PDBsum entry: 2v2t

Transcription

PDB id: 2v2t

Contents

Protein chains

279 a.a. *

313 a.a. *

DNA/RNA

Waters ×34

* Residue conservation analysis

PDB id:

2v2t

Name:

Transcription

Title:

X-ray structure of a nf-kb p50-relb-DNA complex

Structure:

Transcription factor relb. Chain: a. Fragment: residues 91-378. Synonym: relb. Engineered: yes. Nuclear factor nf-kappa-b p105 subunit. Chain: b. Fragment: nuclear factor nf-kappa-b p50 subunit, residues 38-363.

Source:

Mus musculus. Mouse. Organism_taxid: 10090. Cell_line: nf-kb1. Expressed in: escherichia coli. Expression_system_taxid: 511693. Synthetic: yes

Resolution:

3.05Å R-factor: 0.238 R-free: 0.276

Authors:

A.K.Moorthy,D.B.Huang,V.Y.Wang,D.Vu,G.Ghosh

Key ref:

A.K.Moorthy et al. (2007). X-ray structure of a NF-kappaB p50/RelB/DNA complex reveals assembly of multiple dimers on tandem kappaB sites. J Mol Biol, 373, 723-734. PubMed id: 17869269 DOI: 10.1016/j.jmb.2007.08.039

Date:

07-Jun-07 Release date: 03-Jul-07

Protein chain

Q04863  (RELB_MOUSE) -  Transcription factor RelB

Seq: 558 a.a.

Struc: 279 a.a.*

Protein chain

P25799  (NFKB1_MOUSE) -  Nuclear factor NF-kappa-B p105 subunit

Seq: 971 a.a.

Struc: 313 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Cellular component: nucleus (1 term)
• Biological process: regulation of transcription (2 terms)
• Biochemical function: transcription factor activity (1 term)

DOI no: 10.1016/j.jmb.2007.08.039

J Mol Biol 373:723-734 (2007)

PubMed id: 17869269

X-ray structure of a NF-kappaB p50/RelB/DNA complex reveals assembly of multiple dimers on tandem kappaB sites.

A.K.Moorthy, D.B.Huang, V.Y.Wang, D.Vu, G.Ghosh.

ABSTRACT

We describe here the X-ray crystal structure of NF-kappaB p50/RelB heterodimer bound to a kappaB DNA. Although the global modes of subunit association and kappaB DNA recognition are similar to other NF-kappaB/DNA complexes, this complex reveals distinctive features not observed for non-RelB complexes. For example, Lys274 of RelB is removed from the protein-DNA interface whereas the corresponding residues in all other subunits make base-specific contacts. This mode of binding suggests that RelB may allow the recognition of more diverse kappaB sequences. Complementary surfaces on RelB and p50, as revealed by the crystal contacts, are highly suggestive of assembly of multiple p50/RelB heterodimers on tandem kappaB sites in solution. Consistent with this model our in vitro binding experiments reveal optimal assembly of two wild-type p50/RelB heterodimers on tandem HIV kappaB DNA with 2 bp spacing but not by a mutant heterodimer where one of the RelB packing surface is altered. We suggest that multiple NF-kappaB dimers assemble at diverse kappaB promoters through direct interactions utilizing unique protein-protein interaction surfaces.

Selected figure(s)

Figure 2.
Figure 2. Overall structure and the subunit interface of the p50/RelB. (a) The ribbon representation of the complex viewed along the long DNA axis. Throughout the paper the same color code will be maintained for the p50 (green) and RelB (red) subunits. (b) Hydrogen bonding network at the subunit interface. (c) Detailed view of the core of the subunit interface.

Figure 4.
Figure 4. Comparison of the loop 3 conformations. (a) Overlay of the dimerization domains of RelB and p50 reveals difference in their loop 3 conformations. The RelB loop 3 is more helical, which allows more intra-subunit hydrogen bonds between side-chains. (b) A proline at the center of loop 3 breaks the helical structure in p50. (c) Helical conformation in RelB is stabilized by main-chain hydrogen bonds.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 373, 723-734) copyright 2007.

Figures were selected by the author.