2BF0

crystal structure of the rpr of pcf11

• PDB DOI: https://doi.org/10.2210/pdb2BF0/pdb

• Classification: TRANSCRIPTION
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2004-12-02 Released: 2005-01-18 
• Deposition Author(s): Noble, C.G., Hollingworth, D., Martin, S.R., Adeniran, V.E., Smerdon, S.J., Kelly, G., Taylor, I.A., Ramos, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.282 (Depositor) 
• R-Value Work: 
  0.258 (Depositor) 
• R-Value Observed: 
  0.260 (Depositor) 

Literature

Key Features of the Interaction between Pcf11 Cid and RNA Polymerase II Ctd.

Noble, C.G., Hollingworth, D., Martin, S.R., Adeniran, V.E., Smerdon, S.J., Kelly, G., Taylor, I.A., Ramos, A.

(2005) Nat Struct Mol Biol 12: 144

• PubMed: 15665873 
• DOI: https://doi.org/10.1038/nsmb887
• Primary Citation of Related Structures:  
  2BF0


• PubMed Abstract: 
  

  The C-terminal domain (CTD) of the large subunit of RNA polymerase II is a platform for mRNA processing factors and links gene transcription to mRNA capping, splicing and polyadenylation. Pcf11, an essential component of the mRNA cleavage factor IA, contains a CTD-interaction domain that binds in a phospho-dependent manner to the heptad repeats within the RNA polymerase II CTD. We show here that the phosphorylated CTD exists as a dynamic disordered ensemble in solution and, by induced fit, it assumes a structured conformation when bound to Pcf11. In addition, we detected cis-trans populations for the CTD prolines, and found that only the all-trans form is selected for binding. These data suggest that the recognition of the CTD is regulated by independent site-specific modifications (phosphorylation and proline cis-trans isomerization) and, probably, by the local concentration of suitable binding sites.

---

Organizational Affiliation: 

Division of Protein Structure, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.

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: 16.67 kDa 
• Atom Count: 1,131 
• Modelled Residue Count: 131 
• Deposited Residue Count: 143 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PCF11	A [auth X]	143	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P39081 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P39081  Go to UniProtKB:  P39081

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth X]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A [auth X]	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.282 (Depositor) 
• R-Value Work:  0.258 (Depositor) 
• R-Value Observed: 0.260 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.494	α = 90
b = 75.494	β = 90
c = 56.135	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-01-18 
Deposition Author(s): Noble, C.G., Hollingworth, D., Martin, S.R., Adeniran, V.E., Smerdon, S.J., Kelly, G., Taylor, I.A., Ramos, A.

Revision History  

• Version 1.0: 2005-01-18
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-11-06
  Changes: Data collection, Database references, Derived calculations, Structure summary