A
PRO
24
0.09
A
SER
23
A
SER
23
19
A
PRO
24
A
PRO
24
0.18
A
SER
23
A
SER
23
20
A
PRO
24
A
PRO
24
0.04
TFB1_YEAST
UNP
1
1
P32776
MSHSGAAIFEKVSGIIAINEDVSPAELTWRSTDGDKVHTVVLSTIDKLQATPASSEKMMLRLIGKVDESKKRKDNEGNEV
VPKPQRHMFSFNNRTVMDNIKMTLQQIISRYKDAD
1
115
1Y5O
1
115
P32776
A
1
1
115
1
MET
engineered mutation
PRO
1
1Y5O
A
P32776
UNP
1
1
4
3
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
SER
4
A
SER
4
A
ILE
8
A
ILE
8
A
SER
13
A
SER
13
A
ASN
19
A
ASN
19
A
GLU
26
A
GLU
26
A
SER
31
A
SER
31
A
VAL
37
A
VAL
37
A
VAL
41
A
VAL
41
A
GLN
49
A
GLN
49
A
ALA
50
A
ALA
50
A
MET
58
A
MET
58
A
GLY
64
A
GLY
64
A
GLN
85
A
GLN
85
A
PHE
91
A
PHE
91
1
P 1