8VT5 | pdb_00008vt5

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 (Depositor), 0.293 (DCC) 
• R-Value Work: 
  0.250 (Depositor), 0.252 (DCC) 
• R-Value Observed: 
  0.252 (Depositor) 

Starting Model: experimental

Literature

Structural basis of NEAT1 lncRNA maturation and menRNA instability.

Skeparnias, I., Zhang, J.

(2024) Nat Struct Mol Biol 31: 1650-1654

• PubMed: 39026030 
• DOI: https://doi.org/10.1038/s41594-024-01361-z
• Primary Citation 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.
Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA. [e-mail].

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 
• Modeled 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 (Depositor), 0.293 (DCC) 
• R-Value Work:  0.250 (Depositor), 0.252 (DCC) 
• R-Value Observed: 0.252 (Depositor) 

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
• Version 1.2: 2024-11-27
  Changes: Database references, Structure summary