3ZC1

Crystal structure of AfC3PO


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.269 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structural Basis for Duplex RNA Recognition and Cleavage by Archaeoglobus Fulgidus C3Po.

Parizotto, E.A.Lowe, E.D.Parker, J.S.

(2013) Nat.Struct.Mol.Biol. 20: 380

  • DOI: 10.1038/nsmb.2487
  • Primary Citation of Related Structures:  3ZC0

  • PubMed Abstract: 
  • Oligomeric complexes of Trax and Translin proteins, known as C3POs, participate in several eukaryotic nucleic acid metabolism pathways, including RNA interference and tRNA processing. In RNA interference in humans and Drosophila, C3PO activates the R ...

    Oligomeric complexes of Trax and Translin proteins, known as C3POs, participate in several eukaryotic nucleic acid metabolism pathways, including RNA interference and tRNA processing. In RNA interference in humans and Drosophila, C3PO activates the RNA-induced silencing complex (RISC) by removing the passenger strand of the small interfering RNA precursor duplex, using nuclease activity present in Trax. How C3POs engage with nucleic acid substrates is unknown. Here we identify a single protein from Archaeoglobus fulgidus that assembles into an octamer highly similar to human C3PO. The structure in complex with duplex RNA reveals that the octamer entirely encapsulates a single 13-base-pair RNA duplex inside a large inner cavity. Trax-like-subunit catalytic sites target opposite strands of the duplex for cleavage separated by 7 base pairs. The structure provides insight into the mechanism of RNA recognition and cleavage by an archaeal C3PO-like complex.


    Organizational Affiliation

    Department of Biochemistry, University of Oxford, Oxford, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AFTRAX
A, B, C, D, E, F, G, H
199Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)N/A
Find proteins for O28024 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Go to UniProtKB:  O28024
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download SDF File 
Download CCD File 
B, C, D, F, G
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.269 Å
  • R-Value Free: 0.281 
  • R-Value Work: 0.221 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 183.310α = 90.00
b = 183.310β = 90.00
c = 111.280γ = 90.00
Software Package:
Software NamePurpose
SnBphasing
autoSHARPphasing
PHASERphasing
xia2data reduction
xia2data scaling
PHENIXphasing
SCALAdata scaling
Cootphasing
PHENIXrefinement
Cootmodel building
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-23
    Type: Initial release
  • Version 1.1: 2013-01-30
    Type: Database references
  • Version 1.2: 2013-02-27
    Type: Database references
  • Version 1.3: 2013-03-20
    Type: Database references