9E7Q | pdb_00009e7q

Structure of a coiled-coil peptide from C. elegans EDC4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 
    0.170 (Depositor), 0.159 (DCC) 
  • R-Value Work: 
    0.148 (Depositor) 
  • R-Value Observed: 
    0.149 (Depositor) 

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Validation slider image for 9E7Q

This is version 1.2 of the entry. See complete history

Literature

Conserved and divergent features of human mRNA decapping revealed by biochemical reconstitution.

Simko, E.A.J.Muthukumar, S.Myers, T.M.Valkov, A.L.Valkov, E.

(2026) Nat Commun 17

  • DOI: https://doi.org/10.1038/s41467-026-72177-2
  • Primary Citation Related Structures: 
    9E7Q

  • PubMed Abstract: 

    Decapping is a critical step in mRNA decay, but the mechanisms regulating human decapping enzyme DCP2 remain poorly understood. Here, we reconstitute the human decapping network using full-length recombinant proteins and compare it to the yeast system. Unlike in yeast, we find that the C-terminal region of human DCP2 is not autoinhibitory. RNA-binding residues of yeast Dcp2 are not conserved in the human homolog, and we find instead that a charged C-terminal region mediates substrate recognition. Human DCP1 does not stably interact with or directly stimulate DCP2, but mediates activation by the enhancer PNRC2. We also demonstrate that decapping enhancer EDC4 forms tetramers through an extended coiled-coil region, and that both DCP1 and EDC4 homomeric species can further assemble into higher-order oligomers. Furthermore, structural predictions incorporating these findings suggest a model for DCP2 recruitment by EDC4 tetramers. These findings reveal key mechanistic differences between human and yeast decapping regulation and provide insight into the molecular architecture underlying mRNA decay.


  • Organizational Affiliation
    • National Cancer Institute, National Institutes of Health, Frederick, MD, USA.

Macromolecule Content 

  • Total Structure Weight: 7.45 kDa 
  • Atom Count: 443 
  • Modeled Residue Count: 50 
  • Deposited Residue Count: 66 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FHA domain-containing protein
A, B
33Caenorhabditis elegansMutation(s): 0 
Gene Names: edc-4CELE_Y44E3A.6Y44E3A.6
UniProt
Find proteins for Q8ITV7 (Caenorhabditis elegans)
Explore Q8ITV7 
Go to UniProtKB:  Q8ITV7
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8ITV7
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
C [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free:  0.170 (Depositor), 0.159 (DCC) 
  • R-Value Work:  0.148 (Depositor) 
  • R-Value Observed: 0.149 (Depositor) 
Space Group: P 41 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.564α = 90
b = 76.564β = 90
c = 76.564γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Entry History 

& Funding Information

Deposition Data

  • Released Date: 2025-11-12 
  • Deposition Author(s): Valkov, E.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-11-12
    Type: Initial release
  • Version 1.1: 2026-04-29
    Changes: Database references
  • Version 1.2: 2026-05-06
    Changes: Database references