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PDBsum entry 1a3r
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Viral protein/immune system
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PDB id
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1a3r
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Contents |
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220 a.a.
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212 a.a.
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16 a.a.
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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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Crystal structure of a human rhinovirus neutralizing antibody complexed with a peptide derived from viral capsid protein vp2.
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Authors
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J.Tormo,
D.Blaas,
N.R.Parry,
D.Rowlands,
D.Stuart,
I.Fita.
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Ref.
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Embo J, 1994,
13,
2247-2256.
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PubMed id
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Abstract
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The three-dimensional structure of the complex between the Fab fragment of an
anti-human rhinovirus neutralizing antibody (8F5) and a cross-reactive synthetic
peptide from the viral capsid protein VP2 has been determined at 2.5 A
resolution by crystallographic methods. The refinement is presently at an R
factor of 0.18 and the antigen-binding site and viral peptide are well defined.
The peptide antigen adopts a compact fold by two tight turns and interacts
through hydrogen bonds, some with ionic character, and van der Waals contacts
with antibody residues from the six hypervariable loops as well as several
framework amino acids. The conformation adopted by the peptide is closely
related to the corresponding region of the viral protein VP2 on the surface of
human rhinovirus 1A whose three-dimensional structure is known. Implications for
the cross-reactivity between peptides and the viral capsid are discussed. The
peptide-antibody interactions, together with the analysis of mutant viruses that
escape neutralization by 8F5 suggest two different mechanisms for viral escape.
The comparison between the complexed and uncomplexed antibody structures shows
important conformational rearrangements, especially in the hypervariable loops
of the heavy chain. Thus, it constitutes a clear example of the 'induced fit'
molecular recognition mechanism.
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Secondary reference #1
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Title
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Three-Dimensional structure of the FAB fragment of a neutralizing antibody to human rhinovirus serotype 2.
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Authors
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J.Tormo,
E.Stadler,
T.Skern,
H.Auer,
O.Kanzler,
C.Betzel,
D.Blaas,
I.Fita.
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Ref.
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Protein Sci, 1992,
1,
1154-1161.
[DOI no: ]
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PubMed id
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Figure 1.
Fig. 1. model (represented with tom color code) and the electron-density ap (in blue) calculated with coefficients
(2Fo - Fc) n the H-CDR3 region. he quality the map allows most side chains in the pocket to be positioned
with confidence. The sulfate and two nearby water molecules are isible in the upper right side of thephotograph. As men-
tioned (see ext),there ar many aromatic residues around H-CDR3.
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Figure 3.
Fig. 3. Stereo drawing of the a-carbon skeleton of
three 8F5 Fab molecules showing the two groups
of intermolecular crystal contacts. The first type of
contact text) gives ahead-to-tailarrangement
between theconstant module of theFab molecule
closer to the unitcellorign (indicated as R n the fig-
ure) nd the variable module of he symmetrically
related Fab molecule (indicated as I). The second
type of contact is formed he heavy chain
of theconstant domain of the R molecule with the
heavy chain of the variable domain of the symmet-
rical Fab 11.
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The above figures are
reproduced from the cited reference
which is an Open Access publication published by the Protein Society
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Secondary reference #2
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Title
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Crystallization and preliminary X-Ray diffraction studies of the FAB fragment of a neutralizing monoclonal antibody directed against human rhinovirus serotype 2.
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Authors
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J.Tormo,
I.Fita,
O.Kanzler,
D.Blaas.
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Ref.
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J Biol Chem, 1990,
265,
16799-16800.
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PubMed id
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