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PDBsum entry 1hjb
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Transcription/DNA
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PDB id
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1hjb
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structural analyses of DNA recognition by the aml1/runx-1 runt domain and its allosteric control by cbfbeta.
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Authors
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T.H.Tahirov,
T.Inoue-Bungo,
H.Morii,
A.Fujikawa,
M.Sasaki,
K.Kimura,
M.Shiina,
K.Sato,
T.Kumasaka,
M.Yamamoto,
S.Ishii,
K.Ogata.
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Ref.
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Cell, 2001,
104,
755-767.
[DOI no: ]
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PubMed id
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Abstract
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The core binding factor (CBF) heterodimeric transcription factors comprised of
AML/CBFA/PEBP2alpha/Runx and CBFbeta/PEBP2beta subunits are essential for
differentiation of hematopoietic and bone cells, and their mutation is
intimately related to the development of acute leukemias and cleidocranial
dysplasia. Here, we present the crystal structures of the
AML1/Runx-1/CBFalpha(Runt domain)-CBFbeta(core domain)-C/EBPbeta(bZip)-DNA,
AML1/Runx-1/CBFalpha(Runt domain)-C/EBPbeta(bZip)-DNA, and
AML1/Runx-1/CBFalpha(Runt domain)-DNA complexes. The hydrogen bonding network
formed among CBFalpha(Runt domain) and CBFbeta, and CBFalpha(Runt domain) and
DNA revealed the allosteric regulation mechanism of CBFalpha(Runt domain)-DNA
binding by CBFbeta. The point mutations of CBFalpha related to the
aforementioned diseases were also mapped and their effect on DNA binding is
discussed.
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Figure 1.
Figure 1. Overviews of the CBFα-β-C/EBPβ-DNA Quarternary
Complex from Three PerspectivesViews from the front (A), from
the side (B), and from the top (C). Within CBFα, β strands,
and loops are depicted as red arrows and pink tubes,
respectively; within CBFβ, α helices, β strands, and loops
are depicted as green ribbons, blue arrows, and cyan tubes,
respectively. The C-terminal region of the C/EBPβ homodimer
containing the bZip domain is shown as yellow ribbons
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Figure 2.
Figure 2. Sequences, Foldings, and DNA Recognition(A) Amino
acid sequences of CBFα and CBFβ with indications of their
secondary structures; the nucleotide sequence of the 26 bp
double-stranded DNA fragment used for determining the structures
of the CBFα-β-C/EBPβ-DNA and CBFα-C/EBPβ-DNA complexes; and
the sequence of the 16 bp DNA fragment used for determining the
structure of the CBFα-DNA complex.(B and C) Topology diagrams
of the structures of CBFα (B) and CBFβ (C). The first and last
residue numbers of each secondary structure are indicated. The
notations A, B, C, C′, E, F, and G correspond to the β
strands classified as being within the immunoglobulin fold. In
(B), cyan, green, and yellow circles depict the residues
involved in specific DNA base recognition, nonspecific DNA
backbone interactions, and water-mediated interactions,
respectively. In (C), the electron density of a section of L3
(residues 71 to 81) was not observed (dotted line).(D) Schematic
representation of DNA recognition by CBFα. Dashed and solid
lines depict intermolecular hydrogen bonds and van der Waals
contacts, respectively. DNA base labels involved in direct
interactions with amino acids are colored red. A DNA base label
involved in water-mediated base recognitions is colored green.
DNA recognitions by the peptide backbone amide are noted as NH.
Minor groove recognitions are circled with magenta.(E) A stereo
view of the specific interactions between CBFα and DNA. Pink
tubes show the CBFα peptide backbone. Dotted lines depict
intermolecular hydrogen bonds and water molecules are shown as
red balls
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The above figures are
reprinted
by permission from Cell Press:
Cell
(2001,
104,
755-767)
copyright 2001.
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Secondary reference #1
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Title
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Crystallization and preliminary X-Ray analyses of quaternary, Ternary and binary protein-Dna complexes with involvement of aml1/runx-1/cbfalpha runt domain, Cbfbeta and the c/ebpbeta bzip region.
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Authors
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T.H.Tahirov,
T.Inoue-Bungo,
M.Sasaki,
M.Shiina,
K.Kimura,
K.Sato,
T.Kumasaka,
M.Yamamoto,
N.Kamiya,
K.Ogata.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2001,
57,
850-853.
[DOI no: ]
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PubMed id
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Figure 1.
Figure 1 Photomicrographs of crystals of (a) CBF  -DNA,
(b) CBF -C/EBP
 -DNA
and (c) CBF -
-C/EBP
-DNA.
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The above figure is
reproduced from the cited reference
with permission from the IUCr
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