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PDBsum entry 2hye
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Protein binding
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PDB id
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2hye
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Contents |
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1140 a.a.
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180 a.a.
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719 a.a.
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90 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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Molecular architecture and assembly of the ddb1-Cul4a ubiquitin ligase machinery.
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Authors
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S.Angers,
T.Li,
X.Yi,
M.J.Maccoss,
R.T.Moon,
N.Zheng.
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Ref.
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Nature, 2006,
443,
590-593.
[DOI no: ]
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PubMed id
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Abstract
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Protein ubiquitination is a common form of post-translational modification that
regulates a broad spectrum of protein substrates in diverse cellular pathways.
Through a three-enzyme (E1-E2-E3) cascade, the attachment of ubiquitin to
proteins is catalysed by the E3 ubiquitin ligase, which is best represented by
the superfamily of the cullin-RING complexes. Conserved from yeast to human, the
DDB1-CUL4-ROC1 complex is a recently identified cullin-RING ubiquitin ligase,
which regulates DNA repair, DNA replication and transcription, and can also be
subverted by pathogenic viruses to benefit viral infection. Lacking a canonical
SKP1-like cullin adaptor and a defined substrate recruitment module, how the
DDB1-CUL4-ROC1 E3 apparatus is assembled for ubiquitinating various substrates
remains unclear. Here we present crystallographic analyses of the virally
hijacked form of the human DDB1-CUL4A-ROC1 machinery, which show that DDB1 uses
one beta-propeller domain for cullin scaffold binding and a variably attached
separate double-beta-propeller fold for substrate presentation. Through
tandem-affinity purification of human DDB1 and CUL4A complexes followed by mass
spectrometry analysis, we then identify a novel family of WD40-repeat proteins,
which directly bind to the double-propeller fold of DDB1 and serve as the
substrate-recruiting module of the E3. Together, our structural and proteomic
results reveal the structural mechanisms and molecular logic underlying the
assembly and versatility of a new family of cullin-RING E3 complexes.
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Figure 1.
Figure 1: Crystal structure of the DDB1–CUL4A–ROC1 ubiquitin
ligase complex hijacked by the V protein of simian virus 5.
a, b, Two orthogonal views of the complex structure are shown in
ribbon diagram. DDB1, CUL4A, ROC1 and SV5-V are coloured in
blue, green, red and magenta, respectively. The BPB domain of
DDB1 is coloured in cyan. The zinc atoms in ROC1 and SV5-V are
represented as orange spheres. A previously identified
STAT2-binding site^17 of the viral protein, as well as the four
domains of DDB1, are indicated.
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Figure 2.
Figure 2: Binding interfaces and structural flexibility of DDB1
on CUL4A. a, An overall view of the structural elements
mediating the binding of the DDB1 BPB domain (cyan) with the
CUL4A NTD (green). b, The interface between the top surface of
DDB1-BPB (cyan) and the H2–H5 helices of CUL4A (green) viewed
from above with participating side chains shown as sticks (grey
in DDB1 and green in CUL4A). c, Superposition of the H2–H5
helices of CUL4A (green) and CUL1 (grey) with CUL1-bound SKP1
(blue) shown in the background. The view is the same as that
shown in panel b. CUL4A-bound DDB1 is not shown for clarity. d,
The interface between the CUL4A N-terminal extension sequence
(green) and the peripheral side of the DDB1 BPB domain (blue).
e, Superposition analyses of DDB1 alone (right) and DDB1–SV5-V
complex (left) structures in the context of the full
DDB1–CUL4A–ROC1 complex. The models are docked through the
BPB domain and viewed from the same angles as shown in Fig. 1b.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2006,
443,
590-593)
copyright 2006.
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