4PLX | pdb_00004plx

Crystal structure of the triple-helical stability element at the 3' end of MALAT1

• PDB DOI: https://doi.org/10.2210/pdb4PLX/pdb
• NAKB: 4PLX

• Classification: RNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2014-05-19 Released: 2014-06-25 
• Deposition Author(s): Brown, J.A., Bulkley, D., Wang, J., Valenstein, M.L., Yario, T.A., Steitz, T.A., Steitz, J.A.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.255 (Depositor), 0.258 (DCC) 
• R-Value Work: 
  0.220 (Depositor), 0.224 (DCC) 
• R-Value Observed: 
  0.222 (Depositor) 

Literature

Structural insights into the stabilization of MALAT1 noncoding RNA by a bipartite triple helix.

Brown, J.A., Bulkley, D., Wang, J., Valenstein, M.L., Yario, T.A., Steitz, T.A., Steitz, J.A.

(2014) Nat Struct Mol Biol 21: 633-640

• PubMed: 24952594 
• DOI: https://doi.org/10.1038/nsmb.2844
• Primary Citation Related Structures: 
  4PLX


• PubMed Abstract: 
  

  Metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) is a highly abundant nuclear long noncoding RNA that promotes malignancy. A 3'-stem-loop structure is predicted to confer stability by engaging a downstream A-rich tract in a triple helix, similar to the expression and nuclear retention element (ENE) from the KSHV polyadenylated nuclear RNA. The 3.1-Å-resolution crystal structure of the human MALAT1 ENE and A-rich tract reveals a bipartite triple helix containing stacks of five and four U•A-U triples separated by a C+•G-C triplet and C-G doublet, extended by two A-minor interactions. In vivo decay assays indicate that this blunt-ended triple helix, with the 3' nucleotide in a U•A-U triple, inhibits rapid nuclear RNA decay. Interruption of the triple helix by the C-G doublet induces a 'helical reset' that explains why triple-helical stacks longer than six do not occur in nature.

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Organizational Affiliation: 
• Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.
Department of Chemistry, Yale University, New Haven, Connecticut, USA.
Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA.
1] Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA. [2] Department of Chemistry, Yale University, New Haven, Connecticut, USA. [3] Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA.
1] Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA. [2] Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 73.72 kDa 
• Atom Count: 4,744 
• Modeled Residue Count: 220 
• Deposited Residue Count: 228 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Core ENE hairpin and A-rich tract from MALAT1	A, B, C	76	Homo sapiens

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.255 (Depositor), 0.258 (DCC) 
• R-Value Work:  0.220 (Depositor), 0.224 (DCC) 
• R-Value Observed: 0.222 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 162.82	α = 90
b = 162.82	β = 90
c = 65.93	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2014-06-25 
Deposition Author(s): Brown, J.A., Bulkley, D., Wang, J., Valenstein, M.L., Yario, T.A., Steitz, T.A., Steitz, J.A.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM026154
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM022778

Revision History  

• Version 1.0: 2014-06-25
  Type: Initial release
  
• Version 1.1: 2014-07-09
  Changes: Database references
• Version 1.2: 2014-10-01
  Changes: Database references
• Version 1.3: 2017-09-20
  Changes: Author supporting evidence, Derived calculations, Other, Source and taxonomy
• Version 1.4: 2019-12-25
  Changes: Author supporting evidence
• Version 1.5: 2023-12-27
  Changes: Data collection, Database references, Refinement description