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 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/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. 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
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 16 KDA POLYPEPTIDE
A, C, E, G
152Homo sapiensMutation(s): 0 
EC: 2.7.7.6
UniProt & NIH Common Fund Data Resources
Find proteins for O15514 (Homo sapiens)
Explore O15514 
Go to UniProtKB:  O15514
PHAROS:  O15514
GTEx:  ENSG00000144231 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO15514
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA-DIRECTED RNA POLYMERASE II 19 KDA POLYPEPTIDE
B, D, F, H
172Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62487 (Homo sapiens)
Explore P62487 
Go to UniProtKB:  P62487
PHAROS:  P62487
GTEx:  ENSG00000168002 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62487
Sequence Annotations
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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

View Full Validation Report



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
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Other, Refinement description