2C35

Subunits Rpb4 and Rpb7 of human RNA polymerase II

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 

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This is version 1.3 of the entry. See complete history. 


Literature

Crystal Structure and RNA Binding of the Rpb4/Rpb7 Subunits of Human RNA Polymerase II.

Meka, H., Werner, F., Cordell, S.C., Onesti, S., Brick, P.

(2005) Nucleic Acids Res 33: 6435

  • DOI: 10.1093/nar/gki945
  • Primary Citation of Related Structures:  
    2C35

  • PubMed Abstract: 

    • The Rpb4 and Rpb7 subunits of eukaryotic RNA polymerase II (RNAP(II)) form a heterodimer that protrudes from the 10-subunit core of the enzyme. We have obtained crystals of the human Rpb4/Rpb7 heterodimer and determined the structure to 2.7 A resolution. The presence of putative RNA-binding domains on the Rpb7 subunit and the position of the heterodimer close to the RNA exit groove in the 12 subunit yeast polymerase complex strongly suggests a role for the heterodimer in binding and stabilizing the nascent RNA transcript ...

    The Rpb4 and Rpb7 subunits of eukaryotic RNA polymerase II (RNAP(II)) form a heterodimer that protrudes from the 10-subunit core of the enzyme. We have obtained crystals of the human Rpb4/Rpb7 heterodimer and determined the structure to 2.7 A resolution. The presence of putative RNA-binding domains on the Rpb7 subunit and the position of the heterodimer close to the RNA exit groove in the 12 subunit yeast polymerase complex strongly suggests a role for the heterodimer in binding and stabilizing the nascent RNA transcript. We have complemented the structural analysis with biochemical studies directed at dissecting the RNA-binding properties of the human Rpb4/Rpb7 complex and that of the homologous E/F complex from Methanocaldococcus jannaschii. A number of conserved, solvent-exposed residues in both the human Rpb7 subunit and the archaeal E subunit have been modified by site-directed mutagenesis and the mutants tested for RNA binding by performing electrophoretic mobility shift assays. These studies have identified an elongated surface region on the corresponding face of both subunit E and Rpb7 that is involved in RNA binding. The area spans the nucleic acid binding face of the OB fold, including the B4-B5 loop, but also extends towards the N-terminal domain.

    Organizational Affiliation: 

    Department of Biological Sciences, Imperial College London, SW7 2BW, UK.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 16 KDA POLYPEPTIDE A, C, E, G152Homo sapiensMutation(s): 0 
Gene Names: POLR2D
EC: 2.7.7.6
Find proteins for O15514 (Homo sapiens)
Explore O15514 
Go to UniProtKB:  O15514
NIH Common Fund Data Resources
PHAROS:  O15514
GTEx:  ENSG00000144231
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE B, D, F, H172Homo sapiensMutation(s): 0 
Gene Names: POLR2G, RPB7
Find proteins for P62487 (Homo sapiens)
Explore P62487 
Go to UniProtKB:  P62487
NIH Common Fund Data Resources
PHAROS:  P62487
GTEx:  ENSG00000168002
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.230 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.69α = 85.53
b = 83.19β = 81.8
c = 99.31γ = 81.77
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-11-18
    Type: Initial release
  • Version 1.1: 2013-03-27
    Changes: Derived calculations, Non-polymer description, Other, Refinement description, Version format compliance
  • Version 1.2: 2019-03-06
    Changes: Data collection, Experimental preparation, Other
  • Version 1.3: 2019-05-08
    Changes: Data collection, Experimental preparation