9OD4 | pdb_00009od4

Solution structure of the Ebola Transcriptional Regulatory Signal - configuration B

• PDB DOI: https://doi.org/10.2210/pdb9OD4/pdb
• NAKB: 9OD4
• BMRB: 31238

• Classification: RNA
• Organism(s): Ebola virus
• Expression System: in vitro transcription vector pT7-TP(deltai)
• Mutation(s): No 


• Deposited: 2025-04-25 Released: 2025-10-15 
• Deposition Author(s): Edwards, J.M., Kachale, A., Pham, V.V.
• Funding Organization(s): Other private

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

The Ebolavirus Transcription Regulatory Signal Equilibrates Between Two Structural Conformations to Affect VP30 Binding.

Edwards, J.M., Kachale, A., McCleery, S.R., Law, G.A., Patel, V., D'Souza, V.M., Pham, V.V.

(2025) J Mol Biol 437: 169464-169464

• PubMed: 41015113 
• DOI: https://doi.org/10.1016/j.jmb.2025.169464
• Primary Citation Related Structures: 
  9OD4, 9OD5


• PubMed Abstract: 
  

  The transcription of ebolavirus (EBOV) genomes is a major checkpoint in the viral life cycle. Altering the transcription regulatory signal (TRS), an RNA hairpin that forms in the 3' leader sequence of EBOV, affects transcription in a VP30-dependent manner. How this mechanistically occurs is currently unknown. Here, we find that the TRS primarily equilibrates between two structures that differ in their loops. Mutational studies demonstrate that the entire hairpin structure is important in directing both VP30 binding and regulating EBOV transcriptional activity, with the loop being the principal structural element. In doing so, we highlight that the TRS structure is a critical determinant of EBOV transcription.

---

Organizational Affiliation: 
• W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.
Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological Assembly Evidence: NMR Distance Restraints

Macromolecule Content 

• Total Structure Weight: 7.29 kDa 
• Atom Count: 482 
• Modeled Residue Count: 23 
• Deposited Residue Count: 23 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*CP*UP*CP*CP*UP*UP*CP*UP*AP*AP*UP*UP*AP*UP*UP*AP*(AHE)P*AP*AP*GP*GP*AP*G)-3')	A	23	Ebola virus

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-10-15 
Deposition Author(s): Edwards, J.M., Kachale, A., Pham, V.V.

---

Funding Organization	Location	Grant Number
Other private	United States	D'Souza lab startup

Revision History  

• Version 1.0: 2025-10-15
  Type: Initial release
  
• Version 1.1: 2025-10-22
  Changes: Database references