4EYA

Crystal Structure of a Plectonemic RNA Supercoil


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.228 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structure of a plectonemic RNA supercoil.

Stagno, J.R.Ma, B.Li, J.Altieri, A.S.Byrd, R.A.Ji, X.

(2012) Nat Commun 3: 901-901

  • DOI: 10.1038/ncomms1903

  • PubMed Abstract: 
  • Genome packaging is an essential housekeeping process in virtually all organisms for proper storage and maintenance of genetic information. Although the extent and mechanisms of packaging vary, the process involves the formation of nucleic-acid super ...

    Genome packaging is an essential housekeeping process in virtually all organisms for proper storage and maintenance of genetic information. Although the extent and mechanisms of packaging vary, the process involves the formation of nucleic-acid superstructures. Crystal structures of DNA coiled coils indicate that their geometries can vary according to sequence and/or the presence of stabilizers such as proteins or small molecules. However, such superstructures have not been revealed for RNA. Here we report the crystal structure of an RNA supercoil, which displays one level higher molecular organization than previously reported structures of DNA coiled coils. In the presence of an RNA-binding protein, two interlocking RNA coiled coils of double-stranded RNA, a 'coil of coiled coils', form a plectonemic supercoil. Molecular dynamics simulations suggest that protein-RNA interaction is required for the stability of the supercoiled RNA. This study provides structural insight into higher order packaging mechanisms of nucleic acids.


    Organizational Affiliation

    Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, Maryland 21702, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
N utilization substance protein B homolog
A, B, C, D, E, F, G, H
148Aquifex aeolicus (strain VF5)Mutation(s): 0 
Gene Names: nusB
Find proteins for O66530 (Aquifex aeolicus (strain VF5))
Go to UniProtKB:  O66530
Entity ID: 2
MoleculeChainsLengthOrganism
RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')a,c,e,g,i,j,h,f,d,b,k,m,o,q,s,t,r,p,n,l12synthetic construct
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, D, F, H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.228 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 126.424α = 90.00
b = 126.264β = 89.98
c = 144.131γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data scaling
PHENIXrefinement
DENZOdata reduction
PHASERphasing
Blu-Icedata collection
PDB_EXTRACTdata extraction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2012-05-01 
  • Released Date: 2012-06-20 
  • Deposition Author(s): Stagno, J.R., Ji, X.

Revision History 

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description, Source and taxonomy