9ZGN | pdb_00009zgn

Cryo-EM structure of RNase P RNA from Geobacillus stearothermophilus, conformer 5

PDB DOI: https://doi.org/10.2210/pdb9ZGN/pdb
NAKB: 9ZGN
EM Map EMD-74196: EMDB EMDataResource

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

Deposited: 2025-12-03 Released: 2026-05-13
Deposition Author(s): Degenhardt, M.F.S., Stagno, J., Wang, Y.X.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

RNA catalysis emerges from dynamic structural ensembles

Degenhardt, M.F.S., Degenhardt, H.F., Bhoge, B.A., Lee, Y.-T., Yu, P., Zhang, J., Deme, J.C., Stagno, J.R., Wang, Y.-X.

(2026) Nature

DOI: https://doi.org/10.1038/s41586-026-11140-z

Macromolecule Content

Total Structure Weight: 136.3 kDa
Atom Count: 9,004
Modeled Residue Count: 417
Deposited Residue Count: 417
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
RNase P RNA	A	417	Geobacillus stearothermophilus
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain JA [auth A] SDF format, chain L [auth A] SDF format, chain LA [auth A] SDF format, chain MA [auth A] SDF format, chain NA [auth A] SDF format, chain Z [auth A] SDF format, chain Y [auth A] SDF format, chain X [auth A] SDF format, chain W [auth A] SDF format, chain V [auth A] SDF format, chain U [auth A] SDF format, chain T [auth A] SDF format, chain S [auth A] SDF format, chain R [auth A] SDF format, chain Q [auth A] SDF format, chain PA [auth A] SDF format, chain P [auth A] SDF format, chain OA [auth A] SDF format, chain O [auth A] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain KA [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain IA [auth A] SDF format, chain I [auth A] SDF format, chain HA [auth A] SDF format, chain H [auth A] SDF format, chain GA [auth A] SDF format, chain G [auth A] SDF format, chain FA [auth A] SDF format, chain F [auth A] SDF format, chain EA [auth A] SDF format, chain E [auth A] SDF format, chain DA [auth A] SDF format, chain CA [auth A] SDF format, chain C [auth A] SDF format, chain BA [auth A] SDF format, chain B [auth A] SDF format, chain AA [auth A] MOL2 format, chain D [auth A] MOL2 format, chain JA [auth A] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth A] MOL2 format, chain MA [auth A] MOL2 format, chain NA [auth A] MOL2 format, chain Z [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain X [auth A] MOL2 format, chain W [auth A] MOL2 format, chain V [auth A] MOL2 format, chain U [auth A] MOL2 format, chain T [auth A] MOL2 format, chain S [auth A] MOL2 format, chain R [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain PA [auth A] MOL2 format, chain P [auth A] MOL2 format, chain OA [auth A] MOL2 format, chain O [auth A] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain KA [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth A] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth A] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth A] MOL2 format, chain G [auth A] MOL2 format, chain FA [auth A] MOL2 format, chain F [auth A] MOL2 format, chain EA [auth A] MOL2 format, chain E [auth A] MOL2 format, chain DA [auth A] MOL2 format, chain CA [auth A] MOL2 format, chain C [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain B [auth A] MOL2 format, chain AA [auth A] mmCIF format, chain D [auth A] mmCIF format, chain JA [auth A] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth A] mmCIF format, chain MA [auth A] mmCIF format, chain NA [auth A] mmCIF format, chain Z [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain X [auth A] mmCIF format, chain W [auth A] mmCIF format, chain V [auth A] mmCIF format, chain U [auth A] mmCIF format, chain T [auth A] mmCIF format, chain S [auth A] mmCIF format, chain R [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain PA [auth A] mmCIF format, chain P [auth A] mmCIF format, chain OA [auth A] mmCIF format, chain O [auth A] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain KA [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth A] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth A] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth A] mmCIF format, chain G [auth A] mmCIF format, chain FA [auth A] mmCIF format, chain F [auth A] mmCIF format, chain EA [auth A] mmCIF format, chain E [auth A] mmCIF format, chain DA [auth A] mmCIF format, chain CA [auth A] mmCIF format, chain C [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain B [auth A] mmCIF format, chain AA [auth A]	AA [auth A] B [auth A] BA [auth A] C [auth A] CA [auth A] AA [auth A], B [auth A], BA [auth A], C [auth A], CA [auth A], D [auth A], DA [auth A], E [auth A], EA [auth A], F [auth A], FA [auth A], G [auth A], GA [auth A], H [auth A], HA [auth A], I [auth A], IA [auth A], J [auth A], JA [auth A], K [auth A], KA [auth A], L [auth A], LA [auth A], M [auth A], MA [auth A], N [auth A], NA [auth A], O [auth A], OA [auth A], P [auth A], PA [auth A], Q [auth A], R [auth A], S [auth A], T [auth A], U [auth A], V [auth A], W [auth A], X [auth A], Y [auth A], Z [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain B [auth A] Focus chain BA [auth A] Focus chain C [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain E [auth A] Focus chain EA [auth A] Focus chain F [auth A] Focus chain FA [auth A] Focus chain G [auth A] Focus chain GA [auth A] Focus chain H [auth A] Focus chain HA [auth A] Focus chain I [auth A] Focus chain IA [auth A] Focus chain J [auth A] Focus chain JA [auth A] Focus chain K [auth A] Focus chain KA [auth A] Focus chain L [auth A] Focus chain LA [auth A] Focus chain M [auth A] Focus chain MA [auth A] Focus chain N [auth A] Focus chain NA [auth A] Focus chain O [auth A] Focus chain OA [auth A] Focus chain P [auth A] Focus chain PA [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A] Interactions & Density Focus chain AA [auth A] Focus chain B [auth A] Focus chain BA [auth A] Focus chain C [auth A] Focus chain CA [auth A] Focus chain D [auth A] Focus chain DA [auth A] Focus chain E [auth A] Focus chain EA [auth A] Focus chain F [auth A] Focus chain FA [auth A] Focus chain G [auth A] Focus chain GA [auth A] Focus chain H [auth A] Focus chain HA [auth A] Focus chain I [auth A] Focus chain IA [auth A] Focus chain J [auth A] Focus chain JA [auth A] Focus chain K [auth A] Focus chain KA [auth A] Focus chain L [auth A] Focus chain LA [auth A] Focus chain M [auth A] Focus chain MA [auth A] Focus chain N [auth A] Focus chain NA [auth A] Focus chain O [auth A] Focus chain OA [auth A] Focus chain P [auth A] Focus chain PA [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Focus chain T [auth A] Focus chain U [auth A] Focus chain V [auth A] Focus chain W [auth A] Focus chain X [auth A] Focus chain Y [auth A] Focus chain Z [auth A]