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PDBsum entry 1for
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protein Protein-protein interface(s) links
Immunoglobulin PDB id
1for

 

 

 

 

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Contents
Protein chains
210 a.a. *
219 a.a. *
Waters ×157
* Residue conservation analysis
PDB id:
1for
Name: Immunoglobulin
Title: Structure determination of an fab fragment that neutralizes human rhinovirus and analysis of the fab-virus complex
Structure: Igg2a-kappa 17-ia fab (light chain). Chain: l. Engineered: yes. Igg2a-kappa 17-ia fab (heavy chain). Chain: h. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Organism_taxid: 10090
Biol. unit: Dimer (from PQS)
Resolution:
2.75Å     R-factor:   0.174    
Authors: T.J.Smith,H.Liu
Key ref: H.Liu et al. (1994). Structure determination of an Fab fragment that neutralizes human rhinovirus 14 and analysis of the Fab-virus complex. J Mol Biol, 240, 127-137. PubMed id: 8027997
Date:
24-May-94     Release date:   30-Sep-94    
PROCHECK
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 Headers
 References

Protein chain
No UniProt id for this chain
Struc: 210 a.a.
Protein chain
No UniProt id for this chain
Struc: 219 a.a.
Key:    Secondary structure  CATH domain

 

 
J Mol Biol 240:127-137 (1994)
PubMed id: 8027997  
 
 
Structure determination of an Fab fragment that neutralizes human rhinovirus 14 and analysis of the Fab-virus complex.
H.Liu, T.J.Smith, W.M.Lee, A.G.Mosser, R.R.Rueckert, N.H.Olson, R.H.Cheng, T.S.Baker.
 
