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PDBsum entry 1zfd
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Zinc finger DNA binding domain
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PDB id
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1zfd
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References listed in PDB file
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Key reference
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Title
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Solution structures of two zinc-Finger domains from swi5 obtained using two-Dimensional 1h nuclear magnetic resonance spectroscopy. A zinc-Finger structure with a third strand of beta-Sheet.
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Authors
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D.Neuhaus,
Y.Nakaseko,
J.W.Schwabe,
A.Klug.
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Ref.
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J Mol Biol, 1992,
228,
637-651.
[DOI no: ]
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PubMed id
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Abstract
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This paper describes the detailed three-dimensional structures of two
zinc-finger domains from the yeast transcription factor SWI5, calculated using
the results of the n.m.r. experiments described in the accompanying paper. The
structure of finger 2 is essentially similar to those previously obtained by
others for isolated, synthetic single zinc-finger domains in solution, and for
the three zinc-finger peptide Zif268 in its crystalline complex with DNA. The
N-terminal half of the sequence forms a two-stranded, irregular beta-sheet
containing both of the metal-binding cysteine residues, while the remainder of
the structure forms a helix. Approximately the first half of this helix is
alpha-helical, whereas the C-terminal portion, including the two metal-binding
histidine residues, is 3(10) helical. Four invariant hydrophobic residues form a
core to the structure. In contrast to all previously described structures of
zinc-finger domains, finger 1 has an additional strand in the beta-sheet, formed
by residues N-terminal to the formal start of the finger motif. This additional
strand plays a role in stabilising the folded form of finger 1, since a
two-finger peptide lacking the N-terminal residues showed folded structure in
finger 2 but not in finger 1.
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Figure 5.
Figure 5. Schematic representation of the structures of ingers 1 panels and B) and 2 (panels C and D) from SW15,
prepared using the program Molscript (Kraulis, 1991). In each case, the structure having the lowest NOE violations is
shown. iews A and C are related to views B and D by a 90'' rotation bout the vertical. In addition to the schematic
representtion of the backbone, bonds are shown between the non-hydrogen atoms of the side-chains of the metal
binding an conserved hydrophobic residues, nd these rsidues are labelled (not that, because the arrows representing
the /3sheet do not necessarily pass through the actual c'' atom positions, the C''-CB bonds of some side-chains have been
extended with broken lines so as to meet the bacbone representation artificially).
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Figure 6.
Figure 6. Stereoview of a local ackbone superimposition in the turn regio (Cvs44 to Cys49) between the two
P-strands of fingr 2 of SWIS; as in Fig. 3,45 structures are shown. Atoms Nj: NH, C'', e and 0' re shown for all residues,
tog&her with the zinc ions and he non-hydrogen side-chain atoms of Cys44, Pro47 and Cys49. The conformation is
clearly that of tpe II p-turn, characterized by the hydrogen bond between His46 C = 0 and Cys49 ?u'H (indicated hy
the broken line) and by the relative orientation of the Pro47-Gly48 peptide bond.
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The above figures are
reprinted
by permission from Elsevier:
J Mol Biol
(1992,
228,
637-651)
copyright 1992.
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Secondary reference #1
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Title
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Adjacent zinc-Finger motifs in multiple zinc-Finger peptides from swi5 form structurally independent, Flexibly linked domains.
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Authors
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Y.Nakaseko,
D.Neuhaus,
A.Klug,
D.Rhodes.
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Ref.
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J Mol Biol, 1992,
228,
619-636.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3. Sequence specific bining of isolated SW15
peptides containing two and three zinc-finger motifs from
WI5. The autoradiograph shows DNase I footprints of
the two-finger peptide mlOFS and the three-finger peptide
lOFST. The two-finger peptide occupies about 213 of the
inding site of the thre-finger peptide, starting at the 5'
end. The t of the three-finger peptide is very
similar to tht of intact WIS, and is located in the
romoter region o the HO gene at locations - 1290 to
- 1308 from the start of he gene (Stillman et al., 1988).
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Figure 8.
rg30 8.03 383 1.6%1.83$
er3 1 7.58 414 379-385
is32 750 427 303, 314
le33 8.65 347 2.07
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The above figures are
reproduced from the cited reference
with permission from Elsevier
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