1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Kloks, C.P.A.M.
Spronk, C.A.E.M.
Hoffmann, A.
Vuister, G.W.
Grzesiek, S.
Hilbers, C.W.
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
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
316
317
10.1006/JMBI.2001.5334
11851341
The Solution Structure and DNA-Binding Properties of the Cold-Shock Domain of the Human Y-Box Protein Yb-1.
2002
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
SINGLE STRANDED DNA BINDING COLD SHOCK DOMAIN(CSD) OF HUMAN Y-BOX PROTEIN 1 (YB-1)
8754.899
Y-BOX BINDING PROTEIN
COLD SHOCK DOMAIN
1
man
polymer
CSD
no
no
MKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPG
MKKVIATKVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKKNNPRKYLRSVGDGETVEFDVVEGEKGAEAANVTGPG
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
HUMAN
sample
9606
HOMO SAPIENS
469008
ESCHERICHIA COLI
BL21(DE3)
PET11A
repository
Initial release
Version format compliance
Version format compliance
1
0
2002-02-21
1
1
2011-05-07
1
2
2011-07-13
SHEET
DETERMINATION METHOD: AUTHOR PROVIDED.
PDBE
Y
PDBE
2001-02-23
REL
THE SEQUENCE IS MATCHES TO SWISS PROT ENTRY Q90376 (RESIDUES
15-92) WHICH REPRESENTS Y-BOX BINDING PROTEIN FROM COLUMBA LIVIA
(DOMESTIC PIGEON).
N-TERMINAL METHIONINE ADDED IN PDB-SEQUENCE
THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 15N AND 15N/13C LABELLED COLD SHOCK DOMAIN OF HUMAN YB-1
10
10
15N-EDITED NOESY
15N-EDITED ROESY
13C-EDITED NOESY
HNHA
0
6.7
pH
1
atm
303
K
RESTRAINED MD
TORSION ANGLE DYNAMICS FOLLOWED BY RESTRAINED MD
1
NILGES
refinement
MICHEAL NILGES X-PLOR X-PLOR
X-PLOR
structure solution
NMRPIPE
structure solution
PIPP
structure solution
X-PLOR
500
Varian
INOVA
600
Varian
INOVA
750
Bruker
DRX
MET
1
n
1
MET
1
A
LYS
2
n
2
LYS
2
A
LYS
3
n
3
LYS
3
A
VAL
4
n
4
VAL
4
A
ILE
5
n
5
ILE
5
A
ALA
6
n
6
ALA
6
A
THR
7
n
7
THR
7
A
LYS
8
n
8
LYS
8
A
VAL
9
n
9
VAL
9
A
LEU
10
n
10
LEU
10
A
GLY
11
n
11
GLY
11
A
THR
12
n
12
THR
12
A
VAL
13
n
13
VAL
13
A
LYS
14
n
14
LYS
14
A
TRP
15
n
15
TRP
15
A
PHE
16
n
16
PHE
16
A
ASN
17
n
17
ASN
17
A
VAL
18
n
18
VAL
18
A
ARG
19
n
19
ARG
19
A
ASN
20
n
20
ASN
20
A
GLY
21
n
21
GLY
21
A
TYR
22
n
22
TYR
22
A
GLY
23
n
23
GLY
23
A
PHE
24
n
24
PHE
24
A
ILE
25
n
25
ILE
25
A
ASN
26
n
26
ASN
26
A
ARG
27
n
27
ARG
27
A
ASN
28
n
28
ASN
28
A
ASP
29
n
29
ASP
29
A
THR
30
n
30
THR
30
A
LYS
31
n
31
LYS
31
A
GLU
32
n
32
GLU
32
A
ASP
33
n
33
ASP
33
A
VAL
34
n
34
VAL
34
A
PHE
35
n
35
PHE
35
A
VAL
36
n
36
VAL
36
A
HIS
37
n
37
HIS
37
A
GLN
38
n
38
GLN
38
A
THR
39
n
39
THR
39
A
ALA
40
n
40
ALA
40
A
ILE
41
n
41
ILE
41
A
LYS
42
n
42
LYS
42
A
LYS
43
n
43
LYS
43
A
ASN
44
n
44
ASN
44
A
ASN
45
n
45
ASN
45
A
PRO
46
n
46
PRO
46
A
ARG
47
n
