4EYA | pdb_00004eya

Crystal Structure of a Plectonemic RNA Supercoil

• PDB DOI: https://doi.org/10.2210/pdb4EYA/pdb
• NAKB: 4EYA

• Classification: transcription/RNA
• Organism(s): Aquifex aeolicus VF5, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.272 (Depositor), 0.275 (DCC) 
• R-Value Work: 
  0.228 (Depositor), 0.228 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

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

• PubMed: 22692544 
• DOI: https://doi.org/10.1038/ncomms1903
• Primary Citation Related Structures: 
  4EYA


• 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 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.

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Organizational Affiliation: 
• Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, Maryland 21702, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 214.72 kDa 
• Atom Count: 14,060 
• Modeled Residue Count: 1,336 
• Deposited Residue Count: 1,424 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N utilization substance protein B homolog	A, B, C, D, E, F, G, H	148	Aquifex aeolicus VF5	Mutation(s): 0  Gene Names: aq_133, nusB
UniProt
Find proteins for O66530 (Aquifex aeolicus (strain VF5)) Explore O66530  Go to UniProtKB:  O66530

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*GP*GP*CP*UP*CP*CP*UP*UP*GP*GP*CP*A)-3')	AA [auth n], BA [auth l], I [auth a], J [auth c], K [auth e], L [auth g], M [auth i], N [auth j], O [auth h], P [auth f], Q [auth d], R [auth b], S [auth k], T [auth m], U [auth o], V [auth q], W [auth s], X [auth t], Y [auth r], Z [auth p]	12	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	DA [auth B], IA [auth D], MA [auth F], PA [auth H]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	CA [auth A], EA [auth B], FA [auth B], GA [auth C], HA [auth C], JA [auth D], KA [auth E], LA [auth E], NA [auth F], OA [auth G], QA [auth H], RA [auth H]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.272 (Depositor), 0.275 (DCC) 
• R-Value Work:  0.228 (Depositor), 0.228 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 126.424	α = 90
b = 126.264	β = 89.98
c = 144.131	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• 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
  Changes: Refinement description, Source and taxonomy
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 1.3: 2023-09-13
  Changes: Refinement description