8SYK | pdb_00008syk

Crystal structure of RNA device 43 truncation mutant 3 (U100C), holo state

PDB DOI: https://doi.org/10.2210/pdb8SYK/pdb
NAKB: 8SYK

Classification: RNA
Organism(s): synthetic construct
Mutation(s): No

Deposited: 2023-05-25 Released: 2025-02-19
Deposition Author(s): Stagno, J.R., Deme, J.C., Lee, Y.-T., Wang, Y.-X., Lee, H.K., Lea, S.M.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.06 Å
R-Value Free:
0.257 (Depositor), 0.258 (DCC)
R-Value Work:
0.225 (Depositor), 0.225 (DCC)
R-Value Observed:
0.227 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Structural investigation of an RNA device that regulates PD-1 expression in mammalian cells.

Stagno, J.R., Deme, J.C., Dwivedi, V., Lee, Y.T., Lee, H.K., Yu, P., Chen, S.Y., Fan, L., Degenhardt, M.F.S., Chari, R., Young, H.A., Lea, S.M., Wang, Y.X.

(2025) Nucleic Acids Res 53

PubMed: 40071935 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1093/nar/gkaf156
Primary Citation Related Structures:
8SYK, 8T5O, 8TKJ, 8TKK

PubMed Abstract:
Synthetic RNA devices are engineered to control gene expression and offer great potential in both biotechnology and clinical applications. Here, we present multidisciplinary structural and biochemical data for a tetracycline (Tc)-responsive RNA device (D43) in both ligand-free and bound states, providing a structure-dynamical basis for signal transmission. Activation of self-cleavage is achieved via ligand-induced conformational and dynamical changes that stabilize the elongated bridging helix harboring the communication module, which drives proper coordination of the catalytic residues. We then show the utility of CRISPR-integrated D43 in EL4 lymphocytes to regulate programmed cell death protein 1 (PD-1), a key receptor of immune checkpoints. Treatment of these cells with Tc showed a dose-dependent reduction in PD-1 by immunostaining and a decrease in messenger RNA levels by quantitative PCR as compared with wild type. PD-1 expression was recoverable upon removal of Tc. These results provide mechanistic insight into RNA devices with potential for cancer immunotherapy or other applications.

Organizational Affiliation

Protein-Nucleic Acid Interaction Section, Center for Structural Biology, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, United States.

Macromolecule Content

Total Structure Weight: 143.42 kDa
Atom Count: 9,474
Modeled Residue Count: 427
Deposited Residue Count: 428
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
RNA device 43 truncation mutant 3 (U100C)	A, B, C, D	107	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GTP (Subject of Investigation/LOI) Query on GTP Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain E [auth A] SDF format, chain HB [auth D] SDF format, chain PA [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain E [auth A] MOL2 format, chain HB [auth D] MOL2 format, chain PA [auth C] mmCIF format, chain BA [auth B] mmCIF format, chain E [auth A] mmCIF format, chain HB [auth D] mmCIF format, chain PA [auth C]	BA [auth B], E [auth A], HB [auth D], PA [auth C]	GUANOSINE-5'-TRIPHOSPHATE C₁₀ H₁₆ N₅ O₁₄ P₃ XKMLYUALXHKNFT-UUOKFMHZSA-N		Interactions Focus chain BA [auth B] Focus chain E [auth A] Focus chain HB [auth D] Focus chain PA [auth C] Interactions & Density Focus chain BA [auth B] Focus chain E [auth A] Focus chain HB [auth D] Focus chain PA [auth C]
TAC Query on TAC Download:Ideal Coordinates CCD File SDF format, chain CA [auth B] SDF format, chain F [auth A] SDF format, chain IB [auth D] SDF format, chain QA [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain IB [auth D] MOL2 format, chain QA [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain IB [auth D] mmCIF format, chain QA [auth C]	CA [auth B], F [auth A], IB [auth D], QA [auth C]	TETRACYCLINE C₂₂ H₂₄ N₂ O₈ OFVLGDICTFRJMM-WESIUVDSSA-N		Interactions Focus chain CA [auth B] Focus chain F [auth A] Focus chain IB [auth D] Focus chain QA [auth C] Interactions & Density Focus chain CA [auth B] Focus chain F [auth A] Focus chain IB [auth D] Focus chain QA [auth C]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth C] SDF format, chain BB [auth C] SDF format, chain CB [auth C] SDF format, chain DA [auth B] SDF format, chain DB [auth C] SDF format, chain EA [auth B] SDF format, chain EB [auth C] SDF format, chain FA [auth B] SDF format, chain FB [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain GB [auth C] SDF format, chain H [auth A] SDF format, chain HA [auth B] SDF format, chain I [auth A] SDF format, chain IA [auth B] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain JB [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain KB [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain LB [auth D] SDF format, chain M [auth A] SDF format, chain MA [auth B] SDF format, chain MB [auth D] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain NB [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain OB [auth D] SDF format, chain P [auth A] SDF format, chain PB [auth D] SDF format, chain Q [auth A] SDF format, chain QB [auth D] SDF format, chain R [auth A] SDF format, chain RA [auth C] SDF format, chain RB [auth D] SDF format, chain S [auth A] SDF format, chain SA [auth C] SDF format, chain SB [auth D] SDF format, chain T [auth A] SDF format, chain TA [auth C] SDF format, chain TB [auth D] SDF format, chain U [auth A] SDF format, chain UA [auth C] SDF format, chain UB [auth D] SDF format, chain V [auth A] SDF format, chain VA [auth C] SDF format, chain W [auth A] SDF format, chain WA [auth C] SDF format, chain X [auth A] SDF format, chain XA [auth C] SDF format, chain Y [auth A] SDF format, chain YA [auth C] SDF format, chain Z [auth A] SDF format, chain ZA [auth C] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth C] MOL2 format, chain BB [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain DB [auth C] MOL2 format, chain EA [auth B] MOL2 format, chain EB [auth C] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth C] MOL2 format, chain H [auth A] MOL2 format, chain HA [auth B] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain JB [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain LB [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth B] MOL2 format, chain MB [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain NB [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain OB [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PB [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QB [auth D] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain RB [auth D] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth C] MOL2 format, chain SB [auth D] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain TB [auth D] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth C] MOL2 format, chain UB [auth D] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth C] MOL2 format, chain W [auth A] MOL2 format, chain WA [auth C] MOL2 format, chain X [auth A] MOL2 format, chain XA [auth C] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth C] MOL2 format, chain Z [auth A] MOL2 format, chain ZA [auth C] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth C] mmCIF format, chain BB [auth C] mmCIF format, chain CB [auth C] mmCIF format, chain DA [auth B] mmCIF format, chain DB [auth C] mmCIF format, chain EA [auth B] mmCIF format, chain EB [auth C] mmCIF format, chain FA [auth B] mmCIF format, chain FB [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain GB [auth C] mmCIF format, chain H [auth A] mmCIF format, chain HA [auth B] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth B] mmCIF format, chain J [auth A] mmCIF format, chain JA [auth B] mmCIF format, chain JB [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain KB [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain LB [auth D] mmCIF format, chain M [auth A] mmCIF format, chain MA [auth B] mmCIF format, chain MB [auth D] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain NB [auth D] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain OB [auth D] mmCIF format, chain P [auth A] mmCIF format, chain PB [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain QB [auth D] mmCIF format, chain R [auth A] mmCIF format, chain RA [auth C] mmCIF format, chain RB [auth D] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth C] mmCIF format, chain SB [auth D] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth C] mmCIF format, chain TB [auth D] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth C] mmCIF format, chain UB [auth D] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth C] mmCIF format, chain W [auth A] mmCIF format, chain WA [auth C] mmCIF format, chain X [auth A] mmCIF format, chain XA [auth C] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth C] mmCIF format, chain Z [auth A] mmCIF format, chain ZA [auth C]	AA [auth A] AB [auth C] BB [auth C] CB [auth C] DA [auth B] AA [auth A], AB [auth C], BB [auth C], CB [auth C], DA [auth B], DB [auth C], EA [auth B], EB [auth C], FA [auth B], FB [auth C], G [auth A], GA [auth B], GB [auth C], H [auth A], HA [auth B], I [auth A], IA [auth B], J [auth A], JA [auth B], JB [auth D], K [auth A], KA [auth B], KB [auth D], L [auth A], LA [auth B], LB [auth D], M [auth A], MA [auth B], MB [auth D], N [auth A], NA [auth B], NB [auth D], O [auth A], OA [auth B], OB [auth D], P [auth A], PB [auth D], Q [auth A], QB [auth D], R [auth A], RA [auth C], RB [auth D], S [auth A], SA [auth C], SB [auth D], T [auth A], TA [auth C], TB [auth D], U [auth A], UA [auth C], UB [auth D], V [auth A], VA [auth C], W [auth A], WA [auth C], X [auth A], XA [auth C], Y [auth A], YA [auth C], Z [auth A], ZA [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth D] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth D] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RA [auth C] Focus chain RB [auth D] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SB [auth D] Focus chain T [auth A] Focus chain TA [auth C] Focus chain TB [auth D] Focus chain U [auth A] Focus chain UA [auth C] Focus chain UB [auth D] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth C] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain Z [auth A] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth C] Focus chain BB [auth C] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain EB [auth C] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain H [auth A] Focus chain HA [auth B] Focus chain I [auth A] Focus chain IA [auth B] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth D] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth D] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RA [auth C] Focus chain RB [auth D] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SB [auth D] Focus chain T [auth A] Focus chain TA [auth C] Focus chain TB [auth D] Focus chain U [auth A] Focus chain UA [auth C] Focus chain UB [auth D] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth C] Focus chain Y [auth A] Focus chain YA [auth C] Focus chain Z [auth A] Focus chain ZA [auth C]