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PDBsum entry 1k83
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Transcription/toxin
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PDB id
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1k83
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Contents |
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1366 a.a.
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1082 a.a.
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266 a.a.
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213 a.a.
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84 a.a.
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133 a.a.
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122 a.a.
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65 a.a.
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114 a.a.
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45 a.a.
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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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Structural basis of transcription: alpha-Amanitin-Rna polymerase ii cocrystal at 2.8 a resolution.
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Authors
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D.A.Bushnell,
P.Cramer,
R.D.Kornberg.
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Ref.
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Proc Natl Acad Sci U S A, 2002,
99,
1218-1222.
[DOI no: ]
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PubMed id
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Abstract
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The structure of RNA polymerase II in a complex with the inhibitor
alpha-amanitin has been determined by x-ray crystallography. The structure of
the complex indicates the likely basis of inhibition and gives unexpected
insight into the transcription mechanism.
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Figure 2.
Fig. 2. Location of  -amanitin
bound to pol II. (A) Cutaway view of a pol II-transcribing
complex showing the location of -amanitin
binding (red dot) in relation to the nucleic acids and
functional elements of the enzyme. Adapted from ref. 24. (B)
Ribbons representation of the pol II structure (top view in
refs. 1 and 7). Eight zinc atoms are shown in light blue, the
active site magnesium is magenta, the region of Rpb1 around -amanitin
is light green (funnel) and dark green (bridge helix), the
region of Rpb2 near -amanitin
is dark blue, and -amanitin
is red. This figure was prepared by using RIBBONS (25).
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Figure 3.
Fig. 3. Interaction of -amanitin
with pol II. (A) The chemical structure of -amanitin,
with residues of pol II that lie within 4 Å [determined by
using CONTACT (26)] placed near the closest contact. The C s of -amanitin
are labeled with blue numbers. Hydrogen bonds are shown as
dashed lines with the distances indicated. (B) Stereoview of the
-amanitin
binding pocket. Ball and stick models of -amanitin
(red bonds) and of pol II residues within 4 Å (gray bonds)
are shown. Rpb1 from A700 to A809 (funnel region) is light
green. Rpb1 from A810 to A825 (bridge helix) is dark green. Rpb2
from B760 to B769 is blue. This figure was generated by using
BOBSCRIPT and RASTER3D (21-23).
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