3VNB | pdb_00003vnb

Structural insights into small RNA sorting and mRNA binding by Arabidopsis Ago domains

• PDB DOI: https://doi.org/10.2210/pdb3VNB/pdb

• Classification: RNA BINDING PROTEIN
• Organism(s): Arabidopsis thaliana
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2012-01-11 Released: 2012-10-10 
• Deposition Author(s): Yuan, Y.A., Zha, X.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.215 (Depositor), 0.216 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 
  0.189 (Depositor) 

Literature

Structural insights into small RNA sorting and mRNA target binding by Arabidopsis Argonaute Mid domains

Zha, X., Xia, Q., Yuan, Y.A.

(2012) FEBS Lett 586: 3200-3207

• PubMed: 22771475 
• DOI: https://doi.org/10.1016/j.febslet.2012.06.038
• Primary Citation Related Structures: 
  3VNA, 3VNB


• PubMed Abstract: 
  

  The RISC-associated Argonaute (Ago) proteins play the catalytic role for RISC-mediated gene regulation by selecting small RNAs and subsequent targeting and cleavage of complementary mRNAs. Ago Mid domains are proposed to play essential roles in small RNA sorting. Here, we report the crystal structures of Arabidopsis Ago1 Mid domain and its chimera mutant with part of Ago1 replaced by Ago4. The structures demonstrate that a single amino insertion in the nucleotide specificity loop of AtAgo1 will change the nucleotide binding preference of AtAgo1 from "5'-U" to "5'-A". Moreover, we identify a long positively charged groove located along the "5'-end-nucleotide specificity loop" and occupied by several sulfate ions with the distance of 9-11Å distance, indicating a putative mRNA target binding groove.

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Organizational Affiliation: 
• Department of Biological Sciences and Centre for Bioimaging Sciences, National University of Singapore, Singapore.

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: 18 kDa 
• Atom Count: 1,329 
• Modeled Residue Count: 149 
• Deposited Residue Count: 155 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein argonaute 1	A	155	Arabidopsis thaliana	Mutation(s): 3
UniProt
Find proteins for O04379 (Arabidopsis thaliana) Explore O04379  Go to UniProtKB:  O04379

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	B [auth A], C [auth A], D [auth A], E [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.215 (Depositor), 0.216 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.188 (DCC) 
• R-Value Observed: 0.189 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 36.869	α = 90
b = 61.096	β = 90
c = 67.085	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-10-10 
Deposition Author(s): Yuan, Y.A., Zha, X.

Revision History  

• Version 1.0: 2012-10-10
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations