2B8K

12-subunit RNA Polymerase II

Summary for 2B8K

• Entry DOI: 10.2210/pdb2b8k/pdb
• Related: 1WCM
• Descriptor: DNA-directed RNA polymerase II largest subunit, DNA-directed RNA polymerases I/II/III subunit 10, DNA-directed RNA polymerase II 13.6 kDa polypeptide, ... (13 entities in total)
• Functional Keywords: dna-directed rna polymerase, dna-dependent rna polymerase, cellular rna polymerase, metal-binding, nuclear protein, transcription, transferase
• Biological source: Saccharomyces cerevisiae (baker's yeast); More
• Cellular location: Nucleus: P04050 P38902 P08518 P16370 P20433 P20434 P34087 P20436 P27999; Nucleus, nucleolus: P22139 P40422; Cytoplasm: P20435
• Total number of polymer chains: 12
• Total formula weight: 519749.21

Authors

Meyer, P.A.,Ye, P.,Zhang, M.,Suh, M.H.,Fu, J. (deposition date: 2005-10-07, release date: 2006-06-20, Last modification date: 2024-10-30)

Primary citation

Meyer, P.A.,Ye, P.,Zhang, M.,Suh, M.H.,Fu, J.
Phasing RNA Polymerase II Using Intrinsically Bound Zn Atoms: An Updated Structural Model.
Structure, 14:973-982, 2006

PubMed 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.

PubMed: 16765890
DOI: 10.1016/j.str.2006.04.003

Experimental method

X-RAY DIFFRACTION (4.15 Å)