2N4L | pdb_00002n4l

Solution Structure of the HIV-1 Intron Splicing Silencer and its Interactions with the UP1 Domain of hnRNP A1

• PDB DOI: https://doi.org/10.2210/pdb2N4L/pdb
• BMRB: 25671
• NAKB: 2N4L

• Classification: RNA
• Mutation(s): No 


• Deposited: 2015-06-23 Released: 2015-12-02 
• Deposition Author(s): Tolbert, B.S., Jain, N., Morgan, C.E., Rife, B.D., Salemi, M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 256 
• Conformers Submitted: 10 
• Selection Criteria: structures with the least restraint violations 

Literature

Solution Structure of the HIV-1 Intron Splicing Silencer and Its Interactions with the UP1 Domain of Heterogeneous Nuclear Ribonucleoprotein (hnRNP) A1.

Jain, N., Morgan, C.E., Rife, B.D., Salemi, M., Tolbert, B.S.

(2016) J Biological Chem 291: 2331-2344

• PubMed: 26607354 
• DOI: https://doi.org/10.1074/jbc.M115.674564
• Primary Citation Related Structures: 
  2N4L


• PubMed Abstract: 
  

  Splicing patterns in human immunodeficiency virus type 1 (HIV-1) are maintained through cis regulatory elements that recruit antagonistic host RNA-binding proteins. The activity of the 3' acceptor site A7 is tightly regulated through a complex network of an intronic splicing silencer (ISS), a bipartite exonic splicing silencer (ESS3a/b), and an exonic splicing enhancer (ESE3). Because HIV-1 splicing depends on protein-RNA interactions, it is important to know the tertiary structures surrounding the splice sites. Herein, we present the NMR solution structure of the phylogenetically conserved ISS stem loop. ISS adopts a stable structure consisting of conserved UG wobble pairs, a folded 2X2 (GU/UA) internal loop, a UU bulge, and a flexible AGUGA apical loop. Calorimetric and biochemical titrations indicate that the UP1 domain of heterogeneous nuclear ribonucleoprotein A1 binds the ISS apical loop site-specifically and with nanomolar affinity. Collectively, this work provides additional insights into how HIV-1 uses a conserved RNA structure to commandeer a host RNA-binding protein.

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Organizational Affiliation: 
• From the Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078 and.
Department of Pathology, Immunology, and Laboratory of Medicine, College of Medicine and Emerging Pathogens Institute, University of Florida, Gainesville, Florida 32610-3633.
From the Department of Chemistry, Case Western Reserve University, Cleveland, Ohio 44106-7078 and [e-mail].

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 17.01 kDa 
• Atom Count: 1,124 
• Modeled Residue Count: 53 
• Deposited Residue Count: 53 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (53-MER)	A	53	N/A

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 256 
• Conformers Submitted: 10 
• Selection Criteria: structures with the least restraint violations 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-02 
Deposition Author(s): Tolbert, B.S., Jain, N., Morgan, C.E., Rife, B.D., Salemi, M.

Revision History  

• Version 1.0: 2015-12-02
  Type: Initial release
  
• Version 1.1: 2016-03-16
  Changes: Database references
• Version 1.2: 2024-05-01
  Changes: Data collection, Database references