Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 11.84 kDa 
• Atom Count: 831 
• Modelled Residue Count: 100 
• Deposited Residue Count: 100 
• Unique protein chains: 1

2ROK

Solution structure of the cap-binding domain of PARN complexed with the cap analog

• PDB DOI: 10.2210/pdb2ROK/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Mus musculus
• Mutation(s): No 


• Deposited: 2008-03-28 Released: 2009-02-10 
• Deposition Author(s): Nagata, T., Suzuki, S., Endo, R., Shirouzu, M., Terada, T., Inoue, M., Kigawa, T., Guntert, P., Hayashizaki, Y., Muto, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

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

Literature

The RRM domain of poly(A)-specific ribonuclease has a noncanonical binding site for mRNA cap analog recognition.

Nagata, T., Suzuki, S., Endo, R., Shirouzu, M., Terada, T., Inoue, M., Kigawa, T., Kobayashi, N., Guntert, P., Tanaka, A., Hayashizaki, Y., Muto, Y., Yokoyama, S.

(2008) Nucleic Acids Res 36: 4754-4767

• PubMed: 18641416 
• DOI: 10.1093/nar/gkn458
• Primary Citation of Related Structures:  
  2ROK


• PubMed Abstract: 
  

The degradation of the poly(A) tail is crucial for posttranscriptional gene regulation and for quality control of mRNA. Poly(A)-specific ribonuclease (PARN) is one of the major mammalian 3' specific exo-ribonucleases involved in the degradation of the mRNA poly(A) tail, and it is also involved in the regulation of translation in early embryonic development. The interaction between PARN and the m(7)GpppG cap of mRNA plays a key role in stimulating the rate of deadenylation. Here we report the solution structures of the cap-binding domain of mouse PARN with and without the m(7)GpppG cap analog. The structure of the cap-binding domain adopts the RNA recognition motif (RRM) with a characteristic alpha-helical extension at its C-terminus, which covers the beta-sheet surface (hereafter referred to as PARN RRM). In the complex structure of PARN RRM with the cap analog, the base of the N(7)-methyl guanosine (m(7)G) of the cap analog stacks with the solvent-exposed aromatic side chain of the distinctive tryptophan residue 468, located at the C-terminal end of the second beta-strand. These unique structural features in PARN RRM reveal a novel cap-binding mode, which is distinct from the nucleotide recognition mode of the canonical RRM domains.

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Organizational Affiliation: 

Systems and Structural Biology Center, Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
poly(A)-specific ribonuclease	A	100	Mus musculus	Mutation(s): 0  Gene Names: Parn EC: 3.1.13.4
UniProt
Find proteins for Q8VDG3 (Mus musculus) Explore Q8VDG3  Go to UniProtKB:  Q8VDG3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GDP	C [auth A]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
7MG	B [auth A]	7N-METHYL-8-HYDROGUANOSINE-5'-MONOPHOSPHATE C11 H18 N5 O8 P ZMWJGXGSWZFZPJ-KQYNXXCUSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
7MG	PDBBind:  2ROK	Kd: 4.50e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 40 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2ROK Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2008-03-28 
• Released Date: 2009-02-10 
Deposition Author(s): Nagata, T., Suzuki, S., Endo, R., Shirouzu, M., Terada, T., Inoue, M., Kigawa, T., Guntert, P., Hayashizaki, Y., Muto, Y., Yokoyama, S., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History  

• Version 1.0: 2009-02-10
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-16
  Changes: Data collection, Database references, Derived calculations