9DE8

Structure of full-length HIV TAR RNA soaked in CaCl2

PDB DOI: https://doi.org/10.2210/pdb9DE8/pdb

Classification: RNA
Organism(s): Human immunodeficiency virus 1
Mutation(s): Yes

Deposited: 2024-08-28 Released: 2025-03-12
Deposition Author(s): Bou-Nader, C., Zhang, J.
Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.76 Å
R-Value Free:
0.295 (Depositor), 0.294 (DCC)
R-Value Work:
0.245 (Depositor), 0.244 (DCC)
R-Value Observed:
0.248 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structures of complete HIV-1 TAR RNA portray a dynamic platform poised for protein binding and structural remodeling

Bou-Nader, C., Link, K.A., Suddala, K.C., Knutson, J.R., Zhang, J.

(2025) Nat Commun 16: 2252

DOI: https://doi.org/10.1038/s41467-025-57519-w

Macromolecule Content

Total Structure Weight: 18.34 kDa
Atom Count: 1,182
Modelled Residue Count: 56
Deposited Residue Count: 57
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (56-MER)	A	57	Human immunodeficiency virus 1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.76 Å
R-Value Free: 0.295 (Depositor), 0.294 (DCC)
R-Value Work: 0.245 (Depositor), 0.244 (DCC)
R-Value Observed: 0.248 (Depositor)

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 31.588	α = 90
b = 47.266	β = 90
c = 132.729	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-12

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	--

Revision History (Full details and data files)

Version 1.0: 2025-03-12
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.