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PDBsum entry 1llm
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Transcription/DNA
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PDB id
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1llm
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Contents |
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* Residue conservation analysis
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PDB id:
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Transcription/DNA
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Title:
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Crystal structure of a zif23-gcn4 chimera bound to DNA
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Structure:
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5'-d( Tp Cp Cp Cp Ap Cp Gp Cp Gp Tp Gp Gp G)-3'. Chain: a, b. Engineered: yes. Chimera of zif23-gcn4. Chain: c, d. Engineered: yes. Other_details: the zif23 section of the chimera is residues 2-50 and is derived from zif268. The gcn4 section is residues 60-88.
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Source:
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Synthetic: yes. Mus musculus, saccharomyces cerevisiae. House mouse, baker's yeast. Organism_taxid: 10090, 4932. Strain: ,. Expressed in: escherichia coli. Expression_system_taxid: 562.
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Biol. unit:
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Tetramer (from
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Resolution:
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1.50Å
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R-factor:
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0.216
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R-free:
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0.234
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Authors:
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S.A.Wolfe,R.A.Grant,C.O.Pabo
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Key ref:
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S.A.Wolfe
et al.
(2003).
Structure of a designed dimeric zinc finger protein bound to DNA.
Biochemistry,
42,
13401-13409.
PubMed id:
DOI:
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Date:
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29-Apr-02
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Release date:
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30-Sep-03
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PROCHECK
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Headers
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References
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DOI no:
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Biochemistry
42:13401-13409
(2003)
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PubMed id:
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Structure of a designed dimeric zinc finger protein bound to DNA.
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S.A.Wolfe,
R.A.Grant,
C.O.Pabo.
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ABSTRACT
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Proteins that employ dimerization domains to bind cooperatively to DNA have a
number of potential advantages over monomers with regards to gene regulation.
Using a combination of structure-based design and phage display, a dimeric
Cys(2)His(2) zinc finger protein has been created that binds cooperatively to
DNA via an attached leucine zipper dimerization domain. This chimera, derived
from components of Zif268 and GCN4, displayed excellent DNA-binding specificity,
and we now report the 1.5 A resolution cocrystal structure of the Zif268-GCN4
homodimer bound to DNA. This structure shows how phage display has annealed the
DNA binding and dimerization domains into a single functional unit. Moreover,
this chimera provides a potential platform for the creation heterodimeric zinc
finger proteins that can regulate a desired target gene through cooperative DNA
recognition.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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B.Yang,
Y.Zhu,
Y.Wang,
and
G.Chen
(2011).
Interaction identification of Zif268 and TATA(ZF) proteins with GC-/AT-rich DNA sequence: A theoretical study.
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J Comput Chem,
32,
416-428.
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A.W.Reinke,
R.A.Grant,
and
A.E.Keating
(2010).
A synthetic coiled-coil interactome provides heterospecific modules for molecular engineering.
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J Am Chem Soc,
132,
6025-6031.
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PDB codes:
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B.Contreras-Moreira
(2010).
3D-footprint: a database for the structural analysis of protein-DNA complexes.
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Nucleic Acids Res,
38,
D91-D97.
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D.Jantz,
and
J.M.Berg
(2010).
Probing the DNA-binding affinity and specificity of designed zinc finger proteins.
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Biophys J,
98,
852-860.
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M.Y.Jou,
A.F.Philipps,
S.L.Kelleher,
and
B.Lönnerdal
(2010).
Effects of zinc exposure on zinc transporter expression in human intestinal cells of varying maturity.
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J Pediatr Gastroenterol Nutr,
50,
587-595.
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T.W.Siggers,
and
B.Honig
(2007).
Structure-based prediction of C2H2 zinc-finger binding specificity: sensitivity to docking geometry.
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Nucleic Acids Res,
35,
1085-1097.
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D.Endy
(2005).
Foundations for engineering biology.
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Nature,
438,
449-453.
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K.L.Brady,
S.N.Ponnampalam,
M.J.Bumbulis,
and
D.R.Setzer
(2005).
Mutations in TFIIIA that increase stability of the TFIIIA-5 S rRNA gene complex: unusual effects on the kinetics of complex assembly and dissociation.
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J Biol Chem,
280,
26743-26750.
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K.Rothfels,
J.C.Tanny,
E.Molnar,
H.Friesen,
C.Commisso,
and
J.Segall
(2005).
Components of the ESCRT pathway, DFG16, and YGR122w are required for Rim101 to act as a corepressor with Nrg1 at the negative regulatory element of the DIT1 gene of Saccharomyces cerevisiae.
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Mol Cell Biol,
25,
6772-6788.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
