Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 11 kDa 
• Atom Count: 733 
• Modelled Residue Count: 43 
• Deposited Residue Count: 43 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

 6D2U

Solution structure of a ultra-high affinity macrocycle bound to HIV-1 TAR RNA

• PDB DOI:  https://doi.org/10.2210/pdb6D2U/pdb
• NDB: 6D2U
• BMRB: 30452

• Classification: Peptide/RNA
• Organism(s): synthetic construct
• Expression System: synthetic construct
• Mutation(s): No 


• Deposited: 2018-04-13 Released: 2018-12-12 
• Deposition Author(s): Shortridge, M.D., Varani, G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

An ultra-high affinity ligand of HIV-1 TAR reveals the RNA structure recognized by P-TEFb.

Shortridge, M.D., Wille, P.T., Jones, A.N., Davidson, A., Bogdanovic, J., Arts, E., Karn, J., Robinson, J.A., Varani, G.

(2019) Nucleic Acids Res 47: 1523-1531

• PubMed: 30481318 
• DOI: https://doi.org/10.1093/nar/gky1197
• Primary Citation of Related Structures:  
  6D2U


• PubMed Abstract: 
  

The HIV-1 trans-activator protein Tat binds the trans-activation response element (TAR) to facilitate recruitment of the super elongation complex (SEC) to enhance transcription of the integrated pro-viral genome. The Tat-TAR interaction is critical for viral replication and the emergence of the virus from the latent state, therefore, inhibiting this interaction has long been pursued to discover new anti-viral or latency reversal agents. However, discovering active compounds that directly target RNA with high affinity and selectivity remains a significant challenge; limiting pre-clinical development. Here, we report the rational design of a macrocyclic peptide mimic of the arginine rich motif of Tat, which binds to TAR with low pM affinity and 100-fold selectivity against closely homologous RNAs. Despite these unprecedented binding properties, the new ligand (JB181) only moderately inhibits Tat-dependent reactivation in cells and recruitment of positive transcription elongation factor (P-TEFb) to TAR. The NMR structure of the JB181-TAR complex revealed that the ligand induces a structure in the TAR loop that closely mimics the P-TEFb/Tat1:57/AFF4/TAR complex. These results strongly suggest that high-affinity ligands which bind the UCU bulge are not likely to inhibit recruitment of the SEC and suggest that targeting of the TAR loop will be an essential feature of effective Tat inhibitors.

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Organizational Affiliation: 

Department of Chemistry, University of Washington, Seattle, Washington 98195-1700.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DAB-VAL-ARG-THR-ARG-LYS-GLY-ARG-ARG-ILE-NOR-ILE-DPR-PRO	A	14	synthetic construct	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Length	Organism	Image
RNA (29-MER)	B	29	synthetic construct

Small Molecules

Modified Residues  2 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
4J5	A	L-PEPTIDE LINKING	C5 H13 N4 O2		ARG
DAB	A	L-PEPTIDE LINKING	C4 H10 N2 O2		ALA

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-12-12 
Deposition Author(s): Shortridge, M.D., Varani, G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	5R01GM110569

Revision History  

• Version 1.0: 2018-12-12
  Type: Initial release
  
• Version 1.1: 2019-07-03
  Changes: Data collection, Database references
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence