5UX0 | pdb_00005ux0

X-ray crystal structure of Marinitoga piezophila Argonaute in complex with 5' OH guide RNA and target DNA

• PDB DOI: https://doi.org/10.2210/pdb5UX0/pdb
• NAKB: 5UX0

• Classification: HYDROLASE/RNA/DNA
• Organism(s): Marinitoga piezophila, synthetic construct
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-02-21 Released: 2017-05-03 
• Deposition Author(s): Doxzen, K.W., Doudna, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.259 (Depositor), 0.256 (DCC) 
• R-Value Work: 
  0.215 (Depositor), 0.215 (DCC) 
• R-Value Observed: 
  0.218 (Depositor) 

Starting Model: experimental

Literature

DNA recognition by an RNA-guided bacterial Argonaute.

Doxzen, K.W., Doudna, J.A.

(2017) PLoS One 12: e0177097-e0177097

• PubMed: 28520746 
• DOI: https://doi.org/10.1371/journal.pone.0177097
• Primary Citation Related Structures: 
  5UX0


• PubMed Abstract: 
  

  Argonaute (Ago) proteins are widespread in prokaryotes and eukaryotes and share a four-domain architecture capable of RNA- or DNA-guided nucleic acid recognition. Previous studies identified a prokaryotic Argonaute protein from the eubacterium Marinitoga piezophila (MpAgo), which binds preferentially to 5'-hydroxylated guide RNAs and cleaves single-stranded RNA (ssRNA) and DNA (ssDNA) targets. Here we present a 3.2 Å resolution crystal structure of MpAgo bound to a 21-nucleotide RNA guide and a complementary 21-nucleotide ssDNA substrate. Comparison of this ternary complex to other target-bound Argonaute structures reveals a unique orientation of the N-terminal domain, resulting in a straight helical axis of the entire RNA-DNA heteroduplex through the central cleft of the protein. Additionally, mismatches introduced into the heteroduplex reduce MpAgo cleavage efficiency with a symmetric profile centered around the middle of the helix. This pattern differs from the canonical mismatch tolerance of other Argonautes, which display decreased cleavage efficiency for substrates bearing sequence mismatches to the 5' region of the guide strand. This structural analysis of MpAgo bound to a hybrid helix advances our understanding of the diversity of target recognition mechanisms by Argonaute proteins.

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Organizational Affiliation: 
• Biophysics Graduate Group, University of California, Berkeley, California, United States of America.
Department of Molecular and Cell Biology, University of California, Berkeley, California, United States of America.
Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
Center for RNA Systems Biology, University of California, Berkeley, California, United States of America.
Howard Hughes Medical Institute, University of California, Berkeley, California, United States of America.
Innovative Genomics Institute, University of California, Berkeley, California, United States of America.
Department of Chemistry, University of California, Berkeley, California, United States of America.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 178.56 kDa 
• Atom Count: 12,237 
• Modeled Residue Count: 1,345 
• Deposited Residue Count: 1,368 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Argonaute protein	A, D	642	Marinitoga piezophila	Mutation(s): 1  EC: 3.1.24
UniProt
Find proteins for H2J4R4 (Marinitoga piezophila (strain DSM 14283 / JCM 11233 / KA3)) Explore H2J4R4  Go to UniProtKB:  H2J4R4

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*G*GP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP*AP*U)-3')	B, E	21	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*AP*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*CP*C)-3')	C, F	21	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.259 (Depositor), 0.256 (DCC) 
• R-Value Work:  0.215 (Depositor), 0.215 (DCC) 
• R-Value Observed: 0.218 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.003	α = 90
b = 130.993	β = 90
c = 171.468	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-05-03 
Deposition Author(s): Doxzen, K.W., Doudna, J.A.

Revision History  

• Version 1.0: 2017-05-03
  Type: Initial release
  
• Version 1.1: 2017-06-07
  Changes: Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description
• Version 1.3: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary