4B6H | pdb_00004b6h

Structure of hDcp1a in complex with proline rich sequence of PNRC2

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.285 (Depositor), 0.313 (DCC) 
  • R-Value Work: 
    0.234 (Depositor), 0.277 (DCC) 
  • R-Value Observed: 
    0.239 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4B6H

This is version 1.1 of the entry. See complete history. 

Literature

Structural Basis of the Pnrc2-Mediated Link between Mrna Surveillance and Decapping.

Lai, T., Cho, H., Liu, Z., Bowler, M.W., Piao, S., Parker, R., Kim, Y.K., Song, H.

(2012) Structure 20: 2025

  • DOI: https://doi.org/10.1016/j.str.2012.09.009
  • Primary Citation Related Structures: 
    4B6H

  • PubMed Abstract: 

    Nonsense-mediated mRNA decay (NMD) is an important mRNA surveillance system, and human PNRC2 protein mediates the link between mRNA surveillance and decapping. However, the mechanism by which PNRC2 interacts with the mRNA surveillance machinery and stimulates NMD is unknown. Here, we present the crystal structure of Dcp1a in complex with PNRC2. The proline-rich region of PNRC2 is bound to the EVH1 domain of Dcp1a, while its NR-box mediates the interaction with the hyperphosphorylated Upf1. The mode of PNRC2 interaction with Dcp1a is distinct from those observed in other EVH1/proline-rich ligands interactions. Disruption of the interaction of PNRC2 with Dcp1a abolishes its P-body localization and ability to promote mRNA degradation when tethered to mRNAs. PNRC2 acts in synergy with Dcp1a to stimulate the decapping activity of Dcp2 by bridging the interaction between Dcp1a and Dcp2, suggesting that PNRC2 is a decapping coactivator in addition to its adaptor role in NMD.

    • Organizational Affiliation: 
    • Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore 138673.

Macromolecule Content 

  • Total Structure Weight: 61.24 kDa 
  • Atom Count: 2,152 
  • Modeled Residue Count: 259 
  • Deposited Residue Count: 538 
  • Unique protein chains: 2

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MRNA-DECAPPING ENZYME 1A
A, B
134Homo sapiensMutation(s): 0 
EC: 3 (PDB Primary Data), 3.6.1.62 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPI6 (Homo sapiens)
Explore Q9NPI6 
Go to UniProtKB:  Q9NPI6
PHAROS:  Q9NPI6
GTEx:  ENSG00000272886 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NPI6
Sequence Annotations
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Reference Sequence
Find similar proteins by:
|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PROLINE-RICH NUCLEAR RECEPTOR COACTIVATOR 2
C, D
135Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NPJ4 (Homo sapiens)
Explore Q9NPJ4 
Go to UniProtKB:  Q9NPJ4
PHAROS:  Q9NPJ4
GTEx:  ENSG00000189266 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NPJ4
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.285 (Depositor), 0.313 (DCC) 
  • R-Value Work:  0.234 (Depositor), 0.277 (DCC) 
  • R-Value Observed: 0.239 (Depositor) 
Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.091α = 90
b = 97.639β = 90
c = 109.688γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling
SnBphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-06
    Type: Initial release
  • Version 1.1: 2024-05-08
    Changes: Data collection, Database references, Other