9JGM | pdb_00009jgm

The Escherichia coli yybp riboswitch as a tandem riboswitch regulated by Mn2+ and pH

PDB DOI: https://doi.org/10.2210/pdb9JGM/pdb
NAKB: 9JGM

Classification: RNA
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-09-08 Released: 2025-06-04
Deposition Author(s): Xiao, W.W., Liu, G.F., Chen, T., Zhang, Y.L., Ke, A.L., Cai, R.J., Lu, C.R.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.73 Å
R-Value Free:
0.286 (Depositor), 0.287 (DCC)
R-Value Work:
0.236 (Depositor), 0.236 (DCC)
R-Value Observed:
0.239 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Escherichia coli yybP-ykoY Riboswitch as a Tandem Riboswitch Regulated by Mn 2+ and pH.

Xiao, W., Liu, G., Chen, T., Zhang, Y., Ke, A., Cai, R., Lu, C.

(2025) ACS Chem Biol 20: 1010-1019

PubMed: 40252020 Search on PubMed
DOI: https://doi.org/10.1021/acschembio.4c00715
Primary Citation of Related Structures:
9JGM

PubMed Abstract:
The Escherichia coli yybP-ykoY riboswitch regulates mntP and alx gene expression on the translation level. It contains two tandem domains regulated by Mn ²⁺ and pH. This study investigates the tertiary structure and conformational dynamics of the E. coli yybP-ykoY riboswitch using a combination of crystallography, small-angle X-ray scattering (SAXS), and chemical probing. Our crystal structure of the aptamer domain at 3.8 Å reveals that the yybP-ykoY riboswitch aptamer domain forms a coaxial superhelix containing three helices connected by a three-way junction (3WJ), with L1 and L3 creating a pocket-like structure that binds Mg ²⁺ and Mn ²⁺. SHAPE probing and SAXS show that the yybP-ykoY riboswitch maintains a consistent conformation across pH conditions without Mn ²⁺ but exhibits significant conformational changes under alkaline conditions when Mn ²⁺ is present. These findings align with our proposed model, where Mn ²⁺ binding induces a transition from an "OFF" to an "ON" state in alkaline conditions, while the Mn ²⁺ remains bound to the aptamer independent of pH. This regulatory mechanism allows for more sophisticated control of gene expression, providing a finely tuned adaptive response to environmental changes.

Organizational Affiliation

College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, China.

Macromolecule Content

Total Structure Weight: 136.47 kDa
Atom Count: 9,017
Modeled Residue Count: 420
Deposited Residue Count: 420
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
yybP riboswitch	A [auth C], B [auth A], C [auth D], D [auth B]	105	Escherichia coli K-12
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain Y [auth D] SDF format, chain Q [auth A] SDF format, chain N [auth C] SDF format, chain GA [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain N [auth C] MOL2 format, chain GA [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain N [auth C] mmCIF format, chain GA [auth B]	GA [auth B], N [auth C], Q [auth A], Y [auth D]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain GA [auth B] Focus chain N [auth C] Focus chain Q [auth A] Focus chain Y [auth D] Interactions & Density Focus chain GA [auth B] Focus chain N [auth C] Focus chain Q [auth A] Focus chain Y [auth D]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain Z [auth B] SDF format, chain X [auth D] SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain U [auth D] SDF format, chain T [auth D] SDF format, chain S [auth D] SDF format, chain R [auth D] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain M [auth C] SDF format, chain L [auth C] SDF format, chain K [auth C] SDF format, chain J [auth C] SDF format, chain I [auth C] SDF format, chain H [auth C] SDF format, chain G [auth C] SDF format, chain FA [auth B] SDF format, chain F [auth C] SDF format, chain EA [auth B] SDF format, chain E [auth C] SDF format, chain DA [auth B] SDF format, chain CA [auth B] SDF format, chain BA [auth B] SDF format, chain AA [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain X [auth D] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain U [auth D] MOL2 format, chain T [auth D] MOL2 format, chain S [auth D] MOL2 format, chain R [auth D] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain M [auth C] MOL2 format, chain L [auth C] MOL2 format, chain K [auth C] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain H [auth C] MOL2 format, chain G [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain F [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain E [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain AA [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain X [auth D] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain U [auth D] mmCIF format, chain T [auth D] mmCIF format, chain S [auth D] mmCIF format, chain R [auth D] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain M [auth C] mmCIF format, chain L [auth C] mmCIF format, chain K [auth C] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain H [auth C] mmCIF format, chain G [auth C] mmCIF format, chain FA [auth B] mmCIF format, chain F [auth C] mmCIF format, chain EA [auth B] mmCIF format, chain E [auth C] mmCIF format, chain DA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain AA [auth B]	AA [auth B] BA [auth B] CA [auth B] DA [auth B] E [auth C] AA [auth B], BA [auth B], CA [auth B], DA [auth B], E [auth C], EA [auth B], F [auth C], FA [auth B], G [auth C], H [auth C], I [auth C], J [auth C], K [auth C], L [auth C], M [auth C], O [auth A], P [auth A], R [auth D], S [auth D], T [auth D], U [auth D], V [auth D], W [auth D], X [auth D], Z [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth C] Focus chain EA [auth B] Focus chain F [auth C] Focus chain FA [auth B] Focus chain G [auth C] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain DA [auth B] Focus chain E [auth C] Focus chain EA [auth B] Focus chain F [auth C] Focus chain FA [auth B] Focus chain G [auth C] Focus chain H [auth C] Focus chain I [auth C] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth A] Focus chain P [auth A] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth D] Focus chain Z [auth B]