The human Y-box protein 1 (YB-1) is a member of the Y-box protein family, a class of proteins involved in transcriptional and translational regulation of a wide range of genes. Here, we report the solution structure of the cold-shock domain (CSD) of YB-1, which is thought to be responsible for nucleic acid binding. It is the first structure solved of a eukaryotic member of the cold-shock protein family and consists of a closed five-stranded anti-parallel beta-barrel capped by a long flexible loop. The structure of CSD is similar to the OB-fold and a comparison with bacterial cold-shock proteins shows that its structural properties are conserved from bacteria to man. Our data suggest the presence of a DNA-binding site consisting of a patch of positively charged and aromatic residues on the surface of the beta-barrel. Further, it is shown that CSD, which has a preference for binding single-stranded pyrimidine-rich sequences, binds weakly and hardly specifically to DNA. Binding affinities reported for intact YB-1 indicate that domains other than the CSD play a role in DNA binding of YB-1.
M
S
S
E
A
E
T
Q
Q
P
P
A
A
P
P
A
A
P
A
L
S
A
A
D
T
K
P
G
T
T
G
S
G
A
G
S
G
G
P
G
G
L
T
S
A
A
P
A
G
G
D
K
K
V
I
A
T
K
V
L
G
T
V
K
W
F
N
V
R
N
G
Y
G
F
I
N
R
N
D
T
K
E
D
V
F
V
H
Q
T
A
I
K
K
N
N
P
R
K
Y
L
R
S
V
G
D
G
E
T
V
E
F
D
V
V
E
G
E
K
G
A
E
A
A
N
V
T
G
P
G
G
V
P
V
Q
G
S
K
Y
A
A
D
R
N
H
Y
R
R
Y
P
R
R
R
G
P
P
R
N
Y
Q
Q
N
Y
Q
N
S
E
S
G
E
K
N
E
G
S
E
S
A
P
E
G
Q
A
Q
Q
R
R
P
Y
R
R
R
R
F
P
P
Y
Y
M
R
R
P
Y
G
R
R
P
Q
Y
S
N
P
P
V
Q
G
E
V
M
E
G
A
D
N
Q
G
A
G
E
Q
G
R
P
V
R
Q
N
M
Y
R
G
Y
R
P
R
F
R
R
G
P
P
R
Q
R
Q
P
R
E
D
G
N
E
E
D
K
E
N
Q
G
D
E
T
Q
G
Q
Q
P
P
Q
R
R
Y
R
R
N
F
N
Y
R
R
R
R
P
E
N
P
K
P
Q
D
G
K
E
T
K
A
A
D
P
P
A
E
N
S
S
A
P
E
A
E
Q
G
G
A
E