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PDBsum entry 2d03
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Immune system
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PDB id
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2d03
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References listed in PDB file
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Key reference
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Title
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Crystallographic analysis of the nna7 FAB and proposal for the mode of human blood-Group recognition.
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Authors
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K.Xie,
S.C.Song,
S.L.Spitalnik,
J.E.Wedekind.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2005,
61,
1386-1394.
[DOI no: ]
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PubMed id
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Abstract
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The NNA7 Fab antibody fragment recognizes the human N-type blood-group antigen
comprised of the N-terminal glycopeptide of glycophorin A (GPA). A mutant form
of this Fab fragment, NNA7-G91S, exhibits markedly reduced antigen binding. To
provide insight into how these Fab fragments recognize this glycopeptide
antigen, the crystal structures of NNA7 and NNA7-G91S were solved and refined to
1.83 and 1.97 A resolution, respectively. Both molecules are composed of the
same heavy (H) chain Fd fragment, but each contains a slightly different light
(L) chain owing to the G91S substitution. Specifically, the G91S mutation pushes
the backbone of the neighboring H chain away from complementarity-determining
region 3 (CDR3) of the L-chain variable region, allowing an additional glycerol
cryoprotectant molecule to enter the antigen-combining site near the putative
location of O-linked glycosylation. Each Fab fragment also possesses a well
defined 2-(N-morpholino)ethanesulfonic acid (MES) molecule trapped in its
antigen-combining site, as well as a crystallographic symmetry-related molecule
comprising an amino-acid sequence that is virtually identical to the N-terminus
of GPA. The MES molecule interacts with the H-chain CDR in a manner reminiscent
of antibody-carbohydrate complexes. These results suggest a model for
recognition of the glycopeptide antigen that accounts for the deleterious effect
of the G91S substitution.
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Figure 1.
Figure 1
Schematic depiction of the primary sequence of the antigenic GPA glycopeptide. (a) The
polypeptide sequence of the N-terminus depicting the amino-acid polymorphisms that
differentiate the M and N antigens. O-Glycosylated residues are marked with asterisks. (b)
Structures of the O-glycans at positions 2, 3 and 4 that contribute to MN antigenicity.
The sugars are abbreviated as follows: Gal, galactose; GalNAc, N-acetylgalactosamine;
NANA, N-acetylneuraminic (sialic) acid.
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Figure 6.
Figure 6
Superposition of the structures of the antigen-combining sites of NNA7 (yellow) and
NNA7-G91S (blue). Differences in the structures are accentuated by changes in the label
color.
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The above figures are
reprinted
by permission from the IUCr:
Acta Crystallogr D Biol Crystallogr
(2005,
61,
1386-1394)
copyright 2005.
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Secondary reference #1
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Title
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Purification, Crystallization and X-Ray diffraction analysis of a recombinant FAB that recognizes a human blood-Group antigen.
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Authors
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S.C.Song,
K.Xie,
M.Czerwinski,
S.L.Spitalnik,
J.E.Wedekind.
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Ref.
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Acta Crystallogr D Biol Crystallogr, 2004,
60,
788-791.
[DOI no: ]
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PubMed id
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Figure 3.
Figure 3 Representative X-ray diffraction image of an NNA7 Fab
crystal. The inset box is enlarged. Maximum resolution in the
corner of the plate is 1.75 Å. Observed reflections are
overlaid with the predicted diffraction pattern (blue circles).
An arrow indicates Bragg diffraction at 1.88 Å resolution.
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Figure 4.
Figure 4 Representative portion of a (2F[o] - F[c])
electron-density map contoured at the 1.2  level
using  [calc]
from a hybrid model produced by ARP/wARP. The resolution range
for the calculation was 25-1.9 Å. A portion of the model is
shown with a tyrosine residue (red arrowhead) modeled with
`dummy' atoms (isolated yellow spheres). Amino acids for two
glutamines are indicated by ball-and-stick models (bonded blue,
red and yellow spheres are N, O and C atoms, respectively).
Dashed lines with labeled distances indicate potential hydrogen
bonds. A solvent molecule bridges the tyrosine hydroxyl group
and the O atom of the glutamine amide moiety. This figure was
prepared using O (Jones et al., 1991[Jones, T. A., Zou, J. Y.,
Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47,
110-119.]).
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The above figures are
reproduced from the cited reference
with permission from the IUCr
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