9T74 | pdb_00009t74

2'-fluoro-modified pyrimidine (FY) RNA aptamer binding to the receptor binding domain (RBD) of the SARS-CoV-2 spike protein. (focus map: RBD-aptamer)

PDB DOI: https://doi.org/10.2210/pdb9T74/pdb
EM Map EMD-55625: EMDB EMDataResource

Classification: RNA
Organism(s): synthetic RNA, Severe acute respiratory syndrome coronavirus 2
Expression System: synthetic construct, Homo sapiens
Mutation(s): No

Deposited: 2025-11-10 Released: 2026-03-04
Deposition Author(s): Kristoffersen, E.L., Andersen, E.S., Zwergious, N.H.
Funding Organization(s): Novo Nordisk Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.46 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

Serum-stable RNA origami nano-devices

Kristoffersen, E.L., Zwergius, N.H., Vallina, N.S., Gluck, N., Stange, A., Desdorf, L., Civit, L., Geary, C., Kjems, J., Valero, J., Andersen, E.S.

To be published.

Macromolecule Content

Total Structure Weight: 142.16 kDa
Atom Count: 2,673
Modeled Residue Count: 248
Deposited Residue Count: 1,185
Unique protein chains: 1
Unique nucleic acid chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Spike glycoprotein	B	1,134	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0 Gene Names: S, 2
UniProt
Find proteins for P0DTC2 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC2 Go to UniProtKB: P0DTC2
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P0DTC2
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain B	Go to GlyGen: P0DTC2-1
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff)

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA/RNA (51-MER)	A	51	synthetic RNA
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C

Small Molecules

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

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.46 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-03-04

Deposition Author(s):

Kristoffersen, E.L.

Zwergious, N.H.

Funding Organization	Location	Grant Number
Novo Nordisk Foundation	Denmark	NNF21OC0070452

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.