  ABSTRACT  
 
The crystal structure of Fab17-IA, an antigen-binding fragment from a murine immunoglobulin that neutralizes human rhinovirus 14 (HRV14), has been solved to 2.7 A resolution. Fab17-IA crystallized into three different space groups depending upon the method used to purify the intact antibody. The structure was determined by use of molecular and isomorphous replacement methods. The current model has a crystallographic R-factor of approximately 19% for 10,192 independent reflections between 8 and 2.7 A. Correlation coefficient calculations showed that the Fab17-IA structure can be fit into the Fab17-IA/HRV14 image reconstruction density to within 5 A positional accuracy and to within a few degrees of rotation. The resulting interface of the docked antibody was examined and showed extensive charge and shape complementarity with the virus surface that was supported by site-directed mutagenesis experiments. The success of this approach validates the utility of combining X-ray crystallography with cryo-electron microscopy of complex macromolecular assemblies.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20335262 S.Taube, J.R.Rubin, U.Katpally, T.J.Smith, A.Kendall, J.A.Stuckey, and C.E.Wobus (2010).
High-resolution x-ray structure and functional analysis of the murine norovirus 1 capsid protein protruding domain.
  J Virol, 84, 5695-5705.
PDB codes: 3lq6 3lqe
19361425 C.E.Leysath, A.F.Monzingo, J.A.Maynard, J.Barnett, G.Georgiou, B.L.Iverson, and J.D.Robertus (2009).
Crystal structure of the engineered neutralizing antibody M18 complexed to domain 4 of the anthrax protective antigen.
  J Mol Biol, 387, 680-693.
PDB codes: 3esu 3esv 3et9 3etb
19564688 N.Volkmann (2009).
Confidence intervals for fitting of atomic models into low-resolution densities.
  Acta Crystallogr D Biol Crystallogr, 65, 679-689.  
17296314 E.Shacham, B.Sheehan, and N.Volkmann (2007).
Density-based score for selecting near-native atomic models of unknown structures.
  J Struct Biol, 158, 188-195.  
12743303 J.F.Conway, N.R.Watts, D.M.Belnap, N.Cheng, S.J.Stahl, P.T.Wingfield, and A.C.Steven (2003).
Characterization of a conformational epitope on hepatitis B virus core antigen and quasiequivalent variations in antibody binding.
  J Virol, 77, 6466-6473.  
12414964 V.D.Bowman, E.S.Chase, A.W.Franz, P.R.Chipman, X.Zhang, K.L.Perry, T.S.Baker, and T.J.Smith (2002).
An antibody to the putative aphid recognition site on cucumber mosaic virus recognizes pentons but not hexons.
  J Virol, 76, 12250-12258.  
10998630 A.M.Roseman (2000).
Docking structures of domains into maps from cryo-electron microscopy using local correlation.
  Acta Crystallogr D Biol Crystallogr, 56, 1332-1340.  
10223342 K.M.Taylor, C.Porta, T.Lin, J.E.Johnson, P.J.Barker, and G.P.Lomonossoff (1999).
Position-dependent processing of peptides presented on the surface of cowpea mosaic virus.
  Biol Chem, 380, 387-392.  
10024024 N.Kessler, D.Perl-Treves, L.Addadi, and M.Eisenstein (1999).
Structural and chemical complementarity between antibodies and the crystal surfaces they recognize.
  Proteins, 34, 383-394.  
  10585969 T.S.Baker, N.H.Olson, and S.D.Fuller (1999).
Adding the third dimension to virus life cycles: three-dimensional reconstruction of icosahedral viruses from cryo-electron micrographs.
  Microbiol Mol Biol Rev, 63, 862.  
  9557730 E.A.Hewat, T.C.Marlovits, and D.Blaas (1998).
Structure of a neutralizing antibody bound monovalently to human rhinovirus 2.
  J Virol, 72, 4396-4402.  
  9573224 Z.Che, N.H.Olson, D.Leippe, W.M.Lee, A.G.Mosser, R.R.Rueckert, T.S.Baker, and T.J.Smith (1998).
Antibody-mediated neutralization of human rhinovirus 14 explored by means of cryoelectron microscopy and X-ray crystallography of virus-Fab complexes.
  J Virol, 72, 4610-4622.
PDB code: 1a6t
  9007995 E.C.Ohage, W.Graml, M.M.Walter, S.Steinbacher, and B.Steipe (1997).
Beta-turn propensities as paradigms for the analysis of structural motifs to engineer protein stability.
  Protein Sci, 6, 233-241.  
9261076 E.J.Mancini, F.de Haas, and S.D.Fuller (1997).
High-resolution icosahedral reconstruction: fulfilling the promise of cryo-electron microscopy.
  Structure, 5, 741-750.  
9135136 P.L.Stewart, C.Y.Chiu, S.Huang, T.Muir, Y.Zhao, B.Chait, P.Mathias, and G.R.Nemerow (1997).
Cryo-EM visualization of an exposed RGD epitope on adenovirus that escapes antibody neutralization.
  EMBO J, 16, 1189-1198.  
  8612574 E.A.Hewat, and D.Blaas (1996).
Structure of a neutralizing antibody bound bivalently to human rhinovirus 2.
  EMBO J, 15, 1515-1523.  
8913679 T.S.Baker, and J.E.Johnson (1996).
Low resolution meets high: towards a resolution continuum from cells to atoms.
  Curr Opin Struct Biol, 6, 585-594.  
8747455 L.C.Kovari, C.Momany, and M.G.Rossmann (1995).
The use of antibody fragments for crystallization and structure determinations.
  Structure, 3, 1291-1293.  
7539711 M.W.Wien, D.J.Filman, E.A.Stura, S.Guillot, F.Delpeyroux, R.Crainic, and J.M.Hogle (1995).
Structure of the complex between the Fab fragment of a neutralizing antibody for type 1 poliovirus and its viral epitope.
  Nat Struct Biol, 2, 232-243.
PDB code: 1fpt
7479858 T.J.Smith, R.H.Cheng, N.H.Olson, P.Peterson, E.Chase, R.J.Kuhn, and T.S.Baker (1995).
Putative receptor binding sites on alphaviruses as visualized by cryoelectron microscopy.
  Proc Natl Acad Sci U S A, 92, 10648-10652.  
7536111 I.A.Wilson, and R.L.Stanfield (1994).
Antibody-antigen interactions: new structures and new conformational changes.
  Curr Opin Struct Biol, 4, 857-867.  
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 codes are shown on the right.

 

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