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Title: Phasing RNA Polymerase II Using Intrinsically Bound Zn Atoms: An Updated Structural Model

Abstract

Macromolecular assemblies as large as RNA polymerase II (Pol II) can be phased by a few intrinsically bound Zn atoms, by using MAD experiments as described here. A phasing effectiveness of 570 aa/Zn is attained for Pol II. The resulting experimental, unbiased electron density map is of such quality that it confirms the existing crystallographic model and further reveals structural regions not shown by model phases, thus updating the Pol II model at three sites. The mechanistically important fork loop-1 element is observed to be ordered in the absence of nucleic acids, suggesting additional insights into the mechanisms that maintain the stability of the transcription ternary complex and allow its release. Furthermore, a computational experiment with simulated MAD data sets demonstrates that 1 Zn site is able to provide adequate experimental phase information for as many as 1100 amino acids of polypeptide, under the conditions of the current synchrotron and detector technologies.

Authors:
; ; ; ;
Publication Date:
Research Org.:
Brookhaven National Laboratory (BNL) National Synchrotron Light Source
Sponsoring Org.:
Doe - Office Of Science
OSTI Identifier:
914282
Report Number(s):
BNL-78850-2007-JA
TRN: US0802844
DOE Contract Number:
DE-AC02-98CH10886
Resource Type:
Journal Article
Resource Relation:
Journal Name: Structure; Journal Volume: 14; Journal Issue: 6
Country of Publication:
United States
Language:
English
Subject:
43 PARTICLE ACCELERATORS; AMINO ACIDS; ATOMS; ELECTRON DENSITY; NUCLEIC ACIDS; RNA POLYMERASES; STABILITY; STRUCTURAL MODELS; SYNCHROTRONS; TRANSCRIPTION; national synchrotron light source

Citation Formats

Meyer,P., Suh, M., Ye, P., Zhang, M., and Fu, J.. Phasing RNA Polymerase II Using Intrinsically Bound Zn Atoms: An Updated Structural Model. United States: N. p., 2006. Web. doi:10.1016/j.str.2006.04.003.
Meyer,P., Suh, M., Ye, P., Zhang, M., & Fu, J.. Phasing RNA Polymerase II Using Intrinsically Bound Zn Atoms: An Updated Structural Model. United States. doi:10.1016/j.str.2006.04.003.
Meyer,P., Suh, M., Ye, P., Zhang, M., and Fu, J.. Sun . "Phasing RNA Polymerase II Using Intrinsically Bound Zn Atoms: An Updated Structural Model". United States. doi:10.1016/j.str.2006.04.003.
@article{osti_914282,
title = {Phasing RNA Polymerase II Using Intrinsically Bound Zn Atoms: An Updated Structural Model},
author = {Meyer,P. and Suh, M. and Ye, P. and Zhang, M. and Fu, J.},
abstractNote = {Macromolecular assemblies as large as RNA polymerase II (Pol II) can be phased by a few intrinsically bound Zn atoms, by using MAD experiments as described here. A phasing effectiveness of 570 aa/Zn is attained for Pol II. The resulting experimental, unbiased electron density map is of such quality that it confirms the existing crystallographic model and further reveals structural regions not shown by model phases, thus updating the Pol II model at three sites. The mechanistically important fork loop-1 element is observed to be ordered in the absence of nucleic acids, suggesting additional insights into the mechanisms that maintain the stability of the transcription ternary complex and allow its release. Furthermore, a computational experiment with simulated MAD data sets demonstrates that 1 Zn site is able to provide adequate experimental phase information for as many as 1100 amino acids of polypeptide, under the conditions of the current synchrotron and detector technologies.},
doi = {10.1016/j.str.2006.04.003},
journal = {Structure},
number = 6,
volume = 14,
place = {United States},
year = {Sun Jan 01 00:00:00 EST 2006},
month = {Sun Jan 01 00:00:00 EST 2006}
}