47
ARG
47
A
LYS
48
n
48
LYS
48
A
TYR
49
n
49
TYR
49
A
LEU
50
n
50
LEU
50
A
ARG
51
n
51
ARG
51
A
SER
52
n
52
SER
52
A
VAL
53
n
53
VAL
53
A
GLY
54
n
54
GLY
54
A
ASP
55
n
55
ASP
55
A
GLY
56
n
56
GLY
56
A
GLU
57
n
57
GLU
57
A
THR
58
n
58
THR
58
A
VAL
59
n
59
VAL
59
A
GLU
60
n
60
GLU
60
A
PHE
61
n
61
PHE
61
A
ASP
62
n
62
ASP
62
A
VAL
63
n
63
VAL
63
A
VAL
64
n
64
VAL
64
A
GLU
65
n
65
GLU
65
A
GLY
66
n
66
GLY
66
A
GLU
67
n
67
GLU
67
A
LYS
68
n
68
LYS
68
A
GLY
69
n
69
GLY
69
A
ALA
70
n
70
ALA
70
A
GLU
71
n
71
GLU
71
A
ALA
72
n
72
ALA
72
A
ALA
73
n
73
ALA
73
A
ASN
74
n
74
ASN
74
A
VAL
75
n
75
VAL
75
A
THR
76
n
76
THR
76
A
GLY
77
n
77
GLY
77
A
PRO
78
n
78
PRO
78
A
GLY
79
n
79
GLY
79
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
A
N
GLY
11
A
N
GLY
11
A
O
VAL
59
A
O
VAL
59
A
N
VAL
64
A
N
VAL
64
A
O
GLU
71
A
O
GLU
71
A
N
ALA
70
A
N
ALA
70
A
O
ASP
33
A
O
ASP
33
A
N
VAL
36
A
N
VAL
36
A
O
GLY
23
A
O
GLY
23
A
N
ASN
26
A
N
ASN
26
A
O
THR
12
A
O
THR
12
5
A
A
OE1
HZ3
GLU
LYS
65
68
1.60
8
A
A
H3
OE1
MET
GLU
1
32
1.55
3
A
ARG
27
0.107
SIDE CHAIN
4
A
ARG
27
0.108
SIDE CHAIN
4
A
ARG
51
0.083
SIDE CHAIN
6
A
ARG
27
0.080
SIDE CHAIN
7
A
ARG
27
0.125
SIDE CHAIN
10
A
ARG
19
0.086
SIDE CHAIN
1
3.45
0.50
120.30
123.75
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
27
27
27
N
2
3.26
0.50
120.30
123.56
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
51
51
51
N
3
3.62
0.50
120.30
123.92
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
19
19
19
N
3
4.22
0.50
120.30
124.52
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
27
27
27
N
7
-3.08
0.50
120.30
117.22
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
19
19
19
N
7
3.03
0.50
120.30
123.33
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
51
51
51
N
8
3.09
0.50
120.30
123.39
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
27
27
27
N
8
3.31
0.50
120.30
123.61
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
47
47
47
N
8
3.41
0.50
120.30
123.71
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
51
51
51
N
9
3.24
0.50
120.30
123.54
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
47
47
47
N
10
3.27
0.50
120.30
123.57
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
47
47
47
N
1
A
LYS
3
-116.64
-98.61
1
A
ILE
5
-91.37
-61.49
1
A
TRP
15
37.11
63.67
1
A
LYS
43
56.75
-118.54
1
A
ARG
47
-112.19
60.07
1
A
TYR
49
70.77
144.38
1
A
LEU
50
-93.29
-81.30
1
A
VAL
53
-128.27
-77.88
1
A
GLU
67
-100.35
-71.23
1
A
GLU
71
-122.37
-162.86
1
A
THR
76
-96.32
-134.27
2
A
ILE
5
-95.61
-72.87
2
A
LYS
14
-100.32
-87.29
2
A
LYS
42
65.34
-172.53
2
A
ASN
44
53.21
-86.98
2
A
LYS
48
66.74
-157.44
2
A
GLU
67
-95.37
-136.61
2
A
GLU
71
-107.01
-166.71
2
A
THR
76
-125.96
-121.85
