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PDBsum entry 1fl6
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protein ligands Protein-protein interface(s) links
Immune system PDB id
1fl6

 

 

 

 

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Contents
Protein chains
217 a.a. *
219 a.a. *
Ligands
AAH ×2
* Residue conservation analysis
PDB id:
1fl6
Name: Immune system
Title: The hapten complexed germline precursor to sulfide oxidase catalytic antibody 28b4
Structure: Antibody germline precursor to 28b4. Chain: l, a. Fragment: light chain (chains l and a). Engineered: yes. Mutation: yes. Antibody germline precursor to 28b4. Chain: h, b. Fragment: heavy chain (chains h and b). Engineered: yes.
Source: Mus musculus. House mouse. Organism_taxid: 10090. Expressed in: escherichia coli. Expression_system_taxid: 562. Homo sapiens. Human. Organism_taxid: 9606. Expression_system_taxid: 562
Biol. unit: Dimer (from PQS)
Resolution:
2.80Å     R-factor:   0.216     R-free:   0.271
Authors: J.Yin,E.C.Mundorff,P.L.Yang,K.U.Wendt,D.Hanway,R.C.Stevens, P.G.Schultz
Key ref:
J.Yin et al. (2001). A comparative analysis of the immunological evolution of antibody 28B4. Biochemistry, 40, 10764-10773. PubMed id: 11535051 DOI: 10.1021/bi010536c
Date:
11-Aug-00     Release date:   14-Nov-01    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
No UniProt id for this chain
Struc: 217 a.a.
Protein chains
No UniProt id for this chain
Struc: 219 a.a.
Key:    Secondary structure  CATH domain

 

 
DOI no: 10.1021/bi010536c Biochemistry 40:10764-10773 (2001)
PubMed id: 11535051  
 
 
A comparative analysis of the immunological evolution of antibody 28B4.
J.Yin, E.C.Mundorff, P.L.Yang, K.U.Wendt, D.Hanway, R.C.Stevens, P.G.Schultz.
 
