PDBsum entry 3les

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protein ligands links
Immune system PDB id
Protein chains
179 a.a. *
SO4 ×4
Waters ×28
* Residue conservation analysis
PDB id:
Name: Immune system
Title: 2f5 epitope scaffold es2
Structure: RNA polymerase sigma factor. Chain: a, b. Fragment: unp residues 93-271. Engineered: yes
Source: Thermus aquaticus. Organism_taxid: 271. Gene: sigma factor siga. Expressed in: homo sapiens. Expression_system_taxid: 9606.
2.77Å     R-factor:   0.230     R-free:   0.260
Authors: G.Ofek,F.J.Guenaga,W.R.Schief,J.Skinner,R.Wyatt,D.Baker,P.D.
Key ref: G.Ofek et al. (2010). Elicitation of structure-specific antibodies by epitope scaffolds. Proc Natl Acad Sci U S A, 107, 17880-17887. PubMed id: 20876137
15-Jan-10     Release date:   29-Sep-10    
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Protein chains
Pfam   ArchSchema ?
Q9EZJ8  (Q9EZJ8_THEAQ) -  RNA polymerase sigma factor SigA
438 a.a.
179 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 14 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     regulation of transcription, DNA-dependent   2 terms 
  Biochemical function     DNA binding     3 terms  


Proc Natl Acad Sci U S A 107:17880-17887 (2010)
PubMed id: 20876137  
Elicitation of structure-specific antibodies by epitope scaffolds.
G.Ofek, F.J.Guenaga, W.R.Schief, J.Skinner, D.Baker, R.Wyatt, P.D.Kwong.
No abstract given.


Literature references that cite this PDB file's key reference

  PubMed id Reference
23151583 J.Huang, G.Ofek, L.Laub, M.K.Louder, N.A.Doria-Rose, N.S.Longo, H.Imamichi, R.T.Bailer, B.Chakrabarti, S.K.Sharma, S.M.Alam, T.Wang, Y.Yang, B.Zhang, S.A.Migueles, R.Wyatt, B.F.Haynes, P.D.Kwong, J.R.Mascola, and M.Connors (2012).
Broad and potent neutralization of HIV-1 by a gp41-specific human antibody.
  Nature, 491, 406-412.
PDB code: 4g6f
21198670 B.S.Graham (2011).
Biological challenges and technological opportunities for respiratory syncytial virus vaccine development.
  Immunol Rev, 239, 149-166.  
21479208 F.Breden, C.Lepik, N.S.Longo, M.Montero, P.E.Lipsky, and J.K.Scott (2011).
Comparison of antibody repertoires produced by HIV-1 infection, other chronic and acute infections, and systemic autoimmune disease.
  PLoS One, 6, e16857.  
22002224 M.Kim, Z.Y.Sun, K.D.Rand, X.Shi, L.Song, Y.Cheng, A.F.Fahmy, S.Majumdar, G.Ofek, Y.Yang, P.D.Kwong, J.H.Wang, J.R.Engen, G.Wagner, and E.L.Reinherz (2011).
Antibody mechanics on a membrane-bound HIV segment essential for GP41-targeted viral neutralization.
  Nat Struct Mol Biol, 18, 1235-1243.  
20937874 D.R.Burton (2010).
Scaffolding to build a rational vaccine design strategy.
  Proc Natl Acad Sci U S A, 107, 17859-17860.  
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.