5C5W | pdb_00005c5w

1.25 A resolution structure of an RNA 20-mer

• PDB DOI: https://doi.org/10.2210/pdb5C5W/pdb
• NAKB: 5C5W

• Classification: RNA
• Organism(s): Saccharomyces
• Mutation(s): No 


• Deposited: 2015-06-22 Released: 2015-10-14 
• Deposition Author(s): Stewart, M., Valkov, E.
• Funding Organization(s): Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.188 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.183 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

1.25 angstrom resolution structure of an RNA 20-mer that binds to the TREX2 complex.

Valkov, E., Stewart, M.

(2015) Acta Crystallogr F Struct Biol Commun 71: 1318-1321

• PubMed: 26457524 
• DOI: https://doi.org/10.1107/S2053230X1501643X
• Primary Citation Related Structures: 
  5C5W


• PubMed Abstract: 
  

  The 1.25 Å resolution H32:R crystal structure of a 20 nt ribonucleotide that binds to the TREX-2 complex with high affinity shows a double-stranded RNA duplex arranged along a crystallographic 31 axis in which the antiparallel chains overlap by 18 nucleotides and are related by a crystallographic twofold axis. The duplex shows C-A, U-U and C-C noncanonical base pairings together with canonical Watson-Crick A-U and G-C pairs and a G-U wobble.

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Organizational Affiliation: 
• MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, England.

Biological Assembly 1  

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 6.02 kDa 
• Atom Count: 559 
• Modeled Residue Count: 19 
• Deposited Residue Count: 19 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(P*CP*CP*UP*GP*AP*GP*UP*UP*CP*AP*AP*UP*UP*CP*UP*AP*GP*CP*G)-3')	A	19	Saccharomyces

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.188 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.183 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.87	α = 90
b = 39.87	β = 90
c = 156.87	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2015-10-14 
Deposition Author(s): Stewart, M., Valkov, E.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	U105178939

Revision History  

• Version 1.0: 2015-10-14
  Type: Initial release
  
• Version 1.1: 2015-10-28
  Changes: Database references
• Version 1.2: 2017-09-13
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2024-05-08
  Changes: Data collection, Database references