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PDBsum entry 1u2v
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Structural protein
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PDB id
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1u2v
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Contents |
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402 a.a.
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204 a.a.
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357 a.a.
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282 a.a.
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168 a.a.
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166 a.a.
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135 a.a.
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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 structures of actin-Related protein 2/3 complex with bound ATP or ADP.
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Authors
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B.J.Nolen,
R.S.Littlefield,
T.D.Pollard.
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Ref.
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Proc Natl Acad Sci U S A, 2004,
101,
15627-15632.
[DOI no: ]
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PubMed id
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Abstract
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Actin-related protein (Arp) 2/3 complex stimulates formation of actin filaments
at the leading edge of motile cells. Nucleation of filaments depends on
hydrolysis of ATP bound to Arp2. Here we report crystal structures of Arp2/3
complex with bound ATP or ADP. The nucleotides are immobilized on the face of
subdomains 3 and 4 of Arp2, whereas subdomains 1 and 2 are flexible and absent
from the electron density maps. This flexibility may explain why Arp2 does not
hydrolyze ATP until the complex is activated. ATP stabilizes a relatively closed
conformation of Arp3 with the gamma-phosphate bridging loops from opposite sides
of the cleft. ADP binds Arp3 in a unique conformation that favors an open cleft,
revealing a conformational change that may occur in actin and Arps when ATP is
hydrolyzed and phosphate dissociates. These structures provide the an
opportunity to compare all nucleotide-binding states in an actin-related protein
and give insights into the function of both the Arp2/3 complex and actin.
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Figure 3.
Fig. 3. Stereo figure showing conformational changes cased
by ATP binding. (A) Overlay of subdomains 1 and 2 of Arp3 from
the apo-(red) and ATP (blue) complexes. (B) Overlay of Arp3
based on the superposition of the entire Arp3 subunits from
Apo-containing (red), ADP-containing (blue), and ATP-containing
(cyan) complexes. ATP is shown in yellow. DYNDOM-defined
rotation axes required to bring the apo-Arp3 in alignment with
each of the nucleotide-containing structures are blue for
ADP-Arp3 and green for ATP-Arp3. The dotted black lines indicate
distances measured to compare cleft closure. Lengths in Å
of A-C are as follows: apo-Arp3, 9.84, 8.47, and 16.08;
ADP-Arp3, 8.28, 8.84, and 15.02; ATP-Arp3, 8.35, 6.75, and
13.10; actin (PDB entry 1ATN [PDB]
), 8.35, 5.49, and 10.36. The coordinate error estimate by
Luzzati plot is 0.36 Å for the ADP complex and 0.38
Å for the ATP complex (44).
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Figure 5.
Fig. 5. Nucleotide binding to Arp3. (A) Overlay of Arp3
from ATP (yellow) and ADP-Arp2/3 (cyan) complexes based on the
superposition of the entire Arp3 subunit (as in Fig. 3B). ADP is
shown in magenta, and ATP is shown in blue. (B) Interactions of
ATP phosphates with Arp3. (C) Interactions of ADP phosphates
with Arp3. (D) Overlay of actin (PDB entry 1NMD [PDB]
, green) and ATP-Arp3 (yellow) based on superposition of the
entire molecules. ATP and divalent cation from the actin
structure are orange, ATP and Ca^2+ from Arp3 are blue. Select
water molecules from 1NMD [PDB]
are modeled as red spheres.
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