9J9X | pdb_00009j9x

Tetrahymena Ribozyme L-16 complex with small molecule inhibitor ZPT-084

PDB DOI: https://doi.org/10.2210/pdb9J9X/pdb
NAKB: 9J9X
EM Map EMD-61283: EMDB EMDataResource

Classification: RNA
Organism(s): Tetrahymena thermophila
Expression System: in vitro transcription vector pT7-TP(deltai)
Mutation(s): No

Deposited: 2024-08-23 Released: 2026-03-04
Deposition Author(s): Pan, Z.L., Hu, H., Su, Z.M.
Funding Organization(s): Ministry of Science and Technology (MoST, China)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.05 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9J9X

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

Literature

Tetrahymena Ribozyme L-16 complex with small molecule inhibitor ZPT-084

Pan, Z.L., Hu, H., Su, Z.M.

To be published.

Macromolecule Content

Total Structure Weight: 124.66 kDa
Atom Count: 8,236
Modeled Residue Count: 382
Deposited Residue Count: 382
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism	Image
Entity ID: 1
RNA (382-MER)	A [auth N]	382	Tetrahymena thermophila
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1EA7 (Subject of Investigation/LOI) Query on A1EA7 Download:Ideal Coordinates CCD File SDF format, chain IA [auth N] MOL2 format, chain IA [auth N] mmCIF format, chain IA [auth N]	IA [auth N]	1-[4-[(2~{R})-3-[4-[(2~{S})-3-(4-ethanoylphenoxy)-2-oxidanyl-propyl]piperazin-1-yl]-2-oxidanyl-propoxy]phenyl]ethanone C₂₆ H₃₄ N₂ O₆ OAJPQFYTCQEFGQ-PSWAGMNNSA-N		Interactions Focus chain IA [auth N] Interactions & Density Focus chain IA [auth N]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain AA [auth N] SDF format, chain B [auth N] SDF format, chain BA [auth N] SDF format, chain C [auth N] SDF format, chain CA [auth N] SDF format, chain D [auth N] SDF format, chain DA [auth N] SDF format, chain E [auth N] SDF format, chain EA [auth N] SDF format, chain F [auth N] SDF format, chain FA [auth N] SDF format, chain G [auth N] SDF format, chain GA [auth N] SDF format, chain H [auth N] SDF format, chain HA [auth N] SDF format, chain I [auth N] SDF format, chain J [auth N] SDF format, chain K [auth N] SDF format, chain L [auth N] SDF format, chain M [auth N] SDF format, chain N SDF format, chain O [auth N] SDF format, chain P [auth N] SDF format, chain Q [auth N] SDF format, chain R [auth N] SDF format, chain S [auth N] SDF format, chain T [auth N] SDF format, chain U [auth N] SDF format, chain V [auth N] SDF format, chain W [auth N] SDF format, chain X [auth N] SDF format, chain Y [auth N] SDF format, chain Z [auth N] MOL2 format, chain AA [auth N] MOL2 format, chain B [auth N] MOL2 format, chain BA [auth N] MOL2 format, chain C [auth N] MOL2 format, chain CA [auth N] MOL2 format, chain D [auth N] MOL2 format, chain DA [auth N] MOL2 format, chain E [auth N] MOL2 format, chain EA [auth N] MOL2 format, chain F [auth N] MOL2 format, chain FA [auth N] MOL2 format, chain G [auth N] MOL2 format, chain GA [auth N] MOL2 format, chain H [auth N] MOL2 format, chain HA [auth N] MOL2 format, chain I [auth N] MOL2 format, chain J [auth N] MOL2 format, chain K [auth N] MOL2 format, chain L [auth N] MOL2 format, chain M [auth N] MOL2 format, chain N MOL2 format, chain O [auth N] MOL2 format, chain P [auth N] MOL2 format, chain Q [auth N] MOL2 format, chain R [auth N] MOL2 format, chain S [auth N] MOL2 format, chain T [auth N] MOL2 format, chain U [auth N] MOL2 format, chain V [auth N] MOL2 format, chain W [auth N] MOL2 format, chain X [auth N] MOL2 format, chain Y [auth N] MOL2 format, chain Z [auth N] mmCIF format, chain AA [auth N] mmCIF format, chain B [auth N] mmCIF format, chain BA [auth N] mmCIF format, chain C [auth N] mmCIF format, chain CA [auth N] mmCIF format, chain D [auth N] mmCIF format, chain DA [auth N] mmCIF format, chain E [auth N] mmCIF format, chain EA [auth N] mmCIF format, chain F [auth N] mmCIF format, chain FA [auth N] mmCIF format, chain G [auth N] mmCIF format, chain GA [auth N] mmCIF format, chain H [auth N] mmCIF format, chain HA [auth N] mmCIF format, chain I [auth N] mmCIF format, chain J [auth N] mmCIF format, chain K [auth N] mmCIF format, chain L [auth N] mmCIF format, chain M [auth N] mmCIF format, chain N mmCIF format, chain O [auth N] mmCIF format, chain P [auth N] mmCIF format, chain Q [auth N] mmCIF format, chain R [auth N] mmCIF format, chain S [auth N] mmCIF format, chain T [auth N] mmCIF format, chain U [auth N] mmCIF format, chain V [auth N] mmCIF format, chain W [auth N] mmCIF format, chain X [auth N] mmCIF format, chain Y [auth N] mmCIF format, chain Z [auth N]	AA [auth N] B [auth N] BA [auth N] C [auth N] CA [auth N] AA [auth N], B [auth N], BA [auth N], C [auth N], CA [auth N], D [auth N], DA [auth N], E [auth N], EA [auth N], F [auth N], FA [auth N], G [auth N], GA [auth N], H [auth N], HA [auth N], I [auth N], J [auth N], K [auth N], L [auth N], M [auth N], N, O [auth N], P [auth N], Q [auth N], R [auth N], S [auth N], T [auth N], U [auth N], V [auth N], W [auth N], X [auth N], Y [auth N], Z [auth N]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth N] Focus chain B [auth N] Focus chain BA [auth N] Focus chain C [auth N] Focus chain CA [auth N] Focus chain D [auth N] Focus chain DA [auth N] Focus chain E [auth N] Focus chain EA [auth N] Focus chain F [auth N] Focus chain FA [auth N] Focus chain G [auth N] Focus chain GA [auth N] Focus chain H [auth N] Focus chain HA [auth N] Focus chain I [auth N] Focus chain J [auth N] Focus chain K [auth N] Focus chain L [auth N] Focus chain M [auth N] Focus chain N Focus chain O [auth N] Focus chain P [auth N] Focus chain Q [auth N] Focus chain R [auth N] Focus chain S [auth N] Focus chain T [auth N] Focus chain U [auth N] Focus chain V [auth N] Focus chain W [auth N] Focus chain X [auth N] Focus chain Y [auth N] Focus chain Z [auth N] Interactions & Density Focus chain AA [auth N] Focus chain B [auth N] Focus chain BA [auth N] Focus chain C [auth N] Focus chain CA [auth N] Focus chain D [auth N] Focus chain DA [auth N] Focus chain E [auth N] Focus chain EA [auth N] Focus chain F [auth N] Focus chain FA [auth N] Focus chain G [auth N] Focus chain GA [auth N] Focus chain H [auth N] Focus chain HA [auth N] Focus chain I [auth N] Focus chain J [auth N] Focus chain K [auth N] Focus chain L [auth N] Focus chain M [auth N] Focus chain N Focus chain O [auth N] Focus chain P [auth N] Focus chain Q [auth N] Focus chain R [auth N] Focus chain S [auth N] Focus chain T [auth N] Focus chain U [auth N] Focus chain V [auth N] Focus chain W [auth N] Focus chain X [auth N] Focus chain Y [auth N] Focus chain Z [auth N]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.05 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

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):

Funding Organization	Location	Grant Number
Ministry of Science and Technology (MoST, China)	China	2022YFC2303700

Revision History (Full details and data files)

Version 1.0: 2026-03-04
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.