 |
PDBsum entry 2k0a
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Metal binding protein
|
PDB id
|
|
|
|
2k0a
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
References listed in PDB file
|
|
|
Key reference
|
|
|
Title
|
|
Solution structure of the u2 snrnp protein rds3p reveals a knotted zinc-Finger motif.
|
|
|
Authors
|
|
A.M.Van roon,
N.M.Loening,
E.Obayashi,
J.C.Yang,
A.J.Newman,
H.Hernández,
K.Nagai,
D.Neuhaus.
|
|
|
Ref.
|
|
Proc Natl Acad Sci U S A, 2008,
105,
9621-9626.
[DOI no: ]
|
|
|
PubMed id
|
|
|
|
|
|
Abstract
|
|
|
Rds3p, a component of the U2 snRNP subcomplex SF3b, is essential for pre-mRNA
splicing and is extremely well conserved in all eukaryotic species. We report
here the solution structure of Rds3p, which reveals an unusual knotted fold
unrelated to previously known knotted proteins. Rds3p has a triangular shape
with a GATA-like zinc finger at each vertex. Pairs of cysteines contributing to
each finger are arranged nonsequentially in a permuted arrangement reminiscent
of domain-swapping but which here involves segments of subdomains within a
single chain. We suggest that the structure arose through a process of segment
swapping after gene duplication. The fingers are connected through beta-strands
and loops, forming an overall topology strongly resembling a "triquetra knot."
The conservation and surface properties of Rds3p suggest that it functions as a
platform for protein assembly within the multiprotein SF3b complex of U2 snRNP.
The recombinant protein used for structure determination is biologically active,
as it restores splicing activity in a yeast splicing extract depleted of native
Rds3p.
|
|
|
|
|
|
|
|
Figure 4.
Hydrophobic core of Rds3p. (A) The strands connecting the
three zinc fingers form a β-triangle and are highly stabilized
by hydrogen bonds. (B) Conserved hydrophobic residues between
the face of the zinc fingers and the β-triangle stabilize the
core of Rds3p.
|
|
Figure 6.
Electrostatic surface of Rds3p. Regions of positive charge
are shown in blue, and regions of negative charge are shown in
red. (Left) The bottom view (same orientation as in Fig. 1)
shows a basic patch formed by lysine and arginine residues on
strand 2 at the base of the triangle. (Right) The top view (same
orientation as in Fig. 2 B and C) shows a slightly acidic patch,
but otherwise the surface is relatively featureless. The missing
area in the top view results from truncation of the flexible
tails.
|
|
|
|
|
|
|
|
|
|
