9NDD | pdb_00009ndd

RNA scaffold attached to 8-oxoguanine riboswitch aptamer, combined core plus aptamer

PDB DOI: https://doi.org/10.2210/pdb9NDD/pdb
EM Map EMD-49272: EMDB EMDataResource

Classification: RNA
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2025-02-18 Released: 2026-03-04
Deposition Author(s): Jones, C.P., Ferre-D'Amare, A.R.
Funding Organization(s): National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.67 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

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

Literature

Symmetric scaffolds enable de novo modelling of RNA by cryoEM

Jones, C.P., Ferre-D'Amare, A.R.

To be published.

Macromolecule Content

Total Structure Weight: 206.44 kDa
Atom Count: 13,972
Modeled Residue Count: 640
Deposited Residue Count: 640
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff)

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (160-MER)	A, B, C, D	160	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
OXG Query on OXG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth B] SDF format, chain H [auth D] SDF format, chain G [auth C] MOL2 format, chain E [auth A] MOL2 format, chain F [auth B] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] mmCIF format, chain E [auth A] mmCIF format, chain F [auth B] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C]	E [auth A], F [auth B], G [auth C], H [auth D]	8-OXOGUANINE C₅ H₃ N₅ O₂ UBKVUFQGVWHZIR-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.67 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-03-04

Deposition Author(s):

Ferre-D'Amare, A.R.

Funding Organization	Location	Grant Number
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)	United States	--

Revision History (Full details and data files)

Version 1.0: 2026-03-04
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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.