1NT9

Complete 12-subunit RNA polymerase II


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Architecture of initiation-competent 12-subunit RNA polymerase II

Armache, K.-J.Kettenberger, H.Cramer, P.

(2003) Proc Natl Acad Sci U S A 100: 6964-6968

  • DOI: 10.1073/pnas.1030608100
  • Primary Citation of Related Structures:  
    1NT9

  • PubMed Abstract: 
  • RNA polymerase (Pol) II consists of a 10-polypeptide catalytic core and the two-subunit Rpb4/7 complex that is required for transcription initiation. Previous structures of the Pol II core revealed a "clamp," which binds the DNA template strand via t ...

    RNA polymerase (Pol) II consists of a 10-polypeptide catalytic core and the two-subunit Rpb4/7 complex that is required for transcription initiation. Previous structures of the Pol II core revealed a "clamp," which binds the DNA template strand via three "switch regions," and a flexible "linker" to the C-terminal repeat domain (CTD). Here we derived a model of the complete Pol II by fitting structures of the core and Rpb4/7 to a 4.2-A crystallographic electron density map. Rpb4/7 protrudes from the polymerase "upstream face," on which initiation factors assemble for promoter DNA loading. Rpb7 forms a wedge between the clamp and the linker, restricting the clamp to a closed position. The wedge allosterically prevents entry of the promoter DNA duplex into the active center cleft and induces in two switch regions a conformation poised for template-strand binding. Interaction of Rpb4/7 with the linker explains Rpb4-mediated recruitment of the CTD phosphatase to the CTD during Pol II recycling. The core-Rpb7 interaction and some functions of Rpb4/7 are apparently conserved in all eukaryotic and archaeal RNA polymerases but not in the bacterial enzyme.


    Organizational Affiliation

    Institute of Biochemistry and Gene Center, University of Munich, Feodor-Lynen-Strasse 25, 81377 Munich, Germany.



Macromolecules
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II 45 kDa polypeptideC318Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III 23 kDa polypeptideF155Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
Find proteins for P20435 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 19 KD POLYPEPTIDEG171Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerase II 14.2 kDa polypeptideI122Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 13.6 KD POLYPEPTIDEK120Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed RNA polymerases I, II, and III 7.7 kDa polypeptideL70Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II LARGEST SUBUNITA1733Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
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: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-directed polymerase II SECOND LARGEST SUBUNITB1224Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
YEAST DNA-DIRECTED RNA POLYMERASE II 32 KD POLYPEPTIDED221Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
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: 8
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASES I, II, AND III 14.5 KD POLYPEPTIDEH146Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.7.7.6
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 4.20 Å
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 220.4α = 90
b = 391.4β = 90
c = 282.2γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
Omodel building
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-04-22
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance