PDBsum entry 1h8a

Transcription/DNA

PDB id: 1h8a

Contents

Protein chains

68 a.a. *

105 a.a. *

DNA/RNA

Waters ×171

* Residue conservation analysis

PDB id:

1h8a

Name:

Transcription/DNA

Title:

Crystal structure of ternary protein-DNA complex3

Structure:

Caat/enhancer binding protein beta. Chain: a, b. Fragment: residues 259-336. Synonym: c/ebp beta, nfil-6. Engineered: yes. Myb transforming protein. Chain: c. Fragment: residues 1-128. Synonym: amv v-myb.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli. Expression_system_taxid: 469008. Avian myeloblastosis virus. Organism_taxid: 11866. Synthetic: yes. Organism_taxid: 9606

Biol. unit:

Hetero-Pentamer (from PDB file)

Resolution:

2.23Å R-factor: 0.245 R-free: 0.288

Authors:

T.H.Tahirov,K.Ogata

Key ref:

T.H.Tahirov et al. (2002). Mechanism of c-Myb-C/EBP beta cooperation from separated sites on a promoter. Cell, 108, 57-70. PubMed id: 11792321 DOI: 10.1016/S0092-8674(01)00636-5

Date:

31-Jan-01 Release date: 28-Jan-02

Protein chains

P17676  (CEBPB_HUMAN) -  CCAAT/enhancer-binding protein beta from Homo sapiens

Seq: 345 a.a.

Struc: 68 a.a.

Protein chain

P01104  (MYB_AVIMB) -  Transforming protein Myb from Avian myeloblastosis virus

Seq: 382 a.a.

Struc: 105 a.a.

DNA/RNA chains

G-A-T-G-T-G-G-C-G-C-A-A-T-C-C-T-T-A-A-C-G-G-A-C-T-G 26 bases

C-C-A-G-T-C-C-G-T-T-A-A-G-G-A-T-T-G-C-G-C-C-A-C-A-T 26 bases

DOI no: 10.1016/S0092-8674(01)00636-5

Cell 108:57-70 (2002)

PubMed id: 11792321

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

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.

ABSTRACT

c-Myb, but not avian myeloblastosis virus (AMV) v-Myb, cooperates with C/EBP beta to regulate transcription of myeloid-specific genes. To assess the structural basis for that difference, we determined the crystal structures of complexes comprised of the c-Myb or AMV v-Myb DNA-binding domain (DBD), the C/EBP beta DBD, and a promoter DNA fragment. Within the c-Myb complex, a DNA-bound C/EBP beta interacts with R2 of c-Myb bound to a different DNA fragment; point mutations in v-Myb R2 eliminate such interaction within the v-Myb complex. GST pull-down assays, luciferase trans-activation assays, and atomic force microscopy confirmed that the interaction of c-Myb and C/EBP beta observed in crystal mimics their long range interaction on the promoter, which is accompanied by intervening DNA looping.

Selected figure(s)

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 reprinted by permission from Cell Press: Cell (2002, 108, 57-70) copyright 2002.

Figures were selected by an automated process.