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PDBsum entry 1zk9

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Transcription PDB id
1zk9
Jmol
Contents
Protein chain
110 a.a. *
Waters ×103
* Residue conservation analysis
PDB id:
1zk9
Name: Transcription
Title: Nf-kb relb forms an intertwined homodimer
Structure: Transcription factor relb. Chain: a. Fragment: dimerization domain. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Gene: relb. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PDB file)
Resolution:
2.18Å     R-factor:   0.195     R-free:   0.218
Authors: D.B.Huang,D.Vu,G.Ghosh
Key ref:
D.B.Huang et al. (2005). NF-kappaB RelB forms an intertwined homodimer. Structure, 13, 1365-1373. PubMed id: 16154093 DOI: 10.1016/j.str.2005.06.018
Date:
02-May-05     Release date:   10-May-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q04863  (RELB_MOUSE) -  Transcription factor RelB
Seq:
Struc:
 
Seq:
Struc:
558 a.a.
110 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 7 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     regulation of transcription, DNA-dependent   2 terms 
  Biochemical function     sequence-specific DNA binding transcription factor activity     1 term  

 

 
DOI no: 10.1016/j.str.2005.06.018 Structure 13:1365-1373 (2005)
PubMed id: 16154093  
 
 
NF-kappaB RelB forms an intertwined homodimer.
D.B.Huang, D.Vu, G.Ghosh.
 
  ABSTRACT  
 
The X-ray structure of the RelB dimerization domain (DD) reveals that the RelBDD assumes an unexpected intertwined fold topology atypical of other NF-kappaB dimers. All typical NF-kappaB dimers are formed by the association of two independently folded immunoglobulin (Ig) domains. In RelBDD, two polypeptides reconstruct both Ig domains in the dimer with an extra beta sheet connecting the two domains. Residues most critical to NF-kappaB dimer formation are invariant in RelB, and Y300 plays a positive role in RelBDD dimer formation. The presence of RelB-specific nonpolar residues at the surface removes several intradomain surface hydrogen bonds that may render the domain fold unstable. Intertwining may stabilize the RelBDD homodimer by forming the extra beta sheet. We show that, as in the crystal, RelB forms an intertwined homodimer in solution. We suggest that the transiently stable RelB homodimer might prevent its rapid degradation, allowing for heterodimer formation with p50 and p52.
 
  Selected figure(s)  
 
Figure 2.
Figure 2. Detailed Structural Comparisons between the RelBDD Homodimer and the p50DD Homodimer
(A) Overlay of the "b"-"e" b sheets from p50DD and RelBDD . This view is generated by rotating the superimposed Ig-like folds (right) 90 around the long axis of the fold, as shown in Figure 1E. All of the p50 (green) residues are involved in the dimer interface. RelB is shown in red and gray, respectively, for the two chains in the b sheet.
(B and C) Comparison of the orientations of homologous Tyr at the subunit interfaces of the RelBDD and p50DD dimers, respectively.
(D) The b turn connecting b strands "c'" and "e" and the residues present in the turn of p50DD are shown.
(E) The same segment as in (C) in RelBDD is shown. The turn is converted into a strand ("d"), and the two opposing strands connecting the two Ig-like folds of RelBDD are presented. The side chain conformations of His and Gln are completely different in the two dimers.
(F) The hydrogen bonding pattern in the swapped region of the MLAM mutant of p50DD.
 
  The above figure is reprinted by permission from Cell Press: Structure (2005, 13, 1365-1373) copyright 2005.  
  Figure was selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19768810 S.Wang, O.Kirillova, M.Chruszcz, D.Gront, M.D.Zimmerman, M.T.Cymborowski, I.A.Shumilin, T.Skarina, E.Gorodichtchenskaia, A.Savchenko, A.M.Edwards, and W.Minor (2009).
The crystal structure of the AF2331 protein from Archaeoglobus fulgidus DSM 4304 forms an unusual interdigitated dimer with a new type of alpha + beta fold.
  Protein Sci, 18, 2410-2419.
PDB code: 2fdo
  20066103 T.Huxford, and G.Ghosh (2009).
A structural guide to proteins of the NF-kappaB signaling module.
  Cold Spring Harbor Perspect Biol, 1, a000075.  
19020113 X.Chen, B.K.Yoza, M.El Gazzar, J.Y.Hu, S.L.Cousart, and C.E.McCall (2009).
RelB sustains IkappaBalpha expression during endotoxin tolerance.
  Clin Vaccine Immunol, 16, 104-110.  
18321863 A.J.Fusco, O.V.Savinova, R.Talwar, J.D.Kearns, A.Hoffmann, and G.Ghosh (2008).
Stabilization of RelB requires multidomain interactions with p100/p52.
  J Biol Chem, 283, 12324-12332.  
17546045 P.Taneja, A.Mallakin, L.A.Matise, D.P.Frazier, M.Choudhary, and K.Inoue (2007).
Repression of Dmp1 and Arf transcription by anthracyclins: critical roles of the NF-kappaB subunit p65.
  Oncogene, 26, 7457-7466.  
16623771 A.Hoffmann, and D.Baltimore (2006).
Circuitry of nuclear factor kappaB signaling.
  Immunol Rev, 210, 171-186.  
17072323 A.Hoffmann, G.Natoli, and G.Ghosh (2006).
Transcriptional regulation via the NF-kappaB signaling module.
  Oncogene, 25, 6706-6716.  
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 code is shown on the right.