SASDAC9: Varkud Satellite (VS) ribozyme in Tris (Varkud Satellite (VS) rib...

Basic information

• Entry: Database: SASBDB / ID: SASDAC9

Sample

Varkud Satellite (VS) ribozyme in Tris

• Varkud Satellite (VS) ribozyme (RNA), G638A, Neurospora

• Biological species: Neurospora (fungus)
• Citation: Journal: Nat Chem Biol / Year: 2015; Title: Crystal structure of the Varkud satellite ribozyme.; Authors: Nikolai B Suslov / Saurja DasGupta / Hao Huang / James R Fuller / David M J Lilley / Phoebe A Rice / Joseph A Piccirilli / ; Abstract: The Varkud satellite (VS) ribozyme mediates rolling-circle replication of a plasmid found in the Neurospora mitochondrion. We report crystal structures of this ribozyme from Neurospora intermedia at 3.1 Å resolution, which revealed an intertwined dimer formed by an exchange of substrate helices. In each protomer, an arrangement of three-way helical junctions organizes seven helices into a global fold that creates a docking site for the substrate helix of the other protomer, resulting in the formation of two active sites in trans. This mode of RNA-RNA association resembles the process of domain swapping in proteins and has implications for RNA regulation and evolution. Within each active site, adenine and guanine nucleobases abut the scissile phosphate, poised to serve direct roles in catalysis. Similarities to the active sites of the hairpin and hammerhead ribozymes highlight the functional importance of active-site features, underscore the ability of RNA to access functional architectures from distant regions of sequence space, and suggest convergent evolution.

Contact author

• James Fuller (Uchicago, The University of Chicago, Edward H. Levi Hall 5801 South Ellis Avenue Chicago, Illinois 60637 773.702.1234)

Models

• Model #358: ; Type: dummy / Software: DAMMIN / Radius of dummy atoms: 4.00 A; Search similar-shape structures of this assembly by Omokage search (details)
• Model #359: ; Type: mix / Software: FoXS / Radius of dummy atoms: 1.90 A / Chi-square value: 680.308162367; Search similar-shape structures of this assembly by Omokage search (details)

Sample

• Sample: Name: Varkud Satellite (VS) ribozyme in Tris / Specimen concentration: 1.50-4.50
• Buffer: Name: Tris / Concentration: 10.00 mM / pH: 7.5 / Composition: 25 mM KCl and 5 mM MgCl2

Entity #217

Name: G638A / Type: RNA / Description: Varkud Satellite (VS) ribozyme / Formula weight: 60.15 / Num. of mol.: 2 / Source: Neurospora
Sequence:

GGCGCUGUGU CGCAAUCUGC GAAGGGCGUC GUCGGCCCAA GCGGUAGUAA GCAGGGAACU CACCUCCAAU GAAACACAUU GUCGUAGCAG UUGACUACUG UUAUGUGAUU GGUAGAGGCU AAGUGACGGU AUUGGCGUAA GCCAAUACCG CAGCACAGCA CAAGCCCGCU UGCGAGAUUA CAGCGC

Experimental information

• Beam: Instrument name: Advanced Light Source (ALS) 12.3.1 (SIBYLS); City: Berkeley, CA / 国: USA / Type of source: X-ray synchrotronSynchrotron / Wavelength: 0.103 Å
• Detector: Name: Pilatus 2M

Scan

Title: Structure of the Varkud Satellite (VS) ribozyme / Measurement date: Mar 6, 2012 / Number of frames: 24 / Unit: 1/nm /

	Min	Max
Q	0.2098	3.244

Distance distribution function P(R)

Sofotware P(R): GNOM 5.0 / Number of points: 252 /

	Min	Max
Q	0.02098	0.173615
P(R) point	1	252
R	0	164.3

Result

D max: 16.4 / Type of curve: extrapolated
Comments: SAXS data from a catalytically inactive construct support the overall conformation and dimeric state of the VS ribozyme in its x-ray crystal structure.

	Experimental	Standard	Porod
MW	125 kDa	125 kDa	-
Volume	-	-	239.5 nm3

	P(R)	Guinier
Forward scattering, I0	4491	4298
Radius of gyration, Rg	4.13 nm	3.87 nm