8UTA

yjdF riboswitch from R. gauvreauii in complex with proflavine bound to Fab BL3-6 S97N

PDB DOI: https://doi.org/10.2210/pdb8UTA/pdb
NAKB: 8UTA

Classification: RNA
Organism(s): Ruminococcus gauvreauii, Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2023-10-30 Released: 2024-04-10
Deposition Author(s): Krochmal, D., Lewicka, A., Piccirilli, J.A.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.05 Å
R-Value Free: 0.269
R-Value Work: 0.224
R-Value Observed: 0.227

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Structural basis for promiscuity in ligand recognition by yjdF riboswitch.

Krochmal, D., Roman, C., Lewicka, A., Shao, Y., Piccirilli, J.A.

(2024) Cell Discov 10: 37-37

PubMed: 38565535 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41421-024-00663-2
Primary Citation of Related Structures:
8UIW, 8UTA

Organizational Affiliation

Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.

Macromolecule Content

Total Structure Weight: 179.17 kDa
Atom Count: 12,024
Modelled Residue Count: 1,131
Deposited Residue Count: 1,152
Unique protein chains: 2
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab BL3-6 S97N heavy chain	C [auth A], D [auth H]	233	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab BL3-6 S97N light chain	E [auth B], F [auth L]	215	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
yjdF RNA (R. gauvreauii)	A [auth N], B [auth R]	128	Ruminococcus gauvreauii
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PRL (Subject of Investigation/LOI) Query on PRL Download Ideal Coordinates CCD File SDF format, chain J [auth N] SDF format, chain N [auth R] MOL2 format, chain J [auth N] MOL2 format, chain N [auth R] mmCIF format, chain J [auth N] mmCIF format, chain N [auth R]	J [auth N], N [auth R]	PROFLAVIN C₁₃ H₁₁ N₃ WDVSHHCDHLJJJR-UHFFFAOYSA-N		Interactions Focus chain J [auth N] Focus chain N [auth R] Interactions & Density Focus chain J [auth N] Focus chain N [auth R]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain G [auth N] SDF format, chain H [auth N] SDF format, chain I [auth N] SDF format, chain K [auth R] SDF format, chain L [auth R] SDF format, chain M [auth R] MOL2 format, chain G [auth N] MOL2 format, chain H [auth N] MOL2 format, chain I [auth N] MOL2 format, chain K [auth R] MOL2 format, chain L [auth R] MOL2 format, chain M [auth R] mmCIF format, chain G [auth N] mmCIF format, chain H [auth N] mmCIF format, chain I [auth N] mmCIF format, chain K [auth R] mmCIF format, chain L [auth R] mmCIF format, chain M [auth R]	G [auth N] H [auth N] I [auth N] K [auth R] L [auth R] G [auth N], H [auth N], I [auth N], K [auth R], L [auth R], M [auth R]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain G [auth N] Focus chain H [auth N] Focus chain I [auth N] Focus chain K [auth R] Focus chain L [auth R] Focus chain M [auth R] Interactions & Density Focus chain G [auth N] Focus chain H [auth N] Focus chain I [auth N] Focus chain K [auth R] Focus chain L [auth R] Focus chain M [auth R]