9NAK | pdb_00009nak

RNA scaffold attached to tRNA

PDB DOI: https://doi.org/10.2210/pdb9NAK/pdb
NAKB: 9NAK
EM Map EMD-49197: EMDB EMDataResource

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

Deposited: 2025-02-12 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: 3.67 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9NAK

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: 108.48 kDa
Atom Count: 3,526
Modeled Residue Count: 164
Deposited Residue Count: 336
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 1
Scaffold attached to tRNA	A, B [auth C]	168	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
K Query on K Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth C] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth C] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], F [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth C] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain F [auth C]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.67 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

View more in-depth experimental data

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

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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.