Biological Assembly 1  

 3D View: Structure

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 19.83 kDa 
• Atom Count: 1400 
• Modelled Residue Count: 172 
• Deposited Residue Count: 172 
• Unique protein chains: 2

2LYD

The solution structure of the Dm DCP1 EVH1 domain in complex with the XRN1 DBM peptide

• DOI: 10.2210/pdb2LYD/pdb
• BMRB: 18720

• Classification: TRANSCRIPTION/PROTEIN BINDING
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-09-17 Released: 2012-10-17 
• Deposition Author(s): Truffault, V.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 21 
• Selection Criteria: structures with the lowest energy 

Literature

A direct interaction between DCP1 and XRN1 couples mRNA decapping to 5' exonucleolytic degradation.

Braun, J.E., Truffault, V., Boland, A., Huntzinger, E., Chang, C.T., Haas, G., Weichenrieder, O., Coles, M., Izaurralde, E.

(2012) Nat Struct Mol Biol 19: 1324-1331

• PubMed: 23142987 
• DOI: 10.1038/nsmb.2413
• Primary Citation of Related Structures:  
  2LYD


• PubMed Abstract: 
  

The removal of the mRNA 5' cap structure by the decapping enzyme DCP2 leads to rapid 5'→3' mRNA degradation by XRN1, suggesting that the two processes are coordinated, but the coupling mechanism is unknown. DCP2 associates with the decapping activators EDC4 and DCP1. Here we show that XRN1 directly interacts with EDC4 and DCP1 in human and Drosophila melanogaster cells, respectively. In D. melanogaster cells, this interaction is mediated by the DCP1 EVH1 domain and a DCP1-binding motif (DBM) in the XRN1 C-terminal region. The NMR structure of the DCP1 EVH1 domain bound to the DBM reveals that the peptide docks at a conserved aromatic cleft, which is used by EVH1 domains to recognize proline-rich ligands. Our findings reveal a role for XRN1 in decapping and provide a molecular basis for the coupling of decapping to 5'→3' mRNA degradation.

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Organizational Affiliation: 

Department of Biochemistry, Max Planck Institute for Developmental Biology, Tübingen, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Decapping protein 1	A	134	Drosophila melanogaster	Mutation(s): 0  Gene Names:  Dcp1, CG11183, Dmel_CG11183, DCP1, anon-WO0118547.163, Dcp-1, dcp-1, Dcp1p, dDCP1, dDcp1, Dmel\CG11183
Find proteins for Q9W1H5 (Drosophila melanogaster) Explore Q9W1H5  Go to UniProtKB:  Q9W1H5

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Pacman protein	B	38	Drosophila melanogaster	Mutation(s): 0  Gene Names:  Pcm, pacman, CG3291, pcm, Dmel\CG3291, DmXrn1, dXRN1, XRN1, Xrn1, Xrn1p, Dmel_CG3291 EC: 3.1.13
Find proteins for E1JJR3 (Drosophila melanogaster) Explore E1JJR3  Go to UniProtKB:  E1JJR3

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 21 
• Selection Criteria: structures with the lowest energy 
• OLDERADO: 2LYD Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-09-17 
• Released Date: 2012-10-17 
Deposition Author(s): Truffault, V.

Revision History  

• Version 1.0: 2012-10-17
  Type: Initial release
  
• Version 1.1: 2012-10-31
  Changes: Database references
• Version 1.2: 2012-11-28
  Changes: Database references
• Version 1.3: 2012-12-19
  Changes: Database references