8VT5

Crystal structure of human menRNA

• PDB DOI: https://doi.org/10.2210/pdb8VT5/pdb
• NAKB: 8VT5

• Classification: RNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-01-25 Released: 2024-07-24 
• Deposition Author(s): Skeparnias, I., Zhang, J.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 0.291 
• R-Value Work: 0.250 
• R-Value Observed: 0.252 

Starting Model: experimental

Literature

Structural basis of NEAT1 lncRNA maturation and menRNA instability.

Skeparnias, I., Zhang, J.

(2024) Nat Struct Mol Biol 

• PubMed: 39026030 
• DOI: https://doi.org/10.1038/s41594-024-01361-z
• Primary Citation of Related Structures:  
  8VT5


• PubMed Abstract: 
  

  NEAT1 long noncoding RNA orchestrates paraspeckle assembly and impacts tumorigenesis, fertility and immunity. Its maturation requires RNase P cleavage yielding an unstable transfer RNA-like multiple endocrine neoplasia-β tRNA-like transcript (menRNA) due to CCACCA addition. Here we report the crystal structure of human menRNA, which partially mimics tRNAs to drive RNase P and ELAC2 processing. Biophysical analyses uncover an RNA-centric, riboswitch-like mechanism whereby the nascent CCA reshapes the RNA folding landscape and propels a spontaneous conformational isomerization that directs repeat CCA addition, marking the menRNA and defective tRNAs for degradation.

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Organizational Affiliation: 

Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 19.6 kDa 
• Atom Count: 1,270 
• Modelled Residue Count: 60 
• Deposited Residue Count: 60 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
menRNA	A	60	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.69 Å
• R-Value Free: 0.291 
• R-Value Work: 0.250 
• R-Value Observed: 0.252 
• Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.779	α = 90
b = 48.779	β = 90
c = 288.169	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
AutoSol	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-24 
Deposition Author(s): Skeparnias, I., Zhang, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	--

Revision History  

• Version 1.0: 2024-07-24
  Type: Initial release
  
• Version 1.1: 2024-07-31
  Changes: Database references