3CTR

Crystal structure of the RRM-domain of the poly(A)-specific ribonuclease PARN bound to m7GTP


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of the RRM domain of poly(A)-specific ribonuclease reveals a novel m(7)G-cap-binding mode.

Monecke, T.Schell, S.Dickmanns, A.Ficner, R.

(2008) J Mol Biol 382: 827-834

  • DOI: 10.1016/j.jmb.2008.07.073
  • Primary Citation of Related Structures:  
    3CTR

  • PubMed Abstract: 
  • Poly(A)-specific ribonuclease (PARN) is a processive 3'-exoribonuclease involved in the decay of eukaryotic mRNAs. Interestingly, PARN interacts not only with the 3' end of the mRNA but also with its 5' end as PARN contains an RRM domain that specifically binds both the poly(A) tail and the 7-methylguanosine (m(7)G) cap ...

    Poly(A)-specific ribonuclease (PARN) is a processive 3'-exoribonuclease involved in the decay of eukaryotic mRNAs. Interestingly, PARN interacts not only with the 3' end of the mRNA but also with its 5' end as PARN contains an RRM domain that specifically binds both the poly(A) tail and the 7-methylguanosine (m(7)G) cap. The interaction of PARN with the 5' cap of mRNAs stimulates the deadenylation activity and enhances the processivity of this reaction. We have determined the crystal structure of the PARN-RRM domain with a bound m(7)G triphosphate nucleotide, revealing a novel binding mode for the m(7)G cap. The structure of the m(7)G binding pocket is located outside of the canonical RNA-binding surface of the RRM domain and differs significantly from that of other m(7)G-cap-binding proteins. The crystal structure also shows a remarkable conformational flexibility of the RRM domain, leading to a perfect exchange of two alpha-helices with an adjacent protein molecule in the crystal lattice.


    Organizational Affiliation

    Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik, GZMB, Georg-August-Universität Göttingen, 37077 Göttingen, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Poly(A)-specific ribonuclease PARNA101Homo sapiensMutation(s): 0 
Gene Names: PARNDAN
EC: 3.1.13.4
UniProt & NIH Common Fund Data Resources
Find proteins for O95453 (Homo sapiens)
Explore O95453 
Go to UniProtKB:  O95453
PHAROS:  O95453
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MGP (Subject of Investigation/LOI)
Query on MGP

Download Ideal Coordinates CCD File 
B [auth A]7-METHYL-GUANOSINE-5'-TRIPHOSPHATE
C11 H19 N5 O14 P3
DKVRNHPCAOHRSI-KQYNXXCUSA-O
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
MGP Binding MOAD:  3CTR Kd: 6940 (nM) from 1 assay(s)
PDBBind:  3CTR Kd: 6940 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.243 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.211 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.107α = 90
b = 81.107β = 90
c = 78.058γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
SHELXCDphasing
SHELXEmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-07-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-11-06
    Changes: Data collection
  • Version 1.3: 2017-10-25
    Changes: Refinement description