1DZF

RPB5 from S.cerevisiae

• PDB DOI:  https://doi.org/10.2210/pdb1DZF/pdb

• Classification: TRANSFERASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2000-02-25 Released: 2000-06-09 
• Deposition Author(s): Todone, F., Weinzierl, R.O.J., Brick, P., Onesti, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.271 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 

Literature

Crystal Structure of Rpb5, a Universal Eukaryotic RNA Polymerase Subunit and Trascription Factor Interaction Target

Todone, F., Weinzierl, R.O.J., Brick, P., Onesti, S.

(2000) Proc Natl Acad Sci U S A 97: 6306

• PubMed: 10841537 
• DOI: https://doi.org/10.1073/pnas.97.12.6306
• Primary Citation of Related Structures:  
  1DZF


• PubMed Abstract: 
  

Eukaryotic nuclei contain three different types of RNA polymerases (RNAPs), each consisting of 12-18 different subunits. The evolutionarily highly conserved RNAP subunit RPB5 is shared by all three enzymes and therefore represents a key structural/functional component of all eukaryotic RNAPs. Here we present the crystal structure of the RPB5 subunit from Saccharomyces cerevisiae. The bipartite structure includes a eukaryote-specific N-terminal domain and a C-terminal domain resembling the archaeal RNAP subunit H. RPB5 has been implicated in direct protein-protein contacts with transcription factor IIB, one of the components of the RNAP(II) basal transcriptional machinery, and gene-specific activator proteins, such as the hepatitis B virus transactivator protein X. The experimentally mapped regions of RPB5 involved in these interactions correspond to distinct and surface-exposed alpha-helical structures.

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Organizational Affiliation: 

Blackett Laboratory and Department of Biochemistry, Imperial College, Exhibition Road, London SW7 2AZ, United Kingdom.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 25.12 kDa 
• Atom Count: 1,894 
• Modelled Residue Count: 211 
• Deposited Residue Count: 215 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-DIRECTED RNA POLYMERASES I, II, AND III SUBUNIT RPABC 1	A	215	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: YBR154C OR YBR1204, RPB5, RPA7, RPC9, YBR154C, YBR1204 EC: 2.7.7.6
UniProt
Find proteins for P20434 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P20434  Go to UniProtKB:  P20434

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.271 
• R-Value Work: 0.217 
• R-Value Observed: 0.217 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.05	α = 90
b = 82.22	β = 90
c = 134.81	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
MOSFLM	data reduction
CCP4	data scaling
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-06-09 
Deposition Author(s): Todone, F., Weinzierl, R.O.J., Brick, P., Onesti, S.

Revision History  

• Version 1.0: 2000-06-09
  Type: Initial release
  
• Version 1.1: 2014-02-05
  Changes: Data collection, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance