PDBsum entry 1gtw

Transcription/DNA

PDB id: 1gtw

Contents

Protein chains

66 a.a. *

DNA/RNA

Waters ×316

* Residue conservation analysis

References listed in PDB file

Key reference

Title

Structural basis for flexible base recognition by c/ebpbeta

Authors

T.H.Tahirov, T.Inoue-Bungo, K.Sato, M.Sasaki, K.Ogata.

Ref.

To be Published ...

Secondary reference #1

Title

Mechanism of c-Myb-C/ebp beta cooperation from separated sites on a promoter.

Authors

T.H.Tahirov, K.Sato, E.Ichikawa-Iwata, M.Sasaki, T.Inoue-Bungo, M.Shiina, K.Kimura, S.Takata, A.Fujikawa, H.Morii, T.Kumasaka, M.Yamamoto, S.Ishii, K.Ogata.

Ref.

Cell, 2002, 108, 57-70. [DOI no: 10.1016/S0092-8674(01)00636-5]

PubMed id

11792321

Figure 2.
Figure 2. DNA Recognition by c-Myb and AMV v-Myb(A and B) Schematic representations of DNA recognition by c-Myb (A) and AMV v-Myb (B). Dashed and solid lines depict intermolecular hydrogen bonds and van der Waals contacts, respectively. DNA bases labeled in red are involved in direct interactions with proteins.(C) Stereo view of specific interactions between c-Myb and DNA bases. The peptide backbone of c-Myb is drawn as a pink or blue tube in the R2 and R3 regions, respectively. Thin and bold dotted lines depict intermolecular hydrogen bonds and van der Waals interactions, respectively. Water molecules are shown as red balls.(D and E) Electrostatic surface potential of DNA-bound c-Myb R1R2R3 viewed from the front (D) and back (E); positively and negatively charged areas are colored blue and red, respectively.

Figure 3.
Figure 3. Structural Differences between c-Myb R2 and AMV v-Myb R2 and Close-Up Views of the Interactions among c-Myb, C/EBPβ, and DNA(A) Stereo view of the superimposed R2 domains within c-Myb (pink) and AMV v-Myb (gray) complexes. The peptide backbones are drawn as tubes, and the side chains of residues that are mutated or exhibit different conformations in AMV v-Myb are drawn as sticks.(B) A close-up view of the interactions between the Arg114 and Trp115 backbones and the DNA phosphate oxygens at G4′ within the c-Myb and AMV v-Myb complexes.(C) Stereo view of the c-Myb–C/EBPβ interaction site. Intermolecular hydrogen bonds and K^+-mediated interactions are represented by dotted lines. Parts of c-Myb and C/EBPβ chains A and B are drawn as pink, yellow, and green sticks, respectively. The part of the DNA backbone interacting with the C/EBPβ leucine zipper region is also shown. The metal binding sites of R1, R2, and R3 were confirmed by their high-resolution crystal structures (T.T. et al., submitted).(D) Summary of the intermolecular van der Waals interactions between c-Myb and C/EBPβ.(E) Stereo view of the c-Myb–C/EBPβ-DNA interaction site highlighting the interactions involved in stabilization of the α1–α2 loop of c-Myb R2. The peptide backbones of DNA-bound c-Myb (pink) and C/EBPβ chains A (yellow) and B (green) are drawn as tubes. Free c-Myb R2 (blue) is superimposed on the DNA-bound c-Myb R2. An alternative position for the disordered portion of the α1–α2 loop of the free c-Myb R2 is colored dark blue.

The above figures are reproduced from the cited reference with permission from Cell Press

Secondary reference #2

Title

Crystallization and preliminary X-Ray analysis of the c/ebpbeta c-Terminal region in complex with DNA.

Authors

T.H.Tahirov, T.Inoue-Bungo, M.Sasaki, A.Fujikawa, K.Kimura, K.Sato, S.Adachi, N.Kamiya, K.Ogata.

Ref.

Acta Crystallogr D Biol Crystallogr, 2001, 57, 854-856. [DOI no: 10.1107/S0907444901003912]

PubMed id

11375506

Figure 1.
Figure 1 Diffraction pattern of the C/EBP [VE]-DNA crystal; the rotation range is 1.0° and the exposure time is 8 min. The image was obtained using an R-AXIS IV imaging plate at beamline BL44B2 in SPring-8. The wavelength of X-rays was 0.6 Å and the distance from the crystal to the imaging plate was 400 mm.

The above figure is reproduced from the cited reference with permission from the IUCr

Secondary reference #3

Title

Structural analyses of DNA recognition by the aml1/runx-1 runt domain and its allosteric control by cbfbeta.

Authors

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.

Ref.

Cell, 2001, 104, 755-767. [DOI no: 10.1016/S0092-8674(01)00271-9]

PubMed id

11257229

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

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

The above figures are reproduced from the cited reference with permission from Cell Press

Secondary reference #4

Title

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.

Authors

T.H.Tahirov, T.Inoue-Bungo, M.Sasaki, M.Shiina, K.Kimura, K.Sato, T.Kumasaka, M.Yamamoto, N.Kamiya, K.Ogata.

Ref.

Acta Crystallogr D Biol Crystallogr, 2001, 57, 850-853. [DOI no: 10.1107/S0907444901003900]

PubMed id

11375505

Figure 1.
Figure 1 Photomicrographs of crystals of (a) CBF -DNA, (b) CBF -C/EBP -DNA and (c) CBF - -C/EBP -DNA.

The above figure is reproduced from the cited reference with permission from the IUCr

Secondary reference #5

Title

Crystals of ternary protein-Dna complexes composed of DNA-Binding domains of c-Myb or V-Myb, C/ebpalpha or c/ebpbeta and tom-1a promoter fragment.

Authors

T.H.Tahirov, M.Sasaki, T.Inoue-Bungo, A.Fujikawa, K.Sato, T.Kumasaka, M.Yamamoto, K.Ogata.

Ref.

Acta Crystallogr D Biol Crystallogr, 2001, 57, 1655-1658. [DOI no: 10.1107/S0907444901011982]

PubMed id

11679735

Figure 1.
Figure 1 Photomicrographs of crystals of complexes 1 (a), 2 (b), 3 (c), 4 (d), 5-1 (e) and 5-2 (f). The images were recorded at a wavelength of 1.02 Å, a crystal-to-detector distance of 240 mm and an oscillation angle of 1° (a); 0.97934 Å, 300 mm and 1.5° (b); 1.02 Å, 340 mm and 1° (c); 1.04 Å, 300 mm and 1° (d); 1.02 Å, 340 mm and 1° (e); 1.02 Å, 260 mm and 1° (f).

The above figure is reproduced from the cited reference with permission from the IUCr