2YJY | pdb_00002yjy

A specific and modular binding code for cytosine recognition in PUF domains

• PDB DOI: https://doi.org/10.2210/pdb2YJY/pdb
• NAKB: 2YJY

• Classification: RNA BINDING PROTEIN/RNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2011-05-24 Released: 2011-06-08 
• Deposition Author(s): Dong, S., Wang, Y., Cassidy-Amstutz, C., Lu, G., Qiu, C., Bigler, R., Jezyk, M., Li, C., Hall, T.M.T., Wang, Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.306 (Depositor), 0.304 (DCC) 
• R-Value Work: 
  0.210 (Depositor), 0.217 (DCC) 
• R-Value Observed: 
  0.215 (Depositor) 

Starting Model: experimental

Literature

Specific and Modular Binding Code for Cytosine Recognition in Pumilio/Fbf (Puf) RNA-Binding Domains.

Dong, S., Wang, Y., Cassidy-Amstutz, C., Lu, G., Bigler, R., Jezyk, M.R., Li, C., Hall, T.M., Wang, Z.

(2011) J Biological Chem 286: 26732

• PubMed: 21653694 
• DOI: https://doi.org/10.1074/jbc.M111.244889
• Primary Citation Related Structures: 
  2YJY


• PubMed Abstract: 
  

  Pumilio/fem-3 mRNA-binding factor (PUF) proteins possess a recognition code for bases A, U, and G, allowing designed RNA sequence specificity of their modular Pumilio (PUM) repeats. However, recognition side chains in a PUM repeat for cytosine are unknown. Here we report identification of a cytosine-recognition code by screening random amino acid combinations at conserved RNA recognition positions using a yeast three-hybrid system. This C-recognition code is specific and modular as specificity can be transferred to different positions in the RNA recognition sequence. A crystal structure of a modified PUF domain reveals specific contacts between an arginine side chain and the cytosine base. We applied the C-recognition code to design PUF domains that recognize targets with multiple cytosines and to generate engineered splicing factors that modulate alternative splicing. Finally, we identified a divergent yeast PUF protein, Nop9p, that may recognize natural target RNAs with cytosine. This work deepens our understanding of natural PUF protein target recognition and expands the ability to engineer PUF domains to recognize any RNA sequence.

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Organizational Affiliation: 
• Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 87.29 kDa 
• Atom Count: 6,012 
• Modeled Residue Count: 698 
• Deposited Residue Count: 720 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PUMILIO HOMOLOG 1	A, B	350	Homo sapiens	Mutation(s): 2
UniProt & NIH Common Fund Data Resources
Find proteins for Q14671 (Homo sapiens) Explore Q14671  Go to UniProtKB:  Q14671
PHAROS:  Q14671 GTEx:  ENSG00000134644

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*AP*UP*UP*GP*CP*AP*UP*AP*UP*AP)-3'	C, D	10	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.306 (Depositor), 0.304 (DCC) 
• R-Value Work:  0.210 (Depositor), 0.217 (DCC) 
• R-Value Observed: 0.215 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 35.796	α = 90
b = 59.34	β = 90
c = 344.724	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-08 
Deposition Author(s): Dong, S., Wang, Y., Cassidy-Amstutz, C., Lu, G., Qiu, C., Bigler, R., Jezyk, M., Li, C., Hall, T.M.T., Wang, Z.

Revision History  

• Version 1.0: 2011-06-08
  Type: Initial release
  
• Version 1.1: 2011-08-03
  Changes: Database references, Version format compliance
• Version 1.2: 2015-10-28
  Changes: Source and taxonomy
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Other, Refinement description