Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 21.41 kDa 
• Atom Count: 1412 
• Modelled Residue Count: 66 
• Deposited Residue Count: 66 
• Unique nucleic acid chains: 1

3R4F

Prohead RNA

• PDB DOI: 10.2210/pdb3R4F/pdb
• NDB: NA1024

• Classification: RNA
• Mutation(s): No 


• Deposited: 2011-03-17 Released: 2011-04-20 
• Deposition Author(s): Ding, F., Lu, C., Zhano, W., Rajashankar, K.R., Anderson, D.L., Jardine, P.J., Grimes, S., Ke, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.271 
• R-Value Work: 0.239 

Literature

Structure and assembly of the essential RNA ring component of a viral DNA packaging motor.

Ding, F., Lu, C., Zhao, W., Rajashankar, K.R., Anderson, D.L., Jardine, P.J., Grimes, S., Ke, A.

(2011) Proc Natl Acad Sci U S A 108: 7357-7362

• PubMed: 21471452 
• DOI: 10.1073/pnas.1016690108
• Primary Citation of Related Structures:  
  3R4F


• PubMed Abstract: 
  

Prohead RNA (pRNA) is an essential component in the assembly and operation of the powerful bacteriophage 29 DNA packaging motor. The pRNA forms a multimeric ring via intermolecular base-pairing interactions between protomers that serves to guide the assembly of the ring ATPase that drives DNA packaging. Here we report the quaternary structure of this rare multimeric RNA at 3.5 Å resolution, crystallized as tetrameric rings. Strong quaternary interactions and the inherent flexibility helped rationalize how free pRNA is able to adopt multiple oligomerization states in solution. These characteristics also allowed excellent fitting of the crystallographic pRNA protomers into previous prohead/pRNA cryo-EM reconstructions, supporting the presence of a pentameric, but not hexameric, pRNA ring in the context of the DNA packaging motor. The pentameric pRNA ring anchors itself directly to the phage prohead by interacting specifically with the fivefold symmetric capsid structures that surround the head-tail connector portal. From these contacts, five RNA superhelices project from the pRNA ring, where they serve as scaffolds for binding and assembly of the ring ATPase, and possibly mediate communication between motor components. Construction of structure-based designer pRNAs with little sequence similarity to the wild-type pRNA were shown to fully support the packaging of 29 DNA.

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Organizational Affiliation: 

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
pRNA	A	66	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.50 Å
• R-Value Free: 0.271 
• R-Value Work: 0.239 
• Space Group: I 4 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.197	α = 90
b = 104.197	β = 90
c = 208.793	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
SHELXS	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2011-03-17 
• Released Date: 2011-04-20 
Deposition Author(s): Ding, F., Lu, C., Zhano, W., Rajashankar, K.R., Anderson, D.L., Jardine, P.J., Grimes, S., Ke, A.

Revision History  

• Version 1.0: 2011-04-20
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance