2NAX | pdb_00002nax

Structure of CCHC zinc finger domain of Pcf11

• PDB DOI: https://doi.org/10.2210/pdb2NAX/pdb
• BMRB: 25953

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


• Deposited: 2016-01-12 Released: 2016-11-23 
• Deposition Author(s): Yang, F., Varani, G.

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Literature

The C terminus of Pcf11 forms a novel zinc-finger structure that plays an essential role in mRNA 3'-end processing.

Yang, F., Hsu, P., Lee, S.D., Yang, W., Hoskinson, D., Xu, W., Moore, C., Varani, G.

(2017) RNA 23: 98-107

• PubMed: 27780845 
• DOI: https://doi.org/10.1261/rna.058354.116
• Primary Citation Related Structures: 
  2NAX


• PubMed Abstract: 
  

  3'-End processing of pre-mRNAs prior to packaging and export to the cytoplasm of the mature transcript is a highly regulated process executed by several tens of protein factors that recognize poorly conserved RNA signals. Among them is Pcf11, a highly conserved, multidomain protein that links transcriptional elongation, 3'-end processing, and transcription termination. Here we report the structure and biochemical function of Pcf11's C-terminal domain, which is conserved from yeast to humans. We identify a novel zinc-finger fold, resembling a trillium flower. Structural, biochemical, and genetic analyses reveal a highly conserved surface that plays a critical role in both cleavage and polyadenylation. These findings provide further insight into this important protein and its multiple functional roles during cotranscriptional RNA processing.

---

Organizational Affiliation: 
• Department of Chemistry, University of Washington, Seattle, Washington 98195, USA.
Department of Developmental, Molecular, and Chemical Biology, Tufts University School of Medicine, Boston, Massachusetts 02111, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 8.72 kDa 
• Atom Count: 608 
• Modeled Residue Count: 76 
• Deposited Residue Count: 76 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein PCF11	A	76	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: PCF11, YDR228C, YD9934.13C
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
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-23 
Deposition Author(s): Yang, F., Varani, G.

Revision History  

• Version 1.0: 2016-11-23
  Type: Initial release
  
• Version 1.1: 2023-06-14
  Changes: Data collection, Database references, Derived calculations, Other
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references