2XFM

Complex structure of the MIWI Paz domain bound to methylated single stranded RNA

• PDB DOI: https://doi.org/10.2210/pdb2XFM/pdb
• NAKB: 2XFM

• Classification: RNA/PROTEIN
• Organism(s): Mus musculus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-05-27 Released: 2011-01-26 
• Deposition Author(s): Simon, B., Kirkpatrick, J.P., Eckhardt, S., Sehr, P., Andrade-Navarro, M.A., Pillai, R.S., Carlomagno, T.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: LOWEST ENERGY 

Literature

Recognition of 2'-O-Methylated 3'-End of Pirna by the Paz Domain of a Piwi Protein.

Simon, B., Kirkpatrick, J.P., Eckhardt, S., Reuter, M., Rocha, E.A., Andrade-Navarro, M.A., Sehr, P., Pillai, R.S., Carlomagno, T.

(2011) Structure 19: 172

• PubMed: 21237665 
• DOI: https://doi.org/10.1016/j.str.2010.11.015
• Primary Citation of Related Structures:  
  2XFM


• PubMed Abstract: 
  

  Piwi proteins are germline-specific Argonautes that associate with small RNAs called Piwi-interacting RNAs (piRNAs), and together with these RNAs are implicated in transposon silencing. The PAZ domain of Argonaute proteins recognizes the 3'-end of the RNA, which in the case of piRNAs is invariably modified with a 2'-O-methyl group. Here, we present the solution structure of the PAZ domain from the mouse Piwi protein, MIWI, in complex with an 8-mer piRNA mimic. The methyl group is positioned in a hydrophobic cavity made of conserved amino acids from strand β7 and helix α3, where it is contacted by the side chain of methionine-382. Our structure is similar to that of Ago-PAZ, but subtle differences illustrate how the PAZ domain has evolved to accommodate distinct 3' ends from a variety of RNA substrates.

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Organizational Affiliation: 

Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany.

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: 20.14 kDa 
• Atom Count: 1,151 
• Modelled Residue Count: 128 
• Deposited Residue Count: 158 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PIWI-LIKE PROTEIN 1	A	150	Mus musculus	Mutation(s): 0  EC: 3.1.26
UniProt
Find proteins for Q9JMB7 (Mus musculus) Explore Q9JMB7  Go to UniProtKB:  Q9JMB7

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-R(*AP*CP*CP*GP*AP*CP*UP*(OMU)P)-3'	B	8	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: LOWEST ENERGY 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-01-26 
Deposition Author(s): Simon, B., Kirkpatrick, J.P., Eckhardt, S., Sehr, P., Andrade-Navarro, M.A., Pillai, R.S., Carlomagno, T.

Revision History  

• Version 1.0: 2011-01-26
  Type: Initial release
  
• Version 1.1: 2011-10-26
  Changes: Database references, Derived calculations, Version format compliance
• Version 2.0: 2024-05-15
  Changes: Atomic model, Data collection, Database references, Derived calculations, Other