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PDBsum entry 1a8v
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Transcription termination
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PDB id
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1a8v
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Contents |
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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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The structural basis for terminator recognition by the rho transcription termination factor.
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Authors
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C.E.Bogden,
D.Fass,
N.Bergman,
M.D.Nichols,
J.M.Berger.
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Ref.
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Mol Cell, 1999,
3,
487-493.
[DOI no: ]
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PubMed id
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Abstract
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The E. coli Rho protein disengages newly transcribed RNA from its DNA template,
helping terminate certain transcripts. We have determined the X-ray crystal
structure of the RNA-binding domain of Rho complexed to an RNA ligand. Filters
that screen both ligand size and chemical functionality line the primary nucleic
acid-binding site, imparting sequence specificity to a generic single-stranded
nucleic acid-binding fold and explaining the preference of Rho for cytosine-rich
RNA. The crystal packing reveals two Rho domain protomers bound to a single RNA
with a single base spacer, suggesting that the strong RNA-binding sites of Rho
may arise from pairing of RNA-binding modules. Dimerization of symmetric
subunits on an asymmetric ligand is developed as a model for allosteric control
in the action of the intact Rho hexamer.
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Figure 1.
Figure 1. Structure of Rho13N Bound to RNA(a) Experimental
electron density map superposed on a ball-and-stick model of the
refined RNA. The map was generated using phases from the
3-fold-averaged poly-serine molecular replacement solution and
the observed structure factors. Gold contours are at 1.0 σ and
cyan at 2.5 σ.(b) Refined 2F[o] − F[c], model-phased map of
the same region. Gold contours are at 1.3 σ.(c) Front view of
the secondary structure of Rho13N monomer (green) shown with
bound oligoribocytidine (ball-and-stick) in the OB-fold cleft.
The cleft is formed on the surface of strands β2 and β3, with
the β1–β2 and β4–β5 loops forming parts of the lower and
upper walls, respectively. Helices and strands are labeled.(d)
View as in (c), rotated 90° about the vertical axis ([a] and
[b] generated by BOBSCRIPT and RASTER3D [[40 and 22]]; (c) and
(d) generated by RIBBONS [ [12]]).
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Figure 2.
Figure 2. Specific Interactions of Rho13N with Its Target
RNA(a) The RNA moiety (blue sticks) is shown on a surface
representation of the Rho13N C-terminal subdomain. The C[α]
path of Rho13N is marked by a gold coil, while residues and
atoms that interact directly with the RNA are colored black and
labeled.(b) Stereo view of the environment around the first RNA
cytosine. A Van der Waals dot surface is drawn about the protein
atoms. Hydrogen bonds are indicated by dashed lines.(c) Stereo
view of the Watson/Crick-like recognition of the hydrogen bond
donor/acceptor groups of the second RNA cytosine by Arg-66 and
Asp-78; the cytidine base stacks on the ring of Phe-64. The
orientation of these side chains with respect to the cytosine
base is tilted slightly, analogous to a “propeller
twist.”(d) Stereo view of a DNA C·G base pair (from PDB
accession number 126D [[29]]); the cytosine base is stacked on
the ring of a second cytosine (figure generated by RIBBONS [
[12]]).
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The above figures are
reprinted
by permission from Cell Press:
Mol Cell
(1999,
3,
487-493)
copyright 1999.
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