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PDBsum entry 3k1f
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Transcription
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PDB id
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3k1f
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Contents |
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1416 a.a.
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1120 a.a.
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266 a.a.
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178 a.a.
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214 a.a.
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87 a.a.
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171 a.a.
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134 a.a.
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119 a.a.
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65 a.a.
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114 a.a.
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46 a.a.
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185 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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Rna polymerase ii-Tfiib structure and mechanism of transcription initiation.
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Authors
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D.Kostrewa,
M.E.Zeller,
K.J.Armache,
M.Seizl,
K.Leike,
M.Thomm,
P.Cramer.
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Ref.
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Nature, 2009,
462,
323-330.
[DOI no: ]
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PubMed id
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Abstract
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To initiate gene transcription, RNA polymerase II (Pol II) requires the
transcription factor IIB (B). Here we present the crystal structure of the
complete Pol II-B complex at 4.3 A resolution, and complementary functional
data. The results indicate the mechanism of transcription initiation, including
the transition to RNA elongation. Promoter DNA is positioned over the Pol II
active centre cleft with the 'B-core' domain that binds the wall at the end of
the cleft. DNA is then opened with the help of the 'B-linker' that binds the Pol
II rudder and clamp coiled-coil at the edge of the cleft. The DNA template
strand slips into the cleft and is scanned for the transcription start site with
the help of the 'B-reader' that approaches the active site. Synthesis of the RNA
chain and rewinding of upstream DNA displace the B-reader and B-linker,
respectively, to trigger B release and elongation complex formation.
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Figure 1.
Figure 1: Structure of Pol II–B complex. a, B domain
organization and sequence conservation in the region connecting
the B-ribbon and B-core. Yellow and green highlighting indicates
conserved and invariant residues, respectively, between yeast
(S. cerevisiae), human (Homo sapiens) and the archaeon P.
furiosus (Pfu). b, Ribbon model of B as observed in its complex
with Pol II. A peak in the anomalous difference Fourier
(magenta) defines the zinc ion position (cyan sphere) in the
B-ribbon. The view is from the side. c, Overview of the Pol
II–B structure. Ribbon model with Pol II in silver and B in
colours as in a. Side and front views are used. Pol II domains
that interact with B are highlighted (dock, wheat; wall, blue;
flap loop, light blue; clamp with coiled-coil, red; rudder,
salmon; lid, dark red). The left view is from the side and lacks
most of Rpb2, including the protrusion. The right view is from
the front and includes Rpb2.
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Figure 2.
Figure 2: Models of closed and open complexes. a, Model of
the closed complex (minimal PIC). DNA template and non-template
strands are in blue and cyan, respectively. The TATA element is
in black and the nucleotide in the template strand that
represents position +1 in the open complex is shown as a
space-filling model. Top and bottom views are from the side and
front, respectively. b, Model of the open complex. c, Location
of nucleotides in DNA template strand initiator consensus
sequence and mutations influencing start site selection and DNA
opening. The open complex model is shown around the active
centre. Positions -8 and +1 of the template strand are labelled.
Position -8 lies adjacent to the B-reader helix that contains
residues important for TSS selection (Glu 62, Trp 63, Arg 64,
Phe 66, pale green spheres). The mobile B-reader loop
(green-yellow), which contains residues Arg 78 and Val 79
required for initial transcription and TSS selection, could
reach near positions -1 and +1. Sites of mutations abolishing
DNA opening in archaeal transcription are shown as salmon
spheres.
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The above figures are
reprinted
by permission from Macmillan Publishers Ltd:
Nature
(2009,
462,
323-330)
copyright 2009.
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