4KZ2

Crystal Structure of phi29 pRNA 3WJ Core


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.197 

wwPDB Validation 3D Report Full Report


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Literature

Crystal structure of 3WJ core revealing divalent ion-promoted thermostability and assembly of the Phi29 hexameric motor pRNA.

Zhang, H.Endrizzi, J.A.Shu, Y.Haque, F.Sauter, C.Shlyakhtenko, L.S.Lyubchenko, Y.Guo, P.Chi, Y.I.

(2013) Rna 19: 1226-1237

  • DOI: 10.1261/rna.037077.112

  • PubMed Abstract: 
  • The bacteriophage phi29 DNA packaging motor, one of the strongest biological motors characterized to date, is geared by a packaging RNA (pRNA) ring. When assembled from three RNA fragments, its three-way junction (3WJ) motif is highly thermostable, i ...

    The bacteriophage phi29 DNA packaging motor, one of the strongest biological motors characterized to date, is geared by a packaging RNA (pRNA) ring. When assembled from three RNA fragments, its three-way junction (3WJ) motif is highly thermostable, is resistant to 8 M urea, and remains associated at extremely low concentrations in vitro and in vivo. To elucidate the structural basis for its unusual stability, we solved the crystal structure of this pRNA 3WJ motif at 3.05 Å. The structure revealed two divalent metal ions that coordinate 4 nt of the RNA fragments. Single-molecule fluorescence resonance energy transfer (smFRET) analysis confirmed a structural change of 3WJ upon addition of Mg²⁺. The reported pRNA 3WJ conformation is different from a previously published construct that lacks the metal coordination sites. The phi29 DNA packaging motor contains a dodecameric connector at the vertex of the procapsid, with a central pore for DNA translocation. This portal connector serves as the foothold for pRNA binding to procapsid. Subsequent modeling of a connector/pRNA complex suggests that the pRNA of the phi29 DNA packaging motor exists as a hexameric complex serving as a sheath over the connector. The model of hexameric pRNA on the connector agrees with AFM images of the phi29 pRNA hexamer acquired in air and matches all distance parameters obtained from cross-linking, complementary modification, and chemical modification interference.


    Organizational Affiliation

    Nanobiotechnology Center, Markey Cancer Center and Department of Pharmaceutical Sciences, University of Kentucky, Lexington, Kentucky 40536, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
phi29 pRNA 3WJ core RNA 18 merA18N/A
Entity ID: 2
MoleculeChainsLengthOrganism
phi29 pRNA 3WJ core RNA 20 merB20N/A
Entity ID: 3
MoleculeChainsLengthOrganism
phi29 pRNA 3WJ core RNA 16 merC16N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.197 
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 125.012α = 90.00
b = 125.012β = 90.00
c = 26.989γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
PHENIXphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data collection
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-10-16
    Type: Initial release