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PDBsum entry 3c2a
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Immune system
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PDB id
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3c2a
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Contents |
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216 a.a.
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231 a.a.
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13 a.a.
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* Residue conservation analysis
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PDB id:
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Immune system
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Title:
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Antibody fab fragment 447-52d in complex with ug1033 peptide
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Structure:
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Fab 447-52d light chain. Chain: l, m. Fab 447-52d heavy chain. Chain: h, i. Envelope glycoprotein. Chain: p, q. Engineered: yes
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Source:
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Homo sapiens. Human. Organism_taxid: 9606. Synthetic: yes. Human immunodeficiency virus 1. Organism_taxid: 11676. Other_details: the peptide is naturally found in HIV-1 gp120.
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Resolution:
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2.10Å
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R-factor:
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0.241
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R-free:
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0.298
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Authors:
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A.K.Dhillon,R.L.Stanfield,I.A.Wilson
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Key ref:
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A.K.Dhillon
et al.
(2008).
Structure determination of an anti-HIV-1 Fab 447-52D-peptide complex from an epitaxially twinned data set.
Acta Crystallogr D Biol Crystallogr,
64,
792-802.
PubMed id:
DOI:
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Date:
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24-Jan-08
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Release date:
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08-Jul-08
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PROCHECK
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Headers
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References
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P0DOY2
(IGLC2_HUMAN) -
Immunoglobulin lambda constant 2 from Homo sapiens
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Seq:
Struc:
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106 a.a.
216 a.a.*
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DOI no:
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Acta Crystallogr D Biol Crystallogr
64:792-802
(2008)
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PubMed id:
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Structure determination of an anti-HIV-1 Fab 447-52D-peptide complex from an epitaxially twinned data set.
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A.K.Dhillon,
R.L.Stanfield,
M.K.Gorny,
C.Williams,
S.Zolla-Pazner,
I.A.Wilson.
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ABSTRACT
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Although antibodies against the third variable loop (V3) of the HIV-1 viral
envelope glycoprotein are among the first neutralizing antibodies to be detected
in infected individuals, they are normally restricted in their specificity.
X-ray crystallographic studies of V3-specific antibodies have contributed to a
more thorough understanding of recognition of this epitope and of conserved
features in the V3 loop that could potentially aid in the design of a
multi-component vaccine. The human antibody 447-52D exhibits relatively broad
neutralization of primary viral isolates compared with other V3-loop antibodies.
A crystal structure of Fab 447-52D in complex with a V3 peptide (UG1033) was
determined at 2.1 angstroms resolution. The structure was determined using an
epitaxially twinned data set and in-house programs to detect and remove
overlapping reflections. Although the processed data have lower than desired
completeness and slightly higher than normal R values for the resolution,
good-quality electron-density maps were obtained that enabled structure
determination. The structure revealed an extended CDR H3 loop that forms a
beta-sheet with the peptide, with the predominant contacts being main-chain
hydrogen bonds. The V3 peptide and Fab show high structural homology with the
previously reported structures of other Fab 447-52D complexes, reinforcing the
idea that the V3 loop may adopt a small set of conserved structures,
particularly around the crown of the beta-hairpin.
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Selected figure(s)
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Figure 4.
Figure 4 Binding-site interactions between the UG1033 V3
peptide and Fab 447-52D. The Fab CDR H3 is shown in violet and
the UG1033 peptide in yellow. (a) The mixed three-strand  -sheet
formed by CDR H3 and the V3 peptide is shown. (b) The main-chain
hydrogen-bond interactions in the three-strand -sheet
are represented by black dotted lines. (c) Side-chain
interactions between the UG1033 peptide and the Fab light chain
(cyan) and heavy chain (violet).
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Figure 7.
Figure 7 Comparison of the crystal structure of the UG1033
peptide bound to Fab 447-52D with the NMR structures of the MN
and IIIB peptides bound to 447-52D Fv. The C^  -backbone
structures are shown in a similar orientation for (a) the UG1033
V3 peptide from the crystal structure and (b) MN (PDB code 1n1z
) and (c) IIIB (PDB code 1u6u ) from NMR structures. The
N-terminus of each peptide is oriented to the left.
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The above figures are
reprinted
from an Open Access publication published by the IUCr:
Acta Crystallogr D Biol Crystallogr
(2008,
64,
792-802)
copyright 2008.
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Figures were
selected
by an automated process.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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D.Almond,
T.Kimura,
X.Kong,
J.Swetnam,
S.Zolla-Pazner,
and
T.Cardozo
(2010).
Structural conservation predominates over sequence variability in the crown of HIV type 1's V3 loop.
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AIDS Res Hum Retroviruses,
26,
717-723.
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S.Zolla-Pazner,
and
T.Cardozo
(2010).
Structure-function relationships of HIV-1 envelope sequence-variable regions refocus vaccine design.
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Nat Rev Immunol,
10,
527-535.
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X.Jiang,
V.Burke,
M.Totrov,
C.Williams,
T.Cardozo,
M.K.Gorny,
S.Zolla-Pazner,
and
X.P.Kong
(2010).
Conserved structural elements in the V3 crown of HIV-1 gp120.
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Nat Struct Mol Biol,
17,
955-961.
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PDB codes:
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V.Burke,
C.Williams,
M.Sukumaran,
S.S.Kim,
H.Li,
X.H.Wang,
M.K.Gorny,
S.Zolla-Pazner,
and
X.P.Kong
(2009).
Structural basis of the cross-reactivity of genetically related human anti-HIV-1 mAbs: implications for design of V3-based immunogens.
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Structure,
17,
1538-1546.
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PDB codes:
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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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