1WCM

Complete 12-Subunit RNA Polymerase II at 3.8 Angstrom


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.257 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structures of Complete RNA Polymerase II and its Subcomplex,Rpb4/7

Armache, K.-J.Mitterweger, S.Meinhart, A.Cramer, P.

(2005) J Biol Chem 280: 7131

  • DOI: 10.1074/jbc.M413038200
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • We determined the x-ray structure of the RNA polymerase (Pol) II subcomplex Rpb4/7 at 2.3 A resolution, combined it with a previous structure of the 10-subunit polymerase core, and refined an atomic model of the complete 12-subunit Pol II at 3.8-A re ...

    We determined the x-ray structure of the RNA polymerase (Pol) II subcomplex Rpb4/7 at 2.3 A resolution, combined it with a previous structure of the 10-subunit polymerase core, and refined an atomic model of the complete 12-subunit Pol II at 3.8-A resolution. Comparison of the complete Pol II structure with structures of the Pol II core and free Rpb4/7 shows that the core-Rpb4/7 interaction goes along with formation of an alpha-helix in the linker region of the largest Pol II subunit and with folding of the conserved Rpb7 tip loop. Details of the core-Rpb4/7 interface explain facilitated Rpb4/7 dissociation in a temperature-sensitive Pol II mutant and specific assembly of Pol I with its Rpb4/7 counterpart, A43/14. The refined atomic model of Pol II serves as the new reference structure for analysis of the transcription mechanism and enables structure solution of complexes of the complete enzyme with additional factors and nucleic acids by molecular replacement.


    Organizational Affiliation

    Gene Center, University of Munich (LMU), Department of Chemistry and Biochemistry, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.



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 SECOND LARGEST SUBUNITB1224Saccharomyces 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 POLYPEPTIDED177Saccharomyces 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 KD POLYPEPTIDEG171Saccharomyces 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 14.2 KDA POLYPEPTIDEI122Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
DNA-DIRECTED RNA POLYMERASES I, II AND III 8.3 KDA POLYPEPTIDEJ70Saccharomyces 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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A, B, C, I, J, L
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.80 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.257 
  • R-Value Observed: 0.257 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 222.718α = 90
b = 395.135β = 90
c = 284.3γ = 90
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-12-14
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance