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PDBsum entry 1avz
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Complex (myristylation/transferase)
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PDB id
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1avz
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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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The crystal structure of HIV-1 nef protein bound to the fyn kinase sh3 domain suggests a role for this complex in altered t cell receptor signaling.
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Authors
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S.Arold,
P.Franken,
M.P.Strub,
F.Hoh,
S.Benichou,
R.Benarous,
C.Dumas.
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Ref.
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Structure, 1997,
5,
1361-1372.
[DOI no: ]
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PubMed id
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Abstract
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BACKGROUND: Human immunodeficiency virus (HIV) Nef protein accelerates virulent
progression of acquired immunodeficiency syndrome (AIDS) by its interaction with
specific cellular proteins involved in signal transduction and host cell
activation. Nef has been shown to bind specifically to a subset of the Src
family of kinases. The structures of free Nef and Nef bound to Src homology
region 3 (SH3) domain are important for the elucidation of how the affinity and
specificity for the Src kinase family SH3 domains are achieved, and also for the
development of potential drugs and vaccines against AIDS. RESULTS: We have
determined the crystal structures of the conserved core of HIV-1 Nef protein
alone and in complex with the wild-type SH3 domain of the p59fyn protein
tyrosine kinase (Fyn), at 3.0 A resolution. Comparison of the bound and unbound
Nef structures revealed that a proline-rich motif (Pro-x-x-Pro), which is
implicated in SH3 binding, is partially disordered in the absence of the binding
partner; this motif only fully adopts a left-handed polyproline type II helix
conformation upon complex formation with the Fyn SH3 domain. In addition, the
structures show how an arginine residue (Arg77) of Nef interacts with Asp 100 of
the so-called RT loop within the Fyn SH3 domain, and triggers a hydrogen-bond
rearrangement which allows the loop to adapt to complement the Nef surface. The
Arg96 residue of the Fyn SH3 domain is specifically accommodated in the same
hydrophobic pocket of Nef as the isoleucine residue of a previously described
Fyn SH3 (Arg96-->lle) mutant that binds to Nef with higher affinity than the
wild type. CONCLUSIONS: The three-dimensional structures support evidence that
the Nef-Fyn complex forms in vivo and may have a crucial role in the T cell
perturbating action of Nef by altering T cell receptor signaling. The structures
of bound and unbound Nef reveal that the multivalency of SH3 binding may be
achieved by a ligand induced flexibility in the RT loop. The structures suggest
possible targets for the design of inhibitors which specifically block Nef-SH3
interactions.
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Figure 7.
Figure 7. Superimposition of the crystal structures of
Nef–SH3 complexes. Stereoview of the interface showing the
environment of the Nef polyproline type II helix region
(residues 71–77) and conserved residues. The two Nef isolates
are superimposed: Nef HIV-1[LAI] isolate in green and Nef[T71R]
HIV-1[NL43] isolate (Nef-D molecule in PDB entry 1EFN in red.
The hydrogen bond between the Arg71 sidechain and Tyr137 of
Fyn[R96I] is shown as a dotted white line. The SH3 domains are
coloured in light purple and dark purple for Fyn[wt] and
Fyn[R96I] (SH3-C molecule in PDB entry 1EFN), respectively.
(Figure generated using the program O [69].)
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The above figure is
reprinted
by permission from Cell Press:
Structure
(1997,
5,
1361-1372)
copyright 1997.
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Secondary reference #1
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Title
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Crystal structure of the conserved core of HIV-1 nef complexed with a src family sh3 domain.
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Authors
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C.H.Lee,
K.Saksela,
U.A.Mirza,
B.T.Chait,
J.Kuriyan.
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Ref.
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Cell, 1996,
85,
931-942.
[DOI no: ]
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PubMed id
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Figure 2.
Figure 2. Structure of Nef–SH3 Complex(A and B) Stereo
diagrams of the polypeptide backbones of Nef[core] and Fyn(R96I)
SH3. The N-terminal helical layer of Nef[core] (residues
71–120), which forms the SH3 interaction surface, is colored
yellow. The rest of Nef[core] (residues 121–203) is colored
green. The disordered loop (residues 149–178) between βC and
βD is indicated as a dotted line. The Fyn(R96I) SH3 domain is
in blue. Also shown are the side chains of the conserved
tryptophan of SH3 (residue 119, in red), the
specificity-conferring isoleucine of SH3 (residue 96, in red),
and the two prolines that define the PxxP motif of Nef (residues
72 and 75, in yellow). The views in (A) and (B) are
approximately orthogonal. The figure was prepared using
MOLSCRIPT ([23]) and Raster3D ( [1]).(C) The molecular surface
of Nef[core], with Fyn(R96I) SH3. The local electrostatic
potential of Nef[core] was calculated in the absence of the SH3
domain using GRASP ([27]). The molecular surface is colored
according to the local electrostatic potential, with colors
ranging from dark blue (most positive region) to deep red (most
negative) through white (neutral). The SH3 domain is shown as a
blue tube. The side chains of Trp-119 and Ile-96 of SH3 are
shown in yellow. Trp-113 and Phe-90 of Nef separate the binding
pocket for Ile-96 of SH3 from the hydrophobic crevice that is
available for potential interaction with other molecules.
Arg-106 of Nef, located at the lower left edge of the crevice,
is implicated in the association of Nef with a Ser kinase
activity ( [33]).
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Figure 5.
Figure 5. Tertiary Interactions between Nef[core] and
Fyn(R96I) SH3 Domain(A) Molecular surface of Nef, showing the
binding site for the isoleucine side chain of the SH3 domain.(B)
Comparison of the interactions in the two complexes in the
crystal. The polypeptide backbones of Nef and the SH3 domain
are shown as green and blue tubes, respectively. Side chains of
Nef are shown in pink and in yellow (displayed under their
respective molecular surfaces). SH3 side chains are shown in
red. Hydrogen bonding interactions are shown as dashed lines.
Hydrogen bonds to backbone positions are indicated by the
placement of white circles along the backbone ribbon. For
clarity, the side chain of Ile-96 is not shown, and instead the
Cα position of this residue is indicated with a red circle. The
structure on the left is the complex that is the focus of the
major part of the discussion in the text. The structure on the
right is that of the second independent complex in the crystal.
Note the slight change in the relative orientation of the Nef
and SH3 components of the complex (see text). The side chain of
Asp-86 forms a hydrogen bond with Thr-97 in the RT loop of the
second complex. For clarity, this interaction is not shown.
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The above figures are
reproduced from the cited reference
with permission from Cell Press
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Secondary reference #2
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Title
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The solution structure of HIV-1 nef reveals an unexpected fold and permits delineation of the binding surface for the sh3 domain of hck tyrosine protein kinase.
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Authors
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S.Grzesiek,
A.Bax,
G.M.Clore,
A.M.Gronenborn,
J.S.Hu,
J.Kaufman,
I.Palmer,
S.J.Stahl,
P.T.Wingfield.
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Ref.
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Nat Struct Biol, 1996,
3,
340-345.
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PubMed id
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