Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 135.72 kDa 
• Atom Count: 8,187 
• Modelled Residue Count: 1,030 
• Deposited Residue Count: 1,151 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 2Y35

Crystal structure of Xrn1-substrate complex

• PDB DOI:  https://doi.org/10.2210/pdb2Y35/pdb
• NDB: NA1014

• Classification: HYDROLASE/DNA
• Organism(s): Drosophila melanogaster, synthetic construct
• Expression System: Spodoptera frugiperda
• Mutation(s): Yes 


• Deposited: 2010-12-18 Released: 2011-03-16 
• Deposition Author(s): Jinek, M., Coyle, S.M., Doudna, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.271 
• R-Value Work: 0.225 
• R-Value Observed: 0.227 

Literature

Coupled 5' Nucleotide Recognition and Processivity in Xrn1-Mediated Mrna Decay.

Jinek, M., Coyle, S.M., Doudna, J.A.

(2011) Mol Cell 41: 600

• PubMed: 21362555 
• DOI: https://doi.org/10.1016/j.molcel.2011.02.004
• Primary Citation of Related Structures:  
  2Y35


• PubMed Abstract: 
  

Messenger RNA decay plays a central role in the regulation and surveillance of eukaryotic gene expression. The conserved multidomain exoribonuclease Xrn1 targets cytoplasmic RNA substrates marked by a 5' monophosphate for processive 5'-to-3' degradation by an unknown mechanism. Here, we report the crystal structure of an Xrn1-substrate complex. The single-stranded substrate is held in place by stacking of the 5'-terminal trinucleotide between aromatic side chains while a highly basic pocket specifically recognizes the 5' phosphate. Mutations of residues involved in binding the 5'-terminal nucleotide impair Xrn1 processivity. The substrate recognition mechanism allows Xrn1 to couple processive hydrolysis to duplex melting in RNA substrates with sufficiently long single-stranded 5' overhangs. The Xrn1-substrate complex structure thus rationalizes the exclusive specificity of Xrn1 for 5'-monophosphorylated substrates, ensuring fidelity of mRNA turnover, and posits a model for translocation-coupled unwinding of structured RNA substrates.

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Organizational Affiliation: 

Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LD22664P	A	1,140	Drosophila melanogaster	Mutation(s): 1  Gene Names: pcm, Dmel\CG3291, DmXrn1, dXRN1, Pcm, XRN1, Xrn1, Xrn1p, CG3291, Dmel_CG3291 EC: 3.1.13
UniProt
Find proteins for E1JJR3 (Drosophila melanogaster) Explore E1JJR3  Go to UniProtKB:  E1JJR3

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DT11 (5'-D(*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP*TP)-3'	B	11	synthetic construct

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.271 
• R-Value Work: 0.225 
• R-Value Observed: 0.227 
• Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 149.99	α = 90
b = 149.99	β = 90
c = 154.86	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing
autoSHARP	phasing
PHENIX	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-16 
Deposition Author(s): Jinek, M., Coyle, S.M., Doudna, J.A.

Revision History  

• Version 1.0: 2011-03-16
  Type: Initial release
  
• Version 1.1: 2011-08-03
  Changes: Derived calculations, Version format compliance