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PDBsum entry 1f11
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Immune system
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PDB id
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1f11
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Structure of the FAB fragment from f124, A monoclonal antibody specific for hepatitis b surface antigen.
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Authors
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F.A.Saul,
B.Vulliez-Le normand,
M.Passafiume,
M.M.Riottot,
G.A.Bentley.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2000,
56,
945-951.
[DOI no: ]
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PubMed id
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Abstract
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The crystal structure of the Fab fragment from the monoclonal anti-preS2
antibody F124 (IgG1,kappa) has been solved by molecular replacement and refined
at 3.0 A resolution. The Fab crystallizes with two independent molecules in the
asymmetric unit. F124 recognizes an epitope contained within the preS2 segment
between residues 120 and 132 of the surface antigen of hepatitis B virus. The
antibody shows a high affinity for the glycan N-linked to Asn123, but it also
cross-reacts with the non-glycosylated peptide fragment 120-132. Although
crystallization was performed in the presence of an eightfold excess of the
cross-reactive peptide, no evidence for the ligand was found in the
antigen-binding site, which is close to a neighbouring molecule in the crystal
lattice. The antigen-binding site has a groove-like topology which is modulated
with pocket-like cavities. It is characterized by a large number of tyrosine and
aspartate residues. The importance of germ-line mutations at the binding site is
discussed.
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Figure 1.
Figure 1 Ramachandran plot for the two independent molecules of
Fab F124. A total of 83.6% of the non-glycine residues fall in
the most favoured regions and 15.6% in the additional allowed
region. AlaL51, which is in an unfavoured region, has dihedral
angles that are characteristic of a  -turn
(Milner-White et al., 1988[Milner-White, E. J., Ross, B. M.,
Ismail, R., Belhady-Mostefa, K. & Poet, R. (1988). J. Mol. Biol.
204, 777-782.]). Residues in the unfavoured regions are
labelled; glycines are shown as triangles. (Produced by the
program PROCHECK; Laskowski et al., 1993 [Laskowski, R. A.,
McArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). J. Appl.
Cryst.
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Figure 5.
Figure 5 A stereoview of the antigen-binding site colour-coded
for electrostatic potential; red represents positive and blue
negative. (Prepared with the program GRASP; Nicholls et al.,
1991[Nicholls, A., Sharp, K. A. & Honig, B. (1991). Proteins
Struct. Funct. Genet. 11, 281-296.].)
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2000,
56,
945-951)
copyright 2000.
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Secondary reference #1
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Title
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Sequence analysis of a monoclonal antibody specific for the pres2 region of hepatitis b surface antigen, And the cloning, Expression and characterisation of its single-Chain fv construction.
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Authors
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M.Passafiume,
B.Vulliez-Le normand,
M.M.Riottot,
G.A.Bentley.
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Ref.
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Febs Lett, 1998,
441,
407-412.
[DOI no: ]
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PubMed id
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Figure 2.
Fig. 2. Schematic presentation of the genetic construction
of ScFv F124.
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Figure 5.
Fig. 5. Competitive inhibition of (A) IgG and (B) scFv to
r-HBsAg binding by preS2 peptides 120–132, 120–145 and
148–174. The peptide concentration is shown on a logarithmic
scale. Competition inhibition is expressed as a percentage with
respect to a control made in the absence of peptide.
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The above figures are
reproduced from the cited reference
with permission from the Federation of European Biochemical Societies
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