3
A
LYS
2
-90.58
-76.52
3
A
VAL
4
70.73
86.76
3
A
ILE
5
-80.74
-72.08
3
A
LYS
8
59.18
75.67
3
A
ASN
17
-102.52
76.90
3
A
ASN
28
-62.48
84.95
3
A
ASP
29
-159.42
-76.12
3
A
LYS
31
55.65
81.76
3
A
LYS
48
59.32
-156.52
3
A
LEU
50
-88.32
-143.21
3
A
GLU
67
-78.30
-145.37
3
A
GLU
71
-121.09
-168.10
3
A
ASN
74
34.51
63.36
4
A
LYS
8
53.38
83.01
4
A
THR
30
-143.22
33.89
4
A
TYR
49
-86.81
-147.64
4
A
ARG
51
-139.71
-83.21
4
A
GLU
67
-107.82
-89.57
4
A
THR
76
-113.52
-122.09
5
A
LYS
3
75.38
-98.90
5
A
ASP
29
-76.25
-81.33
5
A
LYS
31
77.57
62.29
5
A
ASN
44
-76.73
-80.39
5
A
TYR
49
66.32
159.74
5
A
GLU
65
-139.95
-111.29
5
A
GLU
67
-101.75
-69.78
6
A
LYS
8
60.95
73.15
6
A
LYS
14
-105.37
-86.95
6
A
ASN
28
-82.54
48.00
6
A
THR
30
-150.34
35.33
6
A
LYS
31
57.87
75.99
6
A
LYS
42
-73.43
-74.91
6
A
TYR
49
-97.93
56.82
6
A
ARG
51
-101.49
79.79
6
A
SER
52
-107.02
-85.57
6
A
VAL
53
-108.42
-106.58
6
A
GLU
67
-123.67
-145.47
6
A
GLU
71
-120.53
-168.04
6
A
THR
76
-83.03
-82.85
7
A
LYS
2
60.83
-72.20
7
A
LYS
3
76.79
88.27
7
A
VAL
4
-113.97
-72.54
7
A
TRP
15
77.83
154.11
7
A
ASP
29
-166.97
-76.56
7
A
LYS
31
51.12
73.39
7
A
ASN
44
69.53
-49.13
7
A
LEU
50
-82.16
-86.83
7
A
GLU
65
-144.26
-77.82
8
A
LYS
3
-48.45
103.29
8
A
VAL
4
61.90
103.64
8
A
TRP
15
-69.83
-79.29
8
A
PHE
16
75.10
114.69
8
A
THR
30
-146.40
24.59
8
A
LYS
31
67.09
76.37
8
A
TYR
49
75.85
166.81
8
A
ARG
51
71.40
112.76
8
A
SER
52
-81.23
-70.37
8
A
GLU
65
-160.25
-122.50
9
A
LYS
3
-79.14
-97.16
9
A
VAL
4
65.61
117.15
9
A
LYS
14
-102.47
-99.14
9
A
ARG
27
-36.12
147.65
9
A
ASP
29
-82.94
-78.51
9
A
LYS
31
60.09
67.53
9
A
ASN
45
-118.53
68.58
9
A
LYS
48
-92.50
-93.38
9
A
LEU
50
74.20
-60.51
9
A
ASP
55
66.71
-137.98
9
A
GLU
67
-89.45
-136.23
9
A
THR
76
-109.14
-158.53
10
A
LYS
3
-145.78
-28.65
10
A
LYS
8
59.06
73.12
10
A
LYS
14
-95.14
-100.69
10
A
ASP
29
-132.42
-72.57
10
A
ARG
47
-107.54
-81.25
10
A
GLU
65
-144.81
-60.30
10
A
GLU
67
-80.12
-85.26
10
A
GLU
71
-117.83
-166.81
10
A
THR
76
-99.32
-103.39
Y-BOX BINDING PROTEIN
Solution structure of the single-stranded DNA-binding Cold Shock Domain (CSD) of human Y-box protein 1 (YB1) determined by NMR (10 lowest energy structures)
1
N
N
A
THR
39
A
THR
39
HELX_P
A
ILE
41
A
ILE
41
5
1
3
TRANSLATION FACTOR
TRANSLATION FACTOR, TRANSCRIPTION FACTOR, OB-FOLD, 5-STRANDED ANTI-PARALLEL BETA-BARREL, SINGLE STRANDED DNA BINDING, COLD SHOCK, Y-BOX
1H95
PDB
1
1H95
1
79
1H95
1
79
1H95
A
1
1
79
6
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
LYS
3
A
LYS
3
A
VAL
18
A
VAL
18
A
GLU
57
A
GLU
57
A
GLU
65
A
GLU
65
A
GLY
69
A
GLY
69
A
THR
76
A
THR
76
A
LYS
31
A
LYS
31
A
HIS
37
A
HIS
37
A
GLY
21
A
GLY
21
A
ASN
28
A
ASN
28
A
LYS
3
A
LYS
3
A
VAL
18
A
VAL
18
1
P 1