9ZBR | pdb_00009zbr

1-methyl-pseudouridine L-21 ScaI Tetrahymena Ribozyme - extended conformation

PDB DOI: https://doi.org/10.2210/pdb9ZBR/pdb
EM Map EMD-73998: EMDB EMDataResource
NAKB: 9ZBR

Classification: RNA
Organism(s): Tetrahymena thermophila
Mutation(s): No

Deposited: 2025-11-21 Released: 2025-12-03
Deposition Author(s): McRae, E.K.S., Yang, H.
Funding Organization(s): Cancer Prevention and Research Institute of Texas (CPRIT)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 7.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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

Literature

Base modifications reshape RNA folding landscapes and structure function relationships in synthetic and natural RNAs

Kumar, D.Y., Yang, H., Lee, S., McRae, E.K.S.

To be published.

Macromolecule Content

Total Structure Weight: 126.46 kDa
Atom Count: 8,380
Modeled Residue Count: 387
Deposited Residue Count: 387
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
1-methyl-pseudouridine L-21 ScaI Tetrahymena Ribozyme	A	387	Tetrahymena thermophila
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 7.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	ISOLDE
MODEL REFINEMENT	PHENIX
MODEL REFINEMENT	Coot
RECONSTRUCTION	cryoSPARC

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2025-12-03

Deposition Author(s):

McRae, E.K.S.

Yang, H.

Funding Organization	Location	Grant Number
Cancer Prevention and Research Institute of Texas (CPRIT)	United States	RR230015

Revision History (Full details and data files)

Version 1.0: 2025-12-03
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.