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PDBsum entry 1en0
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Transcription
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PDB id
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1en0
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Contents |
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1213 a.a.*
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943 a.a.*
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263 a.a.*
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110 a.a.*
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211 a.a.*
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140 a.a.*
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117 a.a.*
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65 a.a.*
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36 a.a.*
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* C-alpha coords only
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References listed in PDB file
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Key reference
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Title
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Architecture of RNA polymerase ii and implications for the transcription mechanism.
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Authors
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P.Cramer,
D.A.Bushnell,
J.Fu,
A.L.Gnatt,
B.Maier-Davis,
N.E.Thompson,
R.R.Burgess,
A.M.Edwards,
P.R.David,
R.D.Kornberg.
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Ref.
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Science, 2000,
288,
640-649.
[DOI no: ]
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PubMed id
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Abstract
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A backbone model of a 10-subunit yeast RNA polymerase II has been derived from
x-ray diffraction data extending to 3 angstroms resolution. All 10 subunits
exhibit a high degree of identity with the corresponding human proteins, and 9
of the 10 subunits are conserved among the three eukaryotic RNA polymerases I,
II, and III. Notable features of the model include a pair of jaws, formed by
subunits Rpb1, Rpb5, and Rpb9, that appear to grip DNA downstream of the active
center. A clamp on the DNA nearer the active center, formed by Rpb1, Rpb2, and
Rpb6, may be locked in the closed position by RNA, accounting for the great
stability of transcribing complexes. A pore in the protein complex beneath the
active center may allow entry of substrates for polymerization and exit of the
transcript during proofreading and passage through pause sites in the DNA.
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Figure 4.
Fig. 4. Jaws. (A) Stereoview of structural elements
constituting the jaws (left) and the location of these elements
within pol II (right). (B) Mobility of the larger,
NH[2]-terminal domain of Rpb5. Backbone models of free Rpb5
[gray (47)] and Rpb5 in pol II (pink) are shown with their
smaller, COOH-terminal domains superimposed. (C) Conservation of
amino acid residues of Rpb5.
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Figure 6.
Fig. 6. Topology of the polymerizing complex, and location of
Rpb4 and Rpb7. (A) Nucleic acid configuration in polymerizing
(top) and backtracking (bottom) complexes. (B) Structural
features of functional significance and their location with
respect to the nucleic acids. A surface representation of pol II
is shown as viewed from the top in Fig. 3. To the surface
representation has been added the DNA-RNA hybrid, modeled as
nine base pairs of canonical A-DNA (DNA template strand, blue;
RNA, red), positioned such that the growing (3') end of the RNA
is adjacent to the active site metal and clashes with the
protein are avoided. The exact orientation of the hybrid remains
to be determined. The nontemplate strand of the DNA within the
transcription bubble, single-stranded RNA and the upstream DNA
duplex are not shown. (C) Cutaway view with schematic of DNA
(blue) and with the helical axis of the DNA-RNA hybrid indicated
(dashed white line). An opening in the floor of the cleft that
binds nucleic acid exposes the DNA-RNA hybrid (pore 1) to the
inverted funnel-shaped cavity below. The plane of section is
indicated by a line in (B), and the direction of view
perpendicular to this plane (side) is as in Fig. 3. (D) Surface
representation as in (B), with direction of view as in (C). The
molecular envelope of pol II determined by electron microscopy
of 2D crystals at 16 Å resolution is indicated (yellow
line), as is the location of subunits Rpb4 and Rpb7 (arrow,
Rpb4/7), determined by difference 2D crystallography (25).
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The above figures are
reprinted
by permission from the AAAs:
Science
(2000,
288,
640-649)
copyright 2000.
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Headers
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