2B8K

12-subunit RNA Polymerase II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.15 Å
  • R-Value Observed: 0.387 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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

Meyer, P.A.Ye, P.Zhang, M.Suh, M.H.Fu, J.

(2006) Structure 14: 973-982

  • DOI: 10.1016/j.str.2006.04.003
  • Structures With Same Primary Citation

  • 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, ...

    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.


    Organizational Affiliation

    Department of Molecular Biology and Genetics, Cornell University, 221 Biotechnology Building, Ithaca, New York 14853, USA.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II largest subunitA1733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II 140 kDa polypeptideB1224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II 45 kDa polypeptideC318Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II 32 kDa polypeptideD221Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III 27 kDa polypeptideE215Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III 23 kDa polypeptideF155Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II 19 kDa polypeptideG215Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III 14.5 kDa polypeptideH146Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II subunit 9I122Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I/II/III subunit 10J70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase II 13.6 kDa polypeptideK120Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptideL70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B, C, I, J, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.15 Å
  • R-Value Observed: 0.387 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 220.69α = 90
b = 394.33β = 90
c = 281.31γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASESphasing
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-06-20
    Type: Initial release
  • Version 1.1: 2007-10-16
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2012-06-13
    Changes: Other