  ABSTRACT  
 
In an effort to gain greater insight into the evolution of the redox active, catalytic antibody 28B4, the germline genes used by the mouse to generate this antibody were cloned and expressed, and the X-ray crystal structures of the unliganded and hapten-bound germline Fab of antibody 28B4 were determined. Comparison with the previously determined structures of the unliganded and hapten-bound affinity-matured Fab [Hsieh-Wilson, L. C., Schultz, P. G., and Stevens, R. C. (1996) Proc. Natl. Acad. Sci. U.S.A. 93, 5363] shows that the germline antibody binds the p-nitrophenyl ring of hapten 3 in an orientation significantly different from that seen in the affinity-matured antibody, whereas the phosphonate moiety is bound in a similar mode by both antibodies. The affinity-matured antibody 28B4 has more electrostatic and hydrophobic interactions with hapten 3 than the germline antibody and binds the hapten in a lock-and-key fashion. In contrast, significant conformational changes occur in the loops of CDR H3 and CDR L1 upon hapten binding to the germline antibody, consistent with the notion of structural plasticity in the germline antibody-combining site [Wedemayer, G. J., Patten, P. A., Wang, L. H., Schultz, P. G., and Stevens, R. C. (1997) Science 276, 1665]. The structural differences are reflected in the differential binding affinities of the germline Fab (K(d) = 25 microM) and 28B4 Fab (K(d) = 37 nM) to hapten 3. Nine replacement mutations were found to accumulate in the affinity-matured antibody 28B4 compared to its germline precursor. The effects of each mutation on the binding affinity of the antibody to hapten 3 were characterized in detail in the contexts of both the germline and the affinity-matured antibodies. One of the mutations, Asp95(H)Trp, leads to a change in the orientation of the bound hapten, and its presence is a prerequisite for other somatic mutations to enhance the binding affinity of the germline antibody for hapten 3. Thus, the germline antibody of 28B4 acquired functionally important mutations in a stepwise manner, which fits into a multicycle mutation, affinity selection, and clonal expansion model for germline antibody evolution. Two other antibodies, 20-1 and NZA6, with very different antigen specificities were found to be highly homologous to the germline antibody of 28B4, consistent with the notion that certain germline variable-region gene combinations can give rise to polyspecific hapten binding sites [Romesberg, F. E., Spiller, B., Schultz, P. G., and Stevens, R. C. (1998) Science 279, 1929]. The ultimate specificity of the polyspecific germline antibody appears to be defined by CDR H3 variability and subsequent somatic mutation. Insights into the evolution of antibody-combining sites provided by this and other structural studies are discussed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21287614 S.E.Wong, B.D.Sellers, and M.P.Jacobson (2011).
Effects of somatic mutations on CDR loop flexibility during affinity maturation.
  Proteins, 79, 821-829.  
20334923 S.P.Persaud, D.L.Donermeyer, K.S.Weber, D.M.Kranz, and P.M.Allen (2010).
High-affinity T cell receptor differentiates cognate peptide-MHC and altered peptide ligands with distinct kinetics and thermodynamics.
  Mol Immunol, 47, 1793-1801.  
17675348 J.Morfill, K.Blank, C.Zahnd, B.Luginbühl, F.Kühner, K.E.Gottschalk, A.Plückthun, and H.E.Gaub (2007).
Affinity-matured recombinant antibody fragments analyzed by single-molecule force spectroscopy.
  Biophys J, 93, 3583-3590.  
16618601 D.K.Sethi, A.Agarwal, V.Manivel, K.V.Rao, and D.M.Salunke (2006).
Differential epitope positioning within the germline antibody paratope enhances promiscuity in the primary immune response.
  Immunity, 24, 429-438.  
16684878 G.Thom, A.C.Cockroft, A.G.Buchanan, C.J.Candotti, E.S.Cohen, D.Lowne, P.Monk, C.P.Shorrock-Hart, L.Jermutus, and R.R.Minter (2006).
Probing a protein-protein interaction by in vitro evolution.
  Proc Natl Acad Sci U S A, 103, 7619-7624.  
16954202 J.Zimmermann, E.L.Oakman, I.F.Thorpe, X.Shi, P.Abbyad, C.L.Brooks, S.G.Boxer, and F.E.Romesberg (2006).
Antibody evolution constrains conformational heterogeneity by tailoring protein dynamics.
  Proc Natl Acad Sci U S A, 103, 13722-13727.  
16434745 K.S.Midelfort, and K.D.Wittrup (2006).
Context-dependent mutations predominate in an engineered high-affinity single chain antibody fragment.
  Protein Sci, 15, 324-334.  
16809065 N.S.Longo, and P.E.Lipsky (2006).
Why do B cells mutate their immunoglobulin receptors?
  Trends Immunol, 27, 374-380.  
16365315 K.S.Weber, D.L.Donermeyer, P.M.Allen, and D.M.Kranz (2005).
Class II-restricted T cell receptor engineered in vitro for higher affinity retains peptide specificity and function.
  Proc Natl Acad Sci U S A, 102, 19033-19038.  
15670909 L.Zheng, R.Manetsch, W.D.Woggon, U.Baumann, and J.L.Reymond (2005).
Mechanistic study of proton transfer and hysteresis in catalytic antibody 16E7 by site-directed mutagenesis and homology modeling.
  Bioorg Med Chem, 13, 1021-1029.  
14988504 L.Zheng, U.Baumann, and J.L.Reymond (2004).
Molecular mechanism of enantioselective proton transfer to carbon in catalytic antibody 14D9.
  Proc Natl Acad Sci U S A, 101, 3387-3392.
PDB codes: 1uwe 1uwg
15001706 R.Jimenez, G.Salazar, J.Yin, T.Joo, and F.E.Romesberg (2004).
Protein dynamics and the immunological evolution of molecular recognition.
  Proc Natl Acad Sci U S A, 101, 3803-3808.  
12552112 J.Yin, S.E.Andryski, A.E.Beuscher, R.C.Stevens, and P.G.Schultz (2003).
Structural evidence for substrate strain in antibody catalysis.
  Proc Natl Acad Sci U S A, 100, 856-861.
PDB codes: 1n7m 1ngw 1ngx 1ngy 1ngz
12501157 R.L.Rich, and D.G.Myszka (2002).
Survey of the year 2001 commercial optical biosensor literature.
  J Mol Recognit, 15, 352-376.  
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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