2LO6

Structure of Nrd1 CID bound to phosphorylated RNAP II CTD

• PDB DOI: https://doi.org/10.2210/pdb2LO6/pdb
• BMRB: 17173

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


• Deposited: 2012-01-17 Released: 2012-12-26 
• Deposition Author(s): Kubicek, K., Cerna, H., Pasulka, J., Holub, P., Hrossova, D., Loehr, F., Hofr, C., Vanacova, S., Stefl, R.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 40 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 7TZ8

Literature

Serine phosphorylation and proline isomerization in RNAP II CTD control recruitment of Nrd1.

Kubicek, K., Cerna, H., Holub, P., Pasulka, J., Hrossova, D., Loehr, F., Hofr, C., Vanacova, S., Stefl, R.

(2012) Genes Dev 26: 1891-1896

• PubMed: 22892239 
• DOI: https://doi.org/10.1101/gad.192781.112
• Primary Citation of Related Structures:  
  2LO6


• PubMed Abstract: 
  

  Recruitment of appropriate RNA processing factors to the site of transcription is controlled by post-translational modifications of the C-terminal domain (CTD) of RNA polymerase II (RNAP II). Here, we report the solution structure of the Ser5 phosphorylated (pSer5) CTD bound to Nrd1. The structure reveals a direct recognition of pSer5 by Nrd1 that requires the cis conformation of the upstream pSer5-Pro6 peptidyl-prolyl bond of the CTD. Mutations at the complex interface diminish binding affinity and impair processing or degradation of noncoding RNAs. These findings underpin the interplay between covalent and noncovalent changes in the CTD structure that constitute the CTD code.

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Organizational Affiliation: 

CEITEC-Central European Institute of Technology, Masaryk University, Brno, 62500, Czech Republic.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19.93 kDa 
• Atom Count: 1,326 
• Modelled Residue Count: 168 
• Deposited Residue Count: 175 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein NRD1	A	161	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: NRD1, YNL251C, N0868
UniProt
Find proteins for P53617 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53617  Go to UniProtKB:  P53617

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-directed RNA polymerase II subunit RPB1	B	14	Saccharomyces cerevisiae S288C	Mutation(s): 0  EC: 2.7.7.6
UniProt
Find proteins for P04050 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04050  Go to UniProtKB:  P04050

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SEP	B	L-PEPTIDE LINKING	C3 H8 N O6 P		SER

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 40 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-12-26 
Deposition Author(s): Kubicek, K., Cerna, H., Pasulka, J., Holub, P., Hrossova, D., Loehr, F., Hofr, C., Vanacova, S., Stefl, R.

Revision History  

• Version 1.0: 2012-12-26
  Type: